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.
Changeset 11967 for NEMO/branches/2019/ENHANCE-02_ISF_nemo_TEST_MERGE/doc/latex/NEMO/subfiles/chap_SBC.tex – NEMO

Ignore:
Timestamp:
2019-11-26T15:11:43+01:00 (4 years ago)
Author:
davestorkey
Message:

2019/ENHANCE-02_ISF_nemo_TEST_MERGE : Update to rev 11953.

Location:
NEMO/branches/2019/ENHANCE-02_ISF_nemo_TEST_MERGE/doc
Files:
5 edited

Legend:

Unmodified
Added
Removed

  • NEMO/branches/2019/ENHANCE-02_ISF_nemo_TEST_MERGE/doc

    • Property svn:externals set to
      ^/utils/badges badges
      ^/utils/logos logos

  • NEMO/branches/2019/ENHANCE-02_ISF_nemo_TEST_MERGE/doc/latex

    • Property svn:ignore deleted

  • NEMO/branches/2019/ENHANCE-02_ISF_nemo_TEST_MERGE/doc/latex/NEMO

    • Property svn:externals set to
      ^/utils/figures/NEMO figures

  • NEMO/branches/2019/ENHANCE-02_ISF_nemo_TEST_MERGE/doc/latex/NEMO/subfiles

    • Property svn:ignore

      •  

        old new  
        1 *.aux 
        2 *.bbl 
        3 *.blg 
        4 *.dvi 
        5 *.fdb* 
        6 *.fls 
        7 *.idx 
         1*.ind 
        82*.ilg 
        9 *.ind 
        10 *.log 
        11 *.maf 
        12 *.mtc* 
        13 *.out 
        14 *.pdf 
        15 *.toc 
        16 _minted-* 

  • NEMO/branches/2019/ENHANCE-02_ISF_nemo_TEST_MERGE/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11179 r11967  
    22 
    33\begin{document} 
    4 % ================================================================ 
    5 % Chapter —— Surface Boundary Condition (SBC, ISF, ICB)  
    6 % ================================================================ 
    7 \chapter{Surface Boundary Condition (SBC, ISF, ICB)} 
     4 
     5\chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB)} 
    86\label{chap:SBC} 
    9 \minitoc 
    10  
    11 \newpage 
    12  
    13 %---------------------------------------namsbc-------------------------------------------------- 
    14  
    15 \nlst{namsbc} 
    16 %-------------------------------------------------------------------------------------------------------------- 
    17  
    18 The ocean needs six fields as surface boundary condition: 
     7 
     8\thispagestyle{plain} 
     9 
     10\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
     26 
     27\begin{listing} 
     28  \nlst{namsbc} 
     29  \caption{\forcode{&namsbc}} 
     30  \label{lst:namsbc} 
     31\end{listing} 
     32 
     33The ocean needs seven fields as surface boundary condition: 
     34 
    1935\begin{itemize} 
    20 \item 
    21   the two components of the surface ocean stress $\left( {\tau_u \;,\;\tau_v} \right)$ 
    22 \item 
    23   the incoming solar and non solar heat fluxes $\left( {Q_{ns} \;,\;Q_{sr} } \right)$ 
    24 \item 
    25   the surface freshwater budget $\left( {\textit{emp}} \right)$ 
    26 \item 
    27   the surface salt flux associated with freezing/melting of seawater $\left( {\textit{sfx}} \right)$ 
     36\item the two components of the surface ocean stress $\left( {\tau_u \;,\;\tau_v} \right)$ 
     37\item the incoming solar and non solar heat fluxes $\left( {Q_{ns} \;,\;Q_{sr} } \right)$ 
     38\item the surface freshwater budget $\left( {\textit{emp}} \right)$ 
     39\item the surface salt flux associated with freezing/melting of seawater $\left( {\textit{sfx}} \right)$ 
     40\item the atmospheric pressure at the ocean surface $\left( p_a \right)$ 
    2841\end{itemize} 
    29 plus an optional field: 
     42 
     43Four different ways are available to provide the seven fields to the ocean. They are controlled by 
     44namelist \nam{sbc}{sbc} variables: 
     45 
    3046\begin{itemize} 
    31    \item the atmospheric pressure at the ocean surface $\left( p_a \right)$ 
     47\item a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk} with four possible bulk algorithms), 
     48\item a flux formulation (\np[=.true.]{ln_flx}{ln\_flx}), 
     49\item a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler), 
     50(\np{ln_cpl}{ln\_cpl} or \np[=.true.]{ln_mixcpl}{ln\_mixcpl}), 
     51\item a user defined formulation (\np[=.true.]{ln_usr}{ln\_usr}). 
    3252\end{itemize} 
    3353 
    34 Four different ways to provide the first six fields to the ocean are available which are controlled by 
    35 namelist \ngn{namsbc} variables: 
    36 an analytical formulation (\np{ln\_ana}\forcode{ = .true.}), 
    37 a flux formulation (\np{ln\_flx}\forcode{ = .true.}), 
    38 a bulk formulae formulation (CORE (\np{ln\_blk\_core}\forcode{ = .true.}), 
    39 CLIO (\np{ln\_blk\_clio}\forcode{ = .true.}) bulk formulae) and 
    40 a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler) 
    41 (\np{ln\_cpl} or \np{ln\_mixcpl}\forcode{ = .true.}).  
    42 When used (\ie \np{ln\_apr\_dyn}\forcode{ = .true.}), 
    43 the atmospheric pressure forces both ocean and ice dynamics. 
    44  
    45 The frequency at which the forcing fields have to be updated is given by the \np{nn\_fsbc} namelist parameter. 
    46 When the fields are supplied from data files (flux and bulk formulations), 
    47 the input fields need not be supplied on the model grid. 
    48 Instead a file of coordinates and weights can be supplied which maps the data from the supplied grid to 
     54The frequency at which the forcing fields have to be updated is given by the \np{nn_fsbc}{nn\_fsbc} namelist parameter. 
     55 
     56When the fields are supplied from data files (bulk, flux and mixed formulations), 
     57the input fields do not need to be supplied on the model grid. 
     58Instead, a file of coordinates and weights can be supplied to map the data from the input fields grid to 
    4959the model points (so called "Interpolation on the Fly", see \autoref{subsec:SBC_iof}). 
    50 If the Interpolation on the Fly option is used, input data belonging to land points (in the native grid), 
    51 can be masked to avoid spurious results in proximity of the coasts as 
     60If the "Interpolation on the Fly" option is used, input data belonging to land points (in the native grid) 
     61should be masked or filled to avoid spurious results in proximity of the coasts, as 
    5262large sea-land gradients characterize most of the atmospheric variables. 
    5363 
    5464In addition, the resulting fields can be further modified using several namelist options. 
    55 These options control  
     65These options control: 
     66 
    5667\begin{itemize} 
    57 \item 
    58   the rotation of vector components supplied relative to an east-north coordinate system onto 
    59   the local grid directions in the model; 
    60 \item 
    61   the addition of a surface restoring term to observed SST and/or SSS (\np{ln\_ssr}\forcode{ = .true.}); 
    62 \item 
    63   the modification of fluxes below ice-covered areas (using observed ice-cover or a sea-ice model) 
    64   (\np{nn\_ice}\forcode{ = 0..3}); 
    65 \item 
    66   the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln\_rnf}\forcode{ = .true.}); 
    67 \item 
    68   the addition of isf melting as lateral inflow (parameterisation) or 
    69   as fluxes applied at the land-ice ocean interface (\np{ln\_isf}) ;  
    70 \item 
    71   the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift 
    72   (\np{nn\_fwb}\forcode{ = 0..2}); 
    73 \item 
    74   the transformation of the solar radiation (if provided as daily mean) into a diurnal cycle 
    75   (\np{ln\_dm2dc}\forcode{ = .true.}); 
    76 \item 
    77   a neutral drag coefficient can be read from an external wave model (\np{ln\_cdgw}\forcode{ = .true.}); 
    78 \item 
    79   the Stokes drift rom an external wave model can be accounted (\np{ln\_sdw}\forcode{ = .true.});  
    80 \item 
    81   the Stokes-Coriolis term can be included (\np{ln\_stcor}\forcode{ = .true.}); 
    82 \item 
    83   the surface stress felt by the ocean can be modified by surface waves (\np{ln\_tauwoc}\forcode{ = .true.}). 
     68\item the rotation of vector components supplied relative to an east-north coordinate system onto 
     69  the local grid directions in the model, 
     70\item the use of a land/sea mask for input fields (\np[=.true.]{nn_lsm}{nn\_lsm}), 
     71\item the addition of a surface restoring term to observed SST and/or SSS (\np[=.true.]{ln_ssr}{ln\_ssr}), 
     72\item the modification of fluxes below ice-covered areas (using climatological ice-cover or a sea-ice model) 
     73  (\np[=0..3]{nn_ice}{nn\_ice}), 
     74\item the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np[=.true.]{ln_rnf}{ln\_rnf}), 
     75\item the addition of ice-shelf melting as lateral inflow (parameterisation) or 
     76  as fluxes applied at the land-ice ocean interface (\np[=.true.]{ln_isf}{ln\_isf}), 
     77\item the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift 
     78  (\np[=0..2]{nn_fwb}{nn\_fwb}), 
     79\item the transformation of the solar radiation (if provided as daily mean) into an analytical diurnal cycle 
     80  (\np[=.true.]{ln_dm2dc}{ln\_dm2dc}), 
     81\item the activation of wave effects from an external wave model  (\np[=.true.]{ln_wave}{ln\_wave}), 
     82\item a neutral drag coefficient is read from an external wave model (\np[=.true.]{ln_cdgw}{ln\_cdgw}), 
     83\item the Stokes drift from an external wave model is accounted for (\np[=.true.]{ln_sdw}{ln\_sdw}), 
     84\item the choice of the Stokes drift profile parameterization (\np[=0..2]{nn_sdrift}{nn\_sdrift}), 
     85\item the surface stress given to the ocean is modified by surface waves (\np[=.true.]{ln_tauwoc}{ln\_tauwoc}), 
     86\item the surface stress given to the ocean is read from an external wave model (\np[=.true.]{ln_tauw}{ln\_tauw}), 
     87\item the Stokes-Coriolis term is included (\np[=.true.]{ln_stcor}{ln\_stcor}), 
     88\item the light penetration in the ocean (\np[=.true.]{ln_traqsr}{ln\_traqsr} with namelist \nam{tra_qsr}{tra\_qsr}), 
     89\item the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np[=.true.]{ln_apr_dyn}{ln\_apr\_dyn} with namelist \nam{sbc_apr}{sbc\_apr}), 
     90\item the effect of sea-ice pressure on the ocean (\np[=.true.]{ln_ice_embd}{ln\_ice\_embd}). 
    8491\end{itemize} 
    8592 
    86 In this chapter, we first discuss where the surface boundary condition appears in the model equations. 
    87 Then we present the five ways of providing the surface boundary condition,  
    88 followed by the description of the atmospheric pressure and the river runoff.  
    89 Next the scheme for interpolation on the fly is described. 
     93In this chapter, we first discuss where the surface boundary conditions appear in the model equations. 
     94Then we present the three ways of providing the surface boundary conditions, 
     95followed by the description of the atmospheric pressure and the river runoff. 
     96Next, the scheme for interpolation on the fly is described. 
    9097Finally, the different options that further modify the fluxes applied to the ocean are discussed. 
    91 One of these is modification by icebergs (see \autoref{sec:ICB_icebergs}), 
     98One of these is modification by icebergs (see \autoref{sec:SBC_ICB_icebergs}), 
    9299which act as drifting sources of fresh water. 
    93 Another example of modification is that due to the ice shelf melting/freezing (see \autoref{sec:SBC_isf}),  
     100Another example of modification is that due to the ice shelf melting/freezing (see \autoref{sec:SBC_isf}), 
    94101which provides additional sources of fresh water. 
    95102 
    96  
    97 % ================================================================ 
    98 % Surface boundary condition for the ocean 
    99 % ================================================================ 
     103%% ================================================================================================= 
    100104\section{Surface boundary condition for the ocean} 
    101 \label{sec:SBC_general} 
     105\label{sec:SBC_ocean} 
    102106 
    103107The surface ocean stress is the stress exerted by the wind and the sea-ice on the ocean. 
    104108It is applied in \mdl{dynzdf} module as a surface boundary condition of the computation of 
    105 the momentum vertical mixing trend (see \autoref{eq:dynzdf_sbc} in \autoref{sec:DYN_zdf}). 
     109the momentum vertical mixing trend (see \autoref{eq:DYN_zdf_sbc} in \autoref{sec:DYN_zdf}). 
    106110As such, it has to be provided as a 2D vector interpolated onto the horizontal velocity ocean mesh, 
    107 \ie resolved onto the model (\textbf{i},\textbf{j}) direction at $u$- and $v$-points. 
     111\ie\ resolved onto the model (\textbf{i},\textbf{j}) direction at $u$- and $v$-points. 
    108112 
    109113The surface heat flux is decomposed into two parts, a non solar and a solar heat flux, 
    110114$Q_{ns}$ and $Q_{sr}$, respectively. 
    111115The former is the non penetrative part of the heat flux 
    112 (\ie the sum of sensible, latent and long wave heat fluxes plus 
    113 the heat content of the mass exchange with the atmosphere and sea-ice). 
     116(\ie\ the sum of sensible, latent and long wave heat fluxes plus 
     117the heat content of the mass exchange between the ocean and sea-ice). 
    114118It is applied in \mdl{trasbc} module as a surface boundary condition trend of 
    115119the first level temperature time evolution equation 
    116 (see \autoref{eq:tra_sbc} and \autoref{eq:tra_sbc_lin} in \autoref{subsec:TRA_sbc}).  
     120(see \autoref{eq:TRA_sbc} and \autoref{eq:TRA_sbc_lin} in \autoref{subsec:TRA_sbc}). 
    117121The latter is the penetrative part of the heat flux. 
    118 It is applied as a 3D trends of the temperature equation (\mdl{traqsr} module) when 
    119 \np{ln\_traqsr}\forcode{ = .true.}. 
     122It is applied as a 3D trend of the temperature equation (\mdl{traqsr} module) when 
     123\np[=.true.]{ln_traqsr}{ln\_traqsr}. 
    120124The way the light penetrates inside the water column is generally a sum of decreasing exponentials 
    121 (see \autoref{subsec:TRA_qsr}).  
     125(see \autoref{subsec:TRA_qsr}). 
    122126 
    123127The surface freshwater budget is provided by the \textit{emp} field. 
    124128It represents the mass flux exchanged with the atmosphere (evaporation minus precipitation) and 
    125129possibly with the sea-ice and ice shelves (freezing minus melting of ice). 
    126 It affects both the ocean in two different ways: 
    127 $(i)$  it changes the volume of the ocean and therefore appears in the sea surface height equation as 
    128 a volume flux, and  
     130It affects the ocean in two different ways: 
     131$(i)$  it changes the volume of the ocean, and therefore appears in the sea surface height equation as      %GS: autoref ssh equation to be added 
     132a volume flux, and 
    129133$(ii)$ it changes the surface temperature and salinity through the heat and salt contents of 
    130 the mass exchanged with the atmosphere, the sea-ice and the ice shelves.  
    131  
     134the mass exchanged with atmosphere, sea-ice and ice shelves. 
    132135 
    133136%\colorbox{yellow}{Miss: } 
    134 % 
    135 %A extensive description of all namsbc namelist (parameter that have to be  
     137%A extensive description of all namsbc namelist (parameter that have to be 
    136138%created!) 
    137 % 
    138 %Especially the \np{nn\_fsbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu  
    139 %ssv) \ie information required by flux computation or sea-ice 
    140 % 
    141 %\mdl{sbc\_oce} containt the definition in memory of the 7 fields (6+runoff), add  
     139%Especially the \np{nn_fsbc}{nn\_fsbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu 
     140%ssv) \ie\ information required by flux computation or sea-ice 
     141%\mdl{sbc\_oce} containt the definition in memory of the 7 fields (6+runoff), add 
    142142%a word on runoff: included in surface bc or add as lateral obc{\ldots}. 
    143 % 
    144143%Sbcmod manage the ``providing'' (fourniture) to the ocean the 7 fields 
    145 % 
    146 %Fluxes update only each nf{\_}sbc time step (namsbc) explain relation  
    147 %between nf{\_}sbc and nf{\_}ice, do we define nf{\_}blk??? ? only one  
    148 %nf{\_}sbc 
    149 % 
     144%Fluxes update only each nf\_sbc time step (namsbc) explain relation 
     145%between nf\_sbc and nf\_ice, do we define nf\_blk??? ? only one 
     146%nf\_sbc 
    150147%Explain here all the namlist namsbc variable{\ldots}. 
    151 %  
    152148% explain : use or not of surface currents 
    153 % 
    154149%\colorbox{yellow}{End Miss } 
    155150 
    156151The ocean model provides, at each time step, to the surface module (\mdl{sbcmod}) 
    157 the surface currents, temperature and salinity.   
    158 These variables are averaged over \np{nn\_fsbc} time-step (\autoref{tab:ssm}), and 
    159 it is these averaged fields which are used to computes the surface fluxes at a frequency of \np{nn\_fsbc} time-step. 
    160  
    161  
    162 %-------------------------------------------------TABLE--------------------------------------------------- 
     152the surface currents, temperature and salinity. 
     153These variables are averaged over \np{nn_fsbc}{nn\_fsbc} time-step (\autoref{tab:SBC_ssm}), and 
     154these averaged fields are used to compute the surface fluxes at the frequency of \np{nn_fsbc}{nn\_fsbc} time-steps. 
     155 
    163156\begin{table}[tb] 
    164   \begin{center} 
    165     \begin{tabular}{|l|l|l|l|} 
    166       \hline 
    167       Variable description             & Model variable  & Units  & point \\  \hline 
    168       i-component of the surface current  & ssu\_m & $m.s^{-1}$   & U \\   \hline 
    169       j-component of the surface current  & ssv\_m & $m.s^{-1}$   & V \\   \hline 
    170       Sea surface temperature          & sst\_m & \r{}$K$      & T \\   \hline 
    171       Sea surface salinty              & sss\_m & $psu$        & T \\   \hline 
    172     \end{tabular} 
    173     \caption{ 
    174       \protect\label{tab:ssm} 
    175       Ocean variables provided by the ocean to the surface module (SBC). 
    176       The variable are averaged over nn{\_}fsbc time step, 
    177       \ie the frequency of computation of surface fluxes. 
    178     } 
    179   \end{center} 
     157  \centering 
     158  \begin{tabular}{|l|l|l|l|} 
     159    \hline 
     160    Variable description                           & Model variable  & Units  & point                 \\ 
     161    \hline 
     162    i-component of the surface current & ssu\_m               & $m.s^{-1}$     & U     \\ 
     163    \hline 
     164    j-component of the surface current & ssv\_m               & $m.s^{-1}$     & V     \\ 
     165    \hline 
     166    Sea surface temperature                  & sst\_m               & \r{}$K$              & T     \\\hline 
     167    Sea surface salinty                         & sss\_m               & $psu$              & T     \\   \hline 
     168  \end{tabular} 
     169  \caption[Ocean variables provided to the surface module)]{ 
     170    Ocean variables provided to the surface module (\texttt{SBC}). 
     171    The variable are averaged over \protect\np{nn_fsbc}{nn\_fsbc} time-step, 
     172    \ie\ the frequency of computation of surface fluxes.} 
     173  \label{tab:SBC_ssm} 
    180174\end{table} 
    181 %-------------------------------------------------------------------------------------------------------------- 
    182  
    183 %\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 
    184  
    185  
    186 % ================================================================ 
    187 %       Input Data  
    188 % ================================================================ 
     175 
     176%\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 
     177 
     178%% ================================================================================================= 
    189179\section{Input data generic interface} 
    190180\label{sec:SBC_input} 
    191181 
    192182A generic interface has been introduced to manage the way input data 
    193 (2D or 3D fields, like surface forcing or ocean T and S) are specify in \NEMO. 
    194 This task is archieved by \mdl{fldread}. 
    195 The module was design with four main objectives in mind:  
     183(2D or 3D fields, like surface forcing or ocean T and S) are specified in \NEMO. 
     184This task is achieved by \mdl{fldread}. 
     185The module is designed with four main objectives in mind: 
    196186\begin{enumerate} 
    197 \item 
    198   optionally provide a time interpolation of the input data at model time-step, whatever their input frequency is, 
     187\item optionally provide a time interpolation of the input data every specified model time-step, whatever their input frequency is, 
    199188  and according to the different calendars available in the model. 
    200 \item 
    201   optionally provide an on-the-fly space interpolation from the native input data grid to the model grid. 
    202 \item 
    203   make the run duration independent from the period cover by the input files. 
    204 \item 
    205   provide a simple user interface and a rather simple developer interface by 
    206   limiting the number of prerequisite information.  
    207 \end{enumerate}   
    208  
    209 As a results the user have only to fill in for each variable a structure in the namelist file to 
     189\item optionally provide an on-the-fly space interpolation from the native input data grid to the model grid. 
     190\item make the run duration independent from the period cover by the input files. 
     191\item provide a simple user interface and a rather simple developer interface by 
     192  limiting the number of prerequisite informations. 
     193\end{enumerate} 
     194 
     195As a result, the user has only to fill in for each variable a structure in the namelist file to 
    210196define the input data file and variable names, the frequency of the data (in hours or months), 
    211197whether its is climatological data or not, the period covered by the input file (one year, month, week or day), 
    212 and three additional parameters for on-the-fly interpolation. 
     198and three additional parameters for the on-the-fly interpolation. 
    213199When adding a new input variable, the developer has to add the associated structure in the namelist, 
    214200read this information by mirroring the namelist read in \rou{sbc\_blk\_init} for example, 
    215201and simply call \rou{fld\_read} to obtain the desired input field at the model time-step and grid points. 
    216202 
    217 The only constraints are that the input file is a NetCDF file, the file name follows a nomenclature  
     203The only constraints are that the input file is a NetCDF file, the file name follows a nomenclature 
    218204(see \autoref{subsec:SBC_fldread}), the period it cover is one year, month, week or day, and, 
    219205if on-the-fly interpolation is used, a file of weights must be supplied (see \autoref{subsec:SBC_iof}). 
    220206 
    221207Note that when an input data is archived on a disc which is accessible directly from the workspace where 
    222 the code is executed, then the use can set the \np{cn\_dir} to the pathway leading to the data. 
    223 By default, the data are assumed to have been copied so that cn\_dir='./'. 
    224  
    225 % ------------------------------------------------------------------------------------------------------------- 
    226 % Input Data specification (\mdl{fldread}) 
    227 % ------------------------------------------------------------------------------------------------------------- 
    228 \subsection[Input data specification (\textit{fldread.F90})] 
    229 {Input data specification (\protect\mdl{fldread})} 
     208the code is executed, then the user can set the \np{cn_dir}{cn\_dir} to the pathway leading to the data. 
     209By default, the data are assumed to be in the same directory as the executable, so that cn\_dir='./'. 
     210 
     211%% ================================================================================================= 
     212\subsection[Input data specification (\textit{fldread.F90})]{Input data specification (\protect\mdl{fldread})} 
    230213\label{subsec:SBC_fldread} 
    231214 
    232215The structure associated with an input variable contains the following information: 
    233216\begin{forlines} 
    234 !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !  
     217!  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    235218!             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    236219\end{forlines} 
    237 where  
    238 \begin{description}   
    239 \item[File name]: 
    240   the stem name of the NetCDF file to be open. 
     220where 
     221\begin{description} 
     222\item [File name]: the stem name of the NetCDF file to be opened. 
    241223  This stem will be completed automatically by the model, with the addition of a '.nc' at its end and 
    242224  by date information and possibly a prefix (when using AGRIF). 
    243   Tab.\autoref{tab:fldread} provides the resulting file name in all possible cases according to 
     225  \autoref{tab:SBC_fldread} provides the resulting file name in all possible cases according to 
    244226  whether it is a climatological file or not, and to the open/close frequency (see below for definition). 
    245  
    246 %--------------------------------------------------TABLE-------------------------------------------------- 
    247227  \begin{table}[htbp] 
    248     \begin{center} 
    249       \begin{tabular}{|l|c|c|c|} 
    250         \hline 
    251         & daily or weekLLL         & monthly                   &   yearly          \\   \hline 
    252         \np{clim}\forcode{ = .false.}  & fn\_yYYYYmMMdDD.nc  &   fn\_yYYYYmMM.nc   &   fn\_yYYYY.nc  \\   \hline 
    253         \np{clim}\forcode{ = .true.}         & not possible                  &  fn\_m??.nc             &   fn                \\   \hline 
    254       \end{tabular} 
    255     \end{center} 
    256     \caption{ 
    257       \protect\label{tab:fldread} 
    258       naming nomenclature for climatological or interannual input file, as a function of the Open/close frequency. 
     228    \centering 
     229    \begin{tabular}{|l|c|c|c|} 
     230      \hline 
     231                                  &  daily or weekLL     &  monthly           &  yearly        \\ 
     232      \hline 
     233      \np[=.false.]{clim}{clim} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\ 
     234      \hline 
     235      \np[=.true.]{clim}{clim}  &  not possible        &  fn\_m??.nc        &  fn            \\ 
     236      \hline 
     237    \end{tabular} 
     238    \caption[Naming nomenclature for climatological or interannual input file]{ 
     239      Naming nomenclature for climatological or interannual input file, 
     240      as a function of the open/close frequency. 
    259241      The stem name is assumed to be 'fn'. 
    260242      For weekly files, the 'LLL' corresponds to the first three letters of the first day of the week 
    261       (\ie 'sun','sat','fri','thu','wed','tue','mon'). 
    262       The 'YYYY', 'MM' and 'DD' should be replaced by the actual year/month/day, always coded with 4 or 2 digits. 
    263       Note that (1) in mpp, if the file is split over each subdomain, the suffix '.nc' is replaced by '\_PPPP.nc', 
     243      (\ie\ 'sun','sat','fri','thu','wed','tue','mon'). 
     244      The 'YYYY', 'MM' and 'DD' should be replaced by the actual year/month/day, 
     245      always coded with 4 or 2 digits. 
     246      Note that (1) in mpp, if the file is split over each subdomain, 
     247      the suffix '.nc' is replaced by '\_PPPP.nc', 
    264248      where 'PPPP' is the process number coded with 4 digits; 
    265       (2) when using AGRIF, the prefix '\_N' is added to files, where 'N'  is the child grid number. 
     249      (2) when using AGRIF, the prefix '\_N' is added to files, where 'N' is the child grid number. 
    266250    } 
     251    \label{tab:SBC_fldread} 
    267252  \end{table} 
    268 %-------------------------------------------------------------------------------------------------------------- 
    269    
    270  
    271 \item[Record frequency]: 
    272   the frequency of the records contained in the input file. 
     253\item [Record frequency]: the frequency of the records contained in the input file. 
    273254  Its unit is in hours if it is positive (for example 24 for daily forcing) or in months if negative 
    274255  (for example -1 for monthly forcing or -12 for annual forcing). 
    275   Note that this frequency must really be an integer and not a real. 
    276   On some computers, seting it to '24.' can be interpreted as 240! 
    277  
    278 \item[Variable name]: 
    279   the name of the variable to be read in the input NetCDF file. 
    280  
    281 \item[Time interpolation]: 
    282   a logical to activate, or not, the time interpolation. 
     256  Note that this frequency must REALLY be an integer and not a real. 
     257  On some computers, setting it to '24.' can be interpreted as 240! 
     258\item [Variable name]: the name of the variable to be read in the input NetCDF file. 
     259\item [Time interpolation]: a logical to activate, or not, the time interpolation. 
    283260  If set to 'false', the forcing will have a steplike shape remaining constant during each forcing period. 
    284261  For example, when using a daily forcing without time interpolation, the forcing remaining constant from 
    285262  00h00'00'' to 23h59'59". 
    286263  If set to 'true', the forcing will have a broken line shape. 
    287   Records are assumed to be dated the middle of the forcing period. 
     264  Records are assumed to be dated at the middle of the forcing period. 
    288265  For example, when using a daily forcing with time interpolation, 
    289   linear interpolation will be performed between mid-day of two consecutive days.  
    290  
    291 \item[Climatological forcing]: 
    292   a logical to specify if a input file contains climatological forcing which can be cycle in time, 
     266  linear interpolation will be performed between mid-day of two consecutive days. 
     267\item [Climatological forcing]: a logical to specify if a input file contains climatological forcing which can be cycle in time, 
    293268  or an interannual forcing which will requires additional files if 
    294   the period covered by the simulation exceed the one of the file. 
    295   See the above the file naming strategy which impacts the expected name of the file to be opened.  
    296  
    297 \item[Open/close frequency]: 
    298   the frequency at which forcing files must be opened/closed. 
     269  the period covered by the simulation exceeds the one of the file. 
     270  See the above file naming strategy which impacts the expected name of the file to be opened. 
     271\item [Open/close frequency]: the frequency at which forcing files must be opened/closed. 
    299272  Four cases are coded: 
    300273  'daily', 'weekLLL' (with 'LLL' the first 3 letters of the first day of the week), 'monthly' and 'yearly' which 
    … …  
    302275  Files are assumed to contain data from the beginning of the open/close period. 
    303276  For example, the first record of a yearly file containing daily data is Jan 1st even if 
    304   the experiment is not starting at the beginning of the year.  
    305  
    306 \item[Others]: 
    307   'weights filename', 'pairing rotation' and 'land/sea mask' are associated with 
     277  the experiment is not starting at the beginning of the year. 
     278\item [Others]:  'weights filename', 'pairing rotation' and 'land/sea mask' are associated with 
    308279  on-the-fly interpolation which is described in \autoref{subsec:SBC_iof}. 
    309  
    310280\end{description} 
    311281 
    … …  
    315285the date of the records read in the input files. 
    316286Following \citet{leclair.madec_OM09}, the date of a time step is set at the middle of the time step. 
    317 For example, for an experiment starting at 0h00'00" with a one hour time-step, 
     287For example, for an experiment starting at 0h00'00" with a one-hour time-step, 
    318288a time interpolation will be performed at the following time: 0h30'00", 1h30'00", 2h30'00", etc. 
    319289However, for forcing data related to the surface module, 
    320 values are not needed at every time-step but at every \np{nn\_fsbc} time-step. 
    321 For example with \np{nn\_fsbc}\forcode{ = 3}, the surface module will be called at time-steps 1, 4, 7, etc. 
    322 The date used for the time interpolation is thus redefined to be at the middle of \np{nn\_fsbc} time-step period. 
    323 In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\  
     290values are not needed at every time-step but at every \np{nn_fsbc}{nn\_fsbc} time-step. 
     291For example with \np[=3]{nn_fsbc}{nn\_fsbc}, the surface module will be called at time-steps 1, 4, 7, etc. 
     292The date used for the time interpolation is thus redefined to the middle of \np{nn_fsbc}{nn\_fsbc} time-step period. 
     293In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\ 
    324294(2) For code readablility and maintenance issues, we don't take into account the NetCDF input file calendar. 
    325295The calendar associated with the forcing field is build according to the information provided by 
    326296user in the record frequency, the open/close frequency and the type of temporal interpolation. 
    327297For example, the first record of a yearly file containing daily data that will be interpolated in time is assumed to 
    328 be start Jan 1st at 12h00'00" and end Dec 31st at 12h00'00". \\ 
     298start Jan 1st at 12h00'00" and end Dec 31st at 12h00'00". \\ 
    329299(3) If a time interpolation is requested, the code will pick up the needed data in the previous (next) file when 
    330300interpolating data with the first (last) record of the open/close period. 
    331 For example, if the input file specifications are ''yearly, containing daily data to be interpolated in time'',  
     301For example, if the input file specifications are ''yearly, containing daily data to be interpolated in time'', 
    332302the values given by the code between 00h00'00" and 11h59'59" on Jan 1st will be interpolated values between 
    333303Dec 31st 12h00'00" and Jan 1st 12h00'00". 
    334304If the forcing is climatological, Dec and Jan will be keep-up from the same year. 
    335305However, if the forcing is not climatological, at the end of 
    336 the open/close period the code will automatically close the current file and open the next one. 
     306the open/close period, the code will automatically close the current file and open the next one. 
    337307Note that, if the experiment is starting (ending) at the beginning (end) of 
    338 an open/close period we do accept that the previous (next) file is not existing. 
     308an open/close period, we do accept that the previous (next) file is not existing. 
    339309In this case, the time interpolation will be performed between two identical values. 
    340310For example, when starting an experiment on Jan 1st of year Y with yearly files and daily data to be interpolated, 
    341311we do accept that the file related to year Y-1 is not existing. 
    342312The value of Jan 1st will be used as the missing one for Dec 31st of year Y-1. 
    343 If the file of year Y-1 exists, the code will read its last record.  
     313If the file of year Y-1 exists, the code will read its last record. 
    344314Therefore, this file can contain only one record corresponding to Dec 31st, 
    345315a useful feature for user considering that it is too heavy to manipulate the complete file for year Y-1. 
    346316 
    347  
    348 % ------------------------------------------------------------------------------------------------------------- 
    349 % Interpolation on the Fly 
    350 % ------------------------------------------------------------------------------------------------------------- 
     317%% ================================================================================================= 
    351318\subsection{Interpolation on-the-fly} 
    352319\label{subsec:SBC_iof} 
    … …  
    354321Interpolation on the Fly allows the user to supply input files required for the surface forcing on 
    355322grids other than the model grid. 
    356 To do this he or she must supply, in addition to the source data file, a file of weights to be used to 
     323To do this, he or she must supply, in addition to the source data file(s), a file of weights to be used to 
    357324interpolate from the data grid to the model grid. 
    358325The original development of this code used the SCRIP package 
    359326(freely available \href{http://climate.lanl.gov/Software/SCRIP}{here} under a copyright agreement). 
    360 In principle, any package can be used to generate the weights, but the variables in 
     327In principle, any package such as CDO can be used to generate the weights, but the variables in 
    361328the input weights file must have the same names and meanings as assumed by the model. 
    362 Two methods are currently available: bilinear and bicubic interpolation. 
     329Two methods are currently available: bilinear and bicubic interpolations. 
    363330Prior to the interpolation, providing a land/sea mask file, the user can decide to remove land points from 
    364331the input file and substitute the corresponding values with the average of the 8 neighbouring points in 
    … …  
    366333Only "sea points" are considered for the averaging. 
    367334The land/sea mask file must be provided in the structure associated with the input variable. 
    368 The netcdf land/sea mask variable name must be 'LSM' it must have the same horizontal and vertical dimensions of 
    369 the associated variable and should be equal to 1 over land and 0 elsewhere. 
    370 The procedure can be recursively applied setting nn\_lsm > 1 in namsbc namelist. 
    371 Note that nn\_lsm=0 forces the code to not apply the procedure even if a file for land/sea mask is supplied. 
    372  
     335The netcdf land/sea mask variable name must be 'LSM' and must have the same horizontal and vertical dimensions as 
     336the associated variables and should be equal to 1 over land and 0 elsewhere. 
     337The procedure can be recursively applied by setting nn\_lsm > 1 in namsbc namelist. 
     338Note that nn\_lsm=0 forces the code to not apply the procedure, even if a land/sea mask file is supplied. 
     339 
     340%% ================================================================================================= 
    373341\subsubsection{Bilinear interpolation} 
    374342\label{subsec:SBC_iof_bilinear} 
    … …  
    376344The input weights file in this case has two sets of variables: 
    377345src01, src02, src03, src04 and wgt01, wgt02, wgt03, wgt04. 
    378 The "src" variables correspond to the point in the input grid to which the weight "wgt" is to be applied. 
     346The "src" variables correspond to the point in the input grid to which the weight "wgt" is applied. 
    379347Each src value is an integer corresponding to the index of a point in the input grid when 
    380348written as a one dimensional array. 
    … …  
    392360and wgt(1) corresponds to variable "wgt01" for example. 
    393361 
     362%% ================================================================================================= 
    394363\subsubsection{Bicubic interpolation} 
    395364\label{subsec:SBC_iof_bicubic} 
    396365 
    397 Again there are two sets of variables: "src" and "wgt". 
    398 But in this case there are 16 of each. 
     366Again, there are two sets of variables: "src" and "wgt". 
     367But in this case, there are 16 of each. 
    399368The symbolic algorithm used to calculate values on the model grid is now: 
    400369 
    … …  
    402371  \begin{split} 
    403372    f_{m}(i,j) =  f_{m}(i,j) +& \sum_{k=1}^{4} {wgt(k)f(idx(src(k)))} 
    404     +   \sum_{k=5}^{8} {wgt(k)\left.\frac{\partial f}{\partial i}\right| _{idx(src(k))} }    \\ 
    405     +& \sum_{k=9}^{12} {wgt(k)\left.\frac{\partial f}{\partial j}\right| _{idx(src(k))} } 
    406     +   \sum_{k=13}^{16} {wgt(k)\left.\frac{\partial ^2 f}{\partial i \partial j}\right| _{idx(src(k))} } 
     373    +  \sum_{k=5 }^{8 } {wgt(k)\left.\frac{\partial f}{\partial i}\right| _{idx(src(k))} }    \\ 
     374    +& \sum_{k=9 }^{12} {wgt(k)\left.\frac{\partial f}{\partial j}\right| _{idx(src(k))} } 
     375    +  \sum_{k=13}^{16} {wgt(k)\left.\frac{\partial ^2 f}{\partial i \partial j}\right| _{idx(src(k))} } 
    407376  \end{split} 
    408377\] 
    409378The gradients here are taken with respect to the horizontal indices and not distances since 
    410 the spatial dependency has been absorbed into the weights. 
    411  
     379the spatial dependency has been included into the weights. 
     380 
     381%% ================================================================================================= 
    412382\subsubsection{Implementation} 
    413383\label{subsec:SBC_iof_imp} 
    … …  
    421391inspecting a global attribute stored in the weights input file. 
    422392This attribute must be called "ew\_wrap" and be of integer type. 
    423 If it is negative, the input non-model grid is assumed not to be cyclic. 
     393If it is negative, the input non-model grid is assumed to be not cyclic. 
    424394If zero or greater, then the value represents the number of columns that overlap. 
    425395$E.g.$ if the input grid has columns at longitudes 0, 1, 2, .... , 359, then ew\_wrap should be set to 0; 
    426396if longitudes are 0.5, 2.5, .... , 358.5, 360.5, 362.5, ew\_wrap should be 2. 
    427397If the model does not find attribute ew\_wrap, then a value of -999 is assumed. 
    428 In this case the \rou{fld\_read} routine defaults ew\_wrap to value 0 and 
     398In this case, the \rou{fld\_read} routine defaults ew\_wrap to value 0 and 
    429399therefore the grid is assumed to be cyclic with no overlapping columns. 
    430 (In fact this only matters when bicubic interpolation is required.) 
     400(In fact, this only matters when bicubic interpolation is required.) 
    431401Note that no testing is done to check the validity in the model, 
    432402since there is no way of knowing the name used for the longitude variable, 
    … …  
    445415or is a copy of one from the first few columns on the opposite side of the grid (cyclical case). 
    446416 
     417%% ================================================================================================= 
    447418\subsubsection{Limitations} 
    448419\label{subsec:SBC_iof_lim} 
    449420 
    450 \begin{enumerate}   
    451 \item 
    452   The case where input data grids are not logically rectangular has not been tested. 
    453 \item 
    454   This code is not guaranteed to produce positive definite answers from positive definite inputs when 
     421\begin{enumerate} 
     422\item The case where input data grids are not logically rectangular (irregular grid case) has not been tested. 
     423\item This code is not guaranteed to produce positive definite answers from positive definite inputs when 
    455424  a bicubic interpolation method is used. 
    456 \item 
    457   The cyclic condition is only applied on left and right columns, and not to top and bottom rows. 
    458 \item 
    459   The gradients across the ends of a cyclical grid assume that the grid spacing between 
     425\item The cyclic condition is only applied on left and right columns, and not to top and bottom rows. 
     426\item The gradients across the ends of a cyclical grid assume that the grid spacing between 
    460427  the two columns involved are consistent with the weights used. 
    461 \item 
    462   Neither interpolation scheme is conservative. (There is a conservative scheme available in SCRIP, 
     428\item Neither interpolation scheme is conservative. (There is a conservative scheme available in SCRIP, 
    463429  but this has not been implemented.) 
    464430\end{enumerate} 
    465431 
     432%% ================================================================================================= 
    466433\subsubsection{Utilities} 
    467434\label{subsec:SBC_iof_util} 
    … …  
    471438(see the directory NEMOGCM/TOOLS/WEIGHTS). 
    472439 
    473 % ------------------------------------------------------------------------------------------------------------- 
    474 % Standalone Surface Boundary Condition Scheme 
    475 % ------------------------------------------------------------------------------------------------------------- 
    476 \subsection{Standalone surface boundary condition scheme} 
    477 \label{subsec:SAS_iof} 
    478  
    479 %---------------------------------------namsbc_ana-------------------------------------------------- 
    480  
    481 \nlst{namsbc_sas} 
    482 %-------------------------------------------------------------------------------------------------------------- 
    483  
    484 In some circumstances it may be useful to avoid calculating the 3D temperature, 
    485 salinity and velocity fields and simply read them in from a previous run or receive them from OASIS.   
     440%% ================================================================================================= 
     441\subsection{Standalone surface boundary condition scheme (SAS)} 
     442\label{subsec:SBC_SAS} 
     443 
     444\begin{listing} 
     445  \nlst{namsbc_sas} 
     446  \caption{\forcode{&namsbc_sas}} 
     447  \label{lst:namsbc_sas} 
     448\end{listing} 
     449 
     450In some circumstances, it may be useful to avoid calculating the 3D temperature, 
     451salinity and velocity fields and simply read them in from a previous run or receive them from OASIS. 
    486452For example: 
    487453 
    488454\begin{itemize} 
    489 \item 
    490   Multiple runs of the model are required in code development to 
     455\item Multiple runs of the model are required in code development to 
    491456  see the effect of different algorithms in the bulk formulae. 
    492 \item 
    493   The effect of different parameter sets in the ice model is to be examined. 
    494 \item 
    495   Development of sea-ice algorithms or parameterizations. 
    496 \item 
    497   Spinup of the iceberg floats 
    498 \item 
    499   Ocean/sea-ice simulation with both media running in parallel (\np{ln\_mixcpl}\forcode{ = .true.}) 
     457\item The effect of different parameter sets in the ice model is to be examined. 
     458\item Development of sea-ice algorithms or parameterizations. 
     459\item Spinup of the iceberg floats 
     460\item Ocean/sea-ice simulation with both models running in parallel (\np[=.true.]{ln_mixcpl}{ln\_mixcpl}) 
    500461\end{itemize} 
    501462 
    502 The StandAlone Surface scheme provides this utility. 
    503 Its options are defined through the \ngn{namsbc\_sas} namelist variables. 
     463The Standalone Surface scheme provides this capacity. 
     464Its options are defined through the \nam{sbc_sas}{sbc\_sas} namelist variables. 
    504465A new copy of the model has to be compiled with a configuration based on ORCA2\_SAS\_LIM. 
    505 However no namelist parameters need be changed from the settings of the previous run (except perhaps nn{\_}date0). 
     466However, no namelist parameters need be changed from the settings of the previous run (except perhaps nn\_date0). 
    506467In this configuration, a few routines in the standard model are overriden by new versions. 
    507468Routines replaced are: 
    508469 
    509470\begin{itemize} 
    510 \item 
    511   \mdl{nemogcm}: 
    512   This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (\mdl{step}). 
     471\item \mdl{nemogcm}: This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (\mdl{step}). 
    513472  Since the ocean state is not calculated all associated initialisations have been removed. 
    514 \item 
    515   \mdl{step}: 
    516   The main time stepping routine now only needs to call the sbc routine (and a few utility functions). 
    517 \item 
    518   \mdl{sbcmod}: 
    519   This has been cut down and now only calculates surface forcing and the ice model required. 
     473\item \mdl{step}: The main time stepping routine now only needs to call the sbc routine (and a few utility functions). 
     474\item \mdl{sbcmod}: This has been cut down and now only calculates surface forcing and the ice model required. 
    520475  New surface modules that can function when only the surface level of the ocean state is defined can also be added 
    521   (\eg icebergs). 
    522 \item 
    523   \mdl{daymod}: 
    524   No ocean restarts are read or written (though the ice model restarts are retained), 
     476  (\eg\ icebergs). 
     477\item \mdl{daymod}: No ocean restarts are read or written (though the ice model restarts are retained), 
    525478  so calls to restart functions have been removed. 
    526479  This also means that the calendar cannot be controlled by time in a restart file, 
    527   so the user must make sure that nn{\_}date0 in the model namelist is correct for his or her purposes. 
    528 \item 
    529   \mdl{stpctl}: 
    530   Since there is no free surface solver, references to it have been removed from \rou{stp\_ctl} module. 
    531 \item 
    532   \mdl{diawri}: 
    533   All 3D data have been removed from the output. 
     480  so the user must check that nn\_date0 in the model namelist is correct for his or her purposes. 
     481\item \mdl{stpctl}: Since there is no free surface solver, references to it have been removed from \rou{stp\_ctl} module. 
     482\item \mdl{diawri}: All 3D data have been removed from the output. 
    534483  The surface temperature, salinity and velocity components (which have been read in) are written along with 
    535484  relevant forcing and ice data. 
    … …  
    539488 
    540489\begin{itemize} 
    541 \item 
    542   \mdl{sbcsas}: 
    543   This module initialises the input files needed for reading temperature, salinity and 
     490\item \mdl{sbcsas}: This module initialises the input files needed for reading temperature, salinity and 
    544491  velocity arrays at the surface. 
    545   These filenames are supplied in namelist namsbc{\_}sas. 
    546   Unfortunately because of limitations with the \mdl{iom} module, 
     492  These filenames are supplied in namelist namsbc\_sas. 
     493  Unfortunately, because of limitations with the \mdl{iom} module, 
    547494  the full 3D fields from the mean files have to be read in and interpolated in time, 
    548495  before using just the top level. 
    … …  
    550497\end{itemize} 
    551498 
    552  
    553 % Missing the description of the 2 following variables: 
    554 %   ln_3d_uve   = .true.    !  specify whether we are supplying a 3D u,v and e3 field 
    555 %   ln_read_frq = .false.    !  specify whether we must read frq or not 
    556  
    557  
    558  
    559 % ================================================================ 
    560 % Analytical formulation (sbcana module)  
    561 % ================================================================ 
    562 \section[Analytical formulation (\textit{sbcana.F90})] 
    563 {Analytical formulation (\protect\mdl{sbcana})} 
    564 \label{sec:SBC_ana} 
    565  
    566 %---------------------------------------namsbc_ana-------------------------------------------------- 
    567 % 
    568 %\nlst{namsbc_ana} 
    569 %-------------------------------------------------------------------------------------------------------------- 
    570  
    571 The analytical formulation of the surface boundary condition is the default scheme. 
    572 In this case, all the six fluxes needed by the ocean are assumed to be uniform in space. 
    573 They take constant values given in the namelist \ngn{namsbc{\_}ana} by 
    574 the variables \np{rn\_utau0}, \np{rn\_vtau0}, \np{rn\_qns0}, \np{rn\_qsr0}, and \np{rn\_emp0} 
    575 ($\textit{emp}=\textit{emp}_S$). 
    576 The runoff is set to zero. 
    577 In addition, the wind is allowed to reach its nominal value within a given number of time steps (\np{nn\_tau000}). 
    578  
    579 If a user wants to apply a different analytical forcing, 
    580 the \mdl{sbcana} module can be modified to use another scheme. 
    581 As an example, the \mdl{sbc\_ana\_gyre} routine provides the analytical forcing for the GYRE configuration 
    582 (see GYRE configuration manual, in preparation). 
    583  
    584  
    585 % ================================================================ 
    586 % Flux formulation  
    587 % ================================================================ 
    588 \section[Flux formulation (\textit{sbcflx.F90})] 
    589 {Flux formulation (\protect\mdl{sbcflx})} 
     499The user can also choose in the \nam{sbc_sas}{sbc\_sas} namelist to read the mean (nn\_fsbc time-step) fraction of solar net radiation absorbed in the 1st T level using 
     500 (\np[=.true.]{ln_flx}{ln\_flx}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln_flx}{ln\_flx}\forcode{=.true.}). In that last case, only the 1st level will be read in. 
     501 
     502%% ================================================================================================= 
     503\section[Flux formulation (\textit{sbcflx.F90})]{Flux formulation (\protect\mdl{sbcflx})} 
    590504\label{sec:SBC_flx} 
    591 %------------------------------------------namsbc_flx---------------------------------------------------- 
    592  
    593 \nlst{namsbc_flx}  
    594 %------------------------------------------------------------------------------------------------------------- 
    595  
    596 In the flux formulation (\np{ln\_flx}\forcode{ = .true.}), 
     505 
     506\begin{listing} 
     507  \nlst{namsbc_flx} 
     508  \caption{\forcode{&namsbc_flx}} 
     509  \label{lst:namsbc_flx} 
     510\end{listing} 
     511 
     512In the flux formulation (\np[=.true.]{ln_flx}{ln\_flx}), 
    597513the surface boundary condition fields are directly read from input files. 
    598 The user has to define in the namelist \ngn{namsbc{\_}flx} the name of the file, 
     514The user has to define in the namelist \nam{sbc_flx}{sbc\_flx} the name of the file, 
    599515the name of the variable read in the file, the time frequency at which it is given (in hours), 
    600516and a logical setting whether a time interpolation to the model time step is required for this field. 
    … …  
    604520See \autoref{subsec:SBC_ssr} for its specification. 
    605521 
    606  
    607 % ================================================================ 
    608 % Bulk formulation 
    609 % ================================================================ 
    610 \section[Bulk formulation {(\textit{sbcblk\{\_core,\_clio\}.F90})}] 
    611 {Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}} 
     522%% ================================================================================================= 
     523\section[Bulk formulation (\textit{sbcblk.F90})]{Bulk formulation (\protect\mdl{sbcblk})} 
    612524\label{sec:SBC_blk} 
    613525 
    614 In the bulk formulation, the surface boundary condition fields are computed using bulk formulae and atmospheric fields and ocean (and ice) variables. 
     526\begin{listing} 
     527  \nlst{namsbc_blk} 
     528  \caption{\forcode{&namsbc_blk}} 
     529  \label{lst:namsbc_blk} 
     530\end{listing} 
     531 
     532In the bulk formulation, the surface boundary condition fields are computed with bulk formulae using atmospheric fields 
     533and ocean (and sea-ice) variables averaged over \np{nn_fsbc}{nn\_fsbc} time-step. 
    615534 
    616535The atmospheric fields used depend on the bulk formulae used. 
    617 Two bulk formulations are available: 
    618 the CORE and the CLIO bulk formulea. 
     536In forced mode, when a sea-ice model is used, a specific bulk formulation is used. 
     537Therefore, different bulk formulae are used for the turbulent fluxes computation 
     538over the ocean and over sea-ice surface. 
     539For the ocean, four bulk formulations are available thanks to the \href{https://brodeau.github.io/aerobulk/}{Aerobulk} package (\citet{brodeau.barnier.ea_JPO16}): 
     540the NCAR (formerly named CORE), COARE 3.0, COARE 3.5 and ECMWF bulk formulae. 
    619541The choice is made by setting to true one of the following namelist variable: 
    620 \np{ln\_core} or \np{ln\_clio}. 
    621  
    622 Note: 
    623 in forced mode, when a sea-ice model is used, a bulk formulation (CLIO or CORE) have to be used. 
    624 Therefore the two bulk (CLIO and CORE) formulea include the computation of the fluxes over 
    625 both an ocean and an ice surface.  
    626  
    627 % ------------------------------------------------------------------------------------------------------------- 
    628 %        CORE Bulk formulea 
    629 % ------------------------------------------------------------------------------------------------------------- 
    630 \subsection[CORE formulea (\textit{sbcblk\_core.F90}, \forcode{ln_core = .true.})] 
    631 {CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})} 
    632 \label{subsec:SBC_blk_core} 
    633 %------------------------------------------namsbc_core---------------------------------------------------- 
    634 % 
    635 %\nlst{namsbc_core} 
    636 %------------------------------------------------------------------------------------------------------------- 
    637  
    638 The CORE bulk formulae have been developed by \citet{large.yeager_rpt04}. 
    639 They have been designed to handle the CORE forcing, a mixture of NCEP reanalysis and satellite data. 
    640 They use an inertial dissipative method to compute the turbulent transfer coefficients 
    641 (momentum, sensible heat and evaporation) from the 10 metre wind speed, air temperature and specific humidity. 
    642 This \citet{large.yeager_rpt04} dataset is available through 
    643 the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. 
    644  
    645 Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
    646 This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
    647  
    648 Options are defined through the  \ngn{namsbc\_core} namelist variables. 
    649 The required 8 input fields are: 
    650  
    651 %--------------------------------------------------TABLE-------------------------------------------------- 
     542 \np{ln_NCAR}{ln\_NCAR}, \np{ln_COARE_3p0}{ln\_COARE\_3p0},  \np{ln_COARE_3p5}{ln\_COARE\_3p5} and  \np{ln_ECMWF}{ln\_ECMWF}. 
     543For sea-ice, three possibilities can be selected: 
     544a constant transfer coefficient (1.4e-3; default value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations 
     545 
     546Common options are defined through the \nam{sbc_blk}{sbc\_blk} namelist variables. 
     547The required 9 input fields are: 
     548 
    652549\begin{table}[htbp] 
    653   \label{tab:CORE} 
    654   \begin{center} 
    655     \begin{tabular}{|l|c|c|c|} 
    656       \hline 
    657       Variable desciption              & Model variable  & Units   & point \\    \hline 
    658       i-component of the 10m air velocity & utau      & $m.s^{-1}$         & T  \\  \hline 
    659       j-component of the 10m air velocity & vtau      & $m.s^{-1}$         & T  \\  \hline 
    660       10m air temperature              & tair      & \r{}$K$            & T   \\ \hline 
    661       Specific humidity             & humi      & \%              & T \\      \hline 
    662       Incoming long wave radiation     & qlw    & $W.m^{-2}$         & T \\      \hline 
    663       Incoming short wave radiation    & qsr    & $W.m^{-2}$         & T \\      \hline 
    664       Total precipitation (liquid + solid)   & precip & $Kg.m^{-2}.s^{-1}$ & T \\   \hline 
    665       Solid precipitation              & snow      & $Kg.m^{-2}.s^{-1}$ & T \\   \hline 
     550  \centering 
     551  \begin{tabular}{|l|c|c|c|} 
     552    \hline 
     553    Variable description                 & Model variable & Units              & point \\ 
     554    \hline 
     555    i-component of the 10m air velocity  & utau           & $m.s^{-1}$         & T     \\ 
     556    \hline 
     557    j-component of the 10m air velocity  & vtau           & $m.s^{-1}$         & T     \\ 
     558    \hline 
     559    10m air temperature                  & tair           & \r{}$K$            & T     \\ 
     560    \hline 
     561    Specific humidity                    & humi           & \%                 & T     \\ 
     562    \hline 
     563    Incoming long wave radiation         & qlw            & $W.m^{-2}$         & T     \\ 
     564    \hline 
     565    Incoming short wave radiation        & qsr            & $W.m^{-2}$         & T     \\ 
     566    \hline 
     567    Total precipitation (liquid + solid) & precip         & $Kg.m^{-2}.s^{-1}$ & T     \\ 
     568    \hline 
     569    Solid precipitation                  & snow           & $Kg.m^{-2}.s^{-1}$ & T     \\ 
     570    \hline 
     571    Mean sea-level pressure              & slp            & $hPa$              & T     \\ 
     572    \hline 
    666573    \end{tabular} 
    667   \end{center} 
     574  \label{tab:SBC_BULK} 
    668575\end{table} 
    669 %-------------------------------------------------------------------------------------------------------------- 
    670576 
    671577Note that the air velocity is provided at a tracer ocean point, not at a velocity ocean point ($u$- and $v$-points). 
    … …  
    673579the ocean grid size is the same or larger than the one of the input atmospheric fields. 
    674580 
    675 The \np{sn\_wndi}, \np{sn\_wndj}, \np{sn\_qsr}, \np{sn\_qlw}, \np{sn\_tair}, \np{sn\_humi}, \np{sn\_prec}, 
    676 \np{sn\_snow}, \np{sn\_tdif} parameters describe the fields and the way they have to be used 
    677 (spatial and temporal interpolations).  
    678  
    679 \np{cn\_dir} is the directory of location of bulk files 
    680 \np{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.) 
    681 \np{rn\_zqt}: is the height of humidity and temperature measurements (m) 
    682 \np{rn\_zu}: is the height of wind measurements (m) 
    683  
    684 Three multiplicative factors are availables:  
    685 \np{rn\_pfac} and \np{rn\_efac} allows to adjust (if necessary) the global freshwater budget by 
     581The \np{sn_wndi}{sn\_wndi}, \np{sn_wndj}{sn\_wndj}, \np{sn_qsr}{sn\_qsr}, \np{sn_qlw}{sn\_qlw}, \np{sn_tair}{sn\_tair}, \np{sn_humi}{sn\_humi}, \np{sn_prec}{sn\_prec}, 
     582\np{sn_snow}{sn\_snow}, \np{sn_tdif}{sn\_tdif} parameters describe the fields and the way they have to be used 
     583(spatial and temporal interpolations). 
     584 
     585\np{cn_dir}{cn\_dir} is the directory of location of bulk files 
     586\np{ln_taudif}{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.) 
     587\np{rn_zqt}{rn\_zqt}: is the height of humidity and temperature measurements (m) 
     588\np{rn_zu}{rn\_zu}: is the height of wind measurements (m) 
     589 
     590Three multiplicative factors are available: 
     591\np{rn_pfac}{rn\_pfac} and \np{rn_efac}{rn\_efac} allow to adjust (if necessary) the global freshwater budget by 
    686592increasing/reducing the precipitations (total and snow) and or evaporation, respectively. 
    687 The third one,\np{rn\_vfac}, control to which extend the ice/ocean velocities are taken into account in 
     593The third one,\np{rn_vfac}{rn\_vfac}, control to which extend the ice/ocean velocities are taken into account in 
    688594the calculation of surface wind stress. 
    689 Its range should be between zero and one, and it is recommended to set it to 0. 
    690  
    691 % ------------------------------------------------------------------------------------------------------------- 
    692 %        CLIO Bulk formulea 
    693 % ------------------------------------------------------------------------------------------------------------- 
    694 \subsection[CLIO formulea (\textit{sbcblk\_clio.F90}, \forcode{ln_clio = .true.})] 
    695 {CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})} 
    696 \label{subsec:SBC_blk_clio} 
    697 %------------------------------------------namsbc_clio---------------------------------------------------- 
    698 % 
    699 %\nlst{namsbc_clio} 
    700 %------------------------------------------------------------------------------------------------------------- 
    701  
    702 The CLIO bulk formulae were developed several years ago for the Louvain-la-neuve coupled ice-ocean model 
    703 (CLIO, \cite{goosse.deleersnijder.ea_JGR99}).  
    704 They are simpler bulk formulae. 
    705 They assume the stress to be known and compute the radiative fluxes from a climatological cloud cover.  
    706  
    707 Options are defined through the  \ngn{namsbc\_clio} namelist variables. 
    708 The required 7 input fields are: 
    709  
    710 %--------------------------------------------------TABLE-------------------------------------------------- 
    711 \begin{table}[htbp] 
    712   \label{tab:CLIO} 
    713   \begin{center} 
    714     \begin{tabular}{|l|l|l|l|} 
    715       \hline 
    716       Variable desciption           & Model variable  & Units           & point \\  \hline 
    717       i-component of the ocean stress     & utau         & $N.m^{-2}$         & U \\   \hline 
    718       j-component of the ocean stress     & vtau         & $N.m^{-2}$         & V \\   \hline 
    719       Wind speed module             & vatm         & $m.s^{-1}$         & T \\   \hline 
    720       10m air temperature              & tair         & \r{}$K$            & T \\   \hline 
    721       Specific humidity                & humi         & \%              & T \\   \hline 
    722       Cloud cover                   &           & \%              & T \\   \hline 
    723       Total precipitation (liquid + solid)   & precip    & $Kg.m^{-2}.s^{-1}$ & T \\   \hline 
    724       Solid precipitation              & snow         & $Kg.m^{-2}.s^{-1}$ & T \\   \hline 
    725     \end{tabular} 
    726   \end{center} 
    727 \end{table} 
    728 %-------------------------------------------------------------------------------------------------------------- 
     595Its range must be between zero and one, and it is recommended to set it to 0 at low-resolution (ORCA2 configuration). 
    729596 
    730597As for the flux formulation, information about the input data required by the model is provided in 
    731 the namsbc\_blk\_core or namsbc\_blk\_clio namelist (see \autoref{subsec:SBC_fldread}).  
    732  
    733 % ================================================================ 
    734 % Coupled formulation 
    735 % ================================================================ 
    736 \section[Coupled formulation (\textit{sbccpl.F90})] 
    737 {Coupled formulation (\protect\mdl{sbccpl})} 
     598the namsbc\_blk namelist (see \autoref{subsec:SBC_fldread}). 
     599 
     600%% ================================================================================================= 
     601\subsection[Ocean-Atmosphere Bulk formulae (\textit{sbcblk\_algo\_coare.F90, sbcblk\_algo\_coare3p5.F90, sbcblk\_algo\_ecmwf.F90, sbcblk\_algo\_ncar.F90})]{Ocean-Atmosphere Bulk formulae (\mdl{sbcblk\_algo\_coare}, \mdl{sbcblk\_algo\_coare3p5}, \mdl{sbcblk\_algo\_ecmwf}, \mdl{sbcblk\_algo\_ncar})} 
     602\label{subsec:SBC_blk_ocean} 
     603 
     604Four different bulk algorithms are available to compute surface turbulent momentum and heat fluxes over the ocean. 
     605COARE 3.0, COARE 3.5 and ECMWF schemes mainly differ by their roughness lenghts computation and consequently 
     606their neutral transfer coefficients relationships with neutral wind. 
     607\begin{itemize} 
     608\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
     609  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
     610  They use an inertial dissipative method to compute the turbulent transfer coefficients 
     611  (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity. 
     612  This \citet{large.yeager_rpt04} dataset is available through 
     613  the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}. 
     614  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
     615  This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
     616\item COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}): See \citet{fairall.bradley.ea_JC03} for more details 
     617\item COARE 3.5 (\np[=.true.]{ln_COARE_3p5}{ln\_COARE\_3p5}): See \citet{edson.jampana.ea_JPO13} for more details 
     618\item ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}): Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation. 
     619  Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}. 
     620\end{itemize} 
     621 
     622%% ================================================================================================= 
     623\subsection{Ice-Atmosphere Bulk formulae} 
     624\label{subsec:SBC_blk_ice} 
     625 
     626Surface turbulent fluxes between sea-ice and the atmosphere can be computed in three different ways: 
     627 
     628\begin{itemize} 
     629\item Constant value (\np[ Cd_ice=1.4e-3 ]{constant value}{constant\ value}): 
     630  default constant value used for momentum and heat neutral transfer coefficients 
     631\item \citet{lupkes.gryanik.ea_JGR12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}): 
     632  This scheme adds a dependency on edges at leads, melt ponds and flows 
     633  of the constant neutral air-ice drag. After some approximations, 
     634  this can be resumed to a dependency on ice concentration (A). 
     635  This drag coefficient has a parabolic shape (as a function of ice concentration) 
     636  starting at 1.5e-3 for A=0, reaching 1.97e-3 for A=0.5 and going down 1.4e-3 for A=1. 
     637  It is theoretically applicable to all ice conditions (not only MIZ). 
     638\item \citet{lupkes.gryanik_JGR15} (\np[=.true.]{ln_Cd_L15}{ln\_Cd\_L15}): 
     639  Alternative turbulent transfer coefficients formulation between sea-ice 
     640  and atmosphere with distinct momentum and heat coefficients depending 
     641  on sea-ice concentration and atmospheric stability (no melt-ponds effect for now). 
     642  The parameterization is adapted from ECHAM6 atmospheric model. 
     643  Compared to Lupkes2012 scheme, it considers specific skin and form drags 
     644  to compute neutral transfer coefficients for both heat and momentum fluxes. 
     645  Atmospheric stability effect on transfer coefficient is also taken into account. 
     646\end{itemize} 
     647 
     648%% ================================================================================================= 
     649\section[Coupled formulation (\textit{sbccpl.F90})]{Coupled formulation (\protect\mdl{sbccpl})} 
    738650\label{sec:SBC_cpl} 
    739 %------------------------------------------namsbc_cpl---------------------------------------------------- 
    740  
    741 \nlst{namsbc_cpl}  
    742 %------------------------------------------------------------------------------------------------------------- 
     651 
     652\begin{listing} 
     653  \nlst{namsbc_cpl} 
     654  \caption{\forcode{&namsbc_cpl}} 
     655  \label{lst:namsbc_cpl} 
     656\end{listing} 
    743657 
    744658In the coupled formulation of the surface boundary condition, 
    745 the fluxes are provided by the OASIS coupler at a frequency which is defined in the OASIS coupler, 
     659the fluxes are provided by the OASIS coupler at a frequency which is defined in the OASIS coupler namelist, 
    746660while sea and ice surface temperature, ocean and ice albedo, and ocean currents are sent to 
    747661the atmospheric component. 
    748662 
    749663A generalised coupled interface has been developed. 
    750 It is currently interfaced with OASIS-3-MCT (\key{oasis3}). 
    751 It has been successfully used to interface \NEMO to most of the European atmospheric GCM 
     664It is currently interfaced with OASIS-3-MCT versions 1 to 4 (\key{oasis3}). 
     665An additional specific CPP key (\key{oa3mct\_v1v2}) is needed for OASIS-3-MCT versions 1 and 2. 
     666It has been successfully used to interface \NEMO\ to most of the European atmospheric GCM 
    752667(ARPEGE, ECHAM, ECMWF, HadAM, HadGAM, LMDz), as well as to \href{http://wrf-model.org/}{WRF} 
    753668(Weather Research and Forecasting Model). 
    754669 
    755 Note that in addition to the setting of \np{ln\_cpl} to true, the \key{coupled} have to be defined. 
    756 The CPP key is mainly used in sea-ice to ensure that the atmospheric fluxes are actually received by 
    757 the ice-ocean system (no calculation of ice sublimation in coupled mode). 
    758 When PISCES biogeochemical model (\key{top} and \key{pisces}) is also used in the coupled system,  
    759 the whole carbon cycle is computed by defining \key{cpl\_carbon\_cycle}. 
     670When PISCES biogeochemical model (\key{top}) is also used in the coupled system, 
     671the whole carbon cycle is computed. 
    760672In this case, CO$_2$ fluxes will be exchanged between the atmosphere and the ice-ocean system 
    761 (and need to be activated in \ngn{namsbc{\_}cpl} ). 
     673(and need to be activated in \nam{sbc_cpl}{sbc\_cpl} ). 
    762674 
    763675The namelist above allows control of various aspects of the coupling fields (particularly for vectors) and 
    764676now allows for any coupling fields to have multiple sea ice categories (as required by LIM3 and CICE). 
    765 When indicating a multi-category coupling field in namsbc{\_}cpl the number of categories will be determined by 
     677When indicating a multi-category coupling field in \nam{sbc_cpl}{sbc\_cpl}, the number of categories will be determined by 
    766678the number used in the sea ice model. 
    767 In some limited cases it may be possible to specify single category coupling fields even when 
     679In some limited cases, it may be possible to specify single category coupling fields even when 
    768680the sea ice model is running with multiple categories - 
    769 in this case the user should examine the code to be sure the assumptions made are satisfactory. 
    770 In cases where this is definitely not possible the model should abort with an error message. 
    771 The new code has been tested using ECHAM with LIM2, and HadGAM3 with CICE but 
    772 although it will compile with \key{lim3} additional minor code changes may be required to run using LIM3. 
    773  
    774  
    775 % ================================================================ 
    776 %        Atmospheric pressure 
    777 % ================================================================ 
    778 \section[Atmospheric pressure (\textit{sbcapr.F90})] 
    779 {Atmospheric pressure (\protect\mdl{sbcapr})} 
     681in this case, the user should examine the code to be sure the assumptions made are satisfactory. 
     682In cases where this is definitely not possible, the model should abort with an error message. 
     683 
     684%% ================================================================================================= 
     685\section[Atmospheric pressure (\textit{sbcapr.F90})]{Atmospheric pressure (\protect\mdl{sbcapr})} 
    780686\label{sec:SBC_apr} 
    781 %------------------------------------------namsbc_apr---------------------------------------------------- 
    782  
    783 \nlst{namsbc_apr}  
    784 %------------------------------------------------------------------------------------------------------------- 
     687 
     688\begin{listing} 
     689  \nlst{namsbc_apr} 
     690  \caption{\forcode{&namsbc_apr}} 
     691  \label{lst:namsbc_apr} 
     692\end{listing} 
    785693 
    786694The optional atmospheric pressure can be used to force ocean and ice dynamics 
    787 (\np{ln\_apr\_dyn}\forcode{ = .true.}, \textit{\ngn{namsbc}} namelist). 
    788 The input atmospheric forcing defined via \np{sn\_apr} structure (\textit{namsbc\_apr} namelist) 
     695(\np[=.true.]{ln_apr_dyn}{ln\_apr\_dyn}, \nam{sbc}{sbc} namelist). 
     696The input atmospheric forcing defined via \np{sn_apr}{sn\_apr} structure (\nam{sbc_apr}{sbc\_apr} namelist) 
    789697can be interpolated in time to the model time step, and even in space when the interpolation on-the-fly is used. 
    790698When used to force the dynamics, the atmospheric pressure is further transformed into 
    … …  
    795703\] 
    796704where $P_{atm}$ is the atmospheric pressure and $P_o$ a reference atmospheric pressure. 
    797 A value of $101,000~N/m^2$ is used unless \np{ln\_ref\_apr} is set to true. 
    798 In this case $P_o$ is set to the value of $P_{atm}$ averaged over the ocean domain, 
    799 \ie the mean value of $\eta_{ib}$ is kept to zero at all time step. 
     705A value of $101,000~N/m^2$ is used unless \np{ln_ref_apr}{ln\_ref\_apr} is set to true. 
     706In this case, $P_o$ is set to the value of $P_{atm}$ averaged over the ocean domain, 
     707\ie\ the mean value of $\eta_{ib}$ is kept to zero at all time steps. 
    800708 
    801709The gradient of $\eta_{ib}$ is added to the RHS of the ocean momentum equation (see \mdl{dynspg} for the ocean). 
    802710For sea-ice, the sea surface height, $\eta_m$, which is provided to the sea ice model is set to $\eta - \eta_{ib}$ 
    803711(see \mdl{sbcssr} module). 
    804 $\eta_{ib}$ can be set in the output. 
     712$\eta_{ib}$ can be written in the output. 
    805713This can simplify altimetry data and model comparison as 
    806714inverse barometer sea surface height is usually removed from these date prior to their distribution. 
    807715 
    808716When using time-splitting and BDY package for open boundaries conditions, 
    809 the equivalent inverse barometer sea surface height $\eta_{ib}$ can be added to BDY ssh data:  
    810 \np{ln\_apr\_obc}  might be set to true. 
    811  
    812 % ================================================================ 
    813 %        Surface Tides Forcing 
    814 % ================================================================ 
    815 \section[Surface tides (\textit{sbctide.F90})] 
    816 {Surface tides (\protect\mdl{sbctide})} 
     717the equivalent inverse barometer sea surface height $\eta_{ib}$ can be added to BDY ssh data: 
     718\np{ln_apr_obc}{ln\_apr\_obc}  might be set to true. 
     719 
     720%% ================================================================================================= 
     721\section[Surface tides (\textit{sbctide.F90})]{Surface tides (\protect\mdl{sbctide})} 
    817722\label{sec:SBC_tide} 
    818723 
    819 %------------------------------------------nam_tide--------------------------------------- 
    820  
    821 \nlst{nam_tide} 
    822 %----------------------------------------------------------------------------------------- 
     724\begin{listing} 
     725  \nlst{nam_tide} 
     726  \caption{\forcode{&nam_tide}} 
     727  \label{lst:nam_tide} 
     728\end{listing} 
    823729 
    824730The tidal forcing, generated by the gravity forces of the Earth-Moon and Earth-Sun sytems, 
    825 is activated if \np{ln\_tide} and \np{ln\_tide\_pot} are both set to \forcode{.true.} in \ngn{nam\_tide}. 
    826 This translates as an additional barotropic force in the momentum equations \ref{eq:PE_dyn} such that: 
     731is activated if \np{ln_tide}{ln\_tide} and \np{ln_tide_pot}{ln\_tide\_pot} are both set to \forcode{.true.} in \nam{_tide}{\_tide}. 
     732This translates as an additional barotropic force in the momentum \autoref{eq:MB_PE_dyn} such that: 
    827733\[ 
    828   % \label{eq:PE_dyn_tides} 
     734  % \label{eq:SBC_PE_dyn_tides} 
    829735  \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= ... 
    830736  +g\nabla (\Pi_{eq} + \Pi_{sal}) 
    … …  
    832738where $\Pi_{eq}$ stands for the equilibrium tidal forcing and 
    833739$\Pi_{sal}$ is a self-attraction and loading term (SAL). 
    834   
     740 
    835741The equilibrium tidal forcing is expressed as a sum over a subset of 
    836742constituents chosen from the set of available tidal constituents 
    837 defined in file \rou{SBC/tide.h90} (this comprises the tidal 
     743defined in file \hf{SBC/tide} (this comprises the tidal 
    838744constituents \textit{M2, N2, 2N2, S2, K2, K1, O1, Q1, P1, M4, Mf, Mm, 
    839745  Msqm, Mtm, S1, MU2, NU2, L2}, and \textit{T2}). Individual 
    840746constituents are selected by including their names in the array 
    841 \np{clname} in \ngn{nam\_tide} (e.g., \np{clname(1) = 'M2', 
    842   clname(2)='S2'} to select solely the tidal consituents \textit{M2} 
    843 and \textit{S2}). Optionally, when \np{ln\_tide\_ramp} is set to 
     747\np{clname}{clname} in \nam{_tide}{\_tide} (e.g., \np{clname}{clname}\forcode{(1)='M2', } 
     748\np{clname}{clname}\forcode{(2)='S2'} to select solely the tidal consituents \textit{M2} 
     749and \textit{S2}). Optionally, when \np{ln_tide_ramp}{ln\_tide\_ramp} is set to 
    844750\forcode{.true.}, the equilibrium tidal forcing can be ramped up 
    845 linearly from zero during the initial \np{rdttideramp} days of the 
     751linearly from zero during the initial \np{rdttideramp}{rdttideramp} days of the 
    846752model run. 
    847753 
    … …  
    850756discussion about the practical implementation of this term). 
    851757Nevertheless, the complex calculations involved would make this 
    852 computationally too expensive.  Here, two options are available: 
     758computationally too expensive. Here, two options are available: 
    853759$\Pi_{sal}$ generated by an external model can be read in 
    854 (\np{ln\_read\_load=.true.}), or a ``scalar approximation'' can be 
    855 used (\np{ln\_scal\_load=.true.}). In the latter case 
     760(\np[=.true.]{ln_read_load}{ln\_read\_load}), or a ``scalar approximation'' can be 
     761used (\np[=.true.]{ln_scal_load}{ln\_scal\_load}). In the latter case 
    856762\[ 
    857763  \Pi_{sal} = \beta \eta, 
    858764\] 
    859 where $\beta$ (\np{rn\_scal\_load} with a default value of 0.094) is a 
     765where $\beta$ (\np{rn_scal_load}{rn\_scal\_load} with a default value of 0.094) is a 
    860766spatially constant scalar, often chosen to minimize tidal prediction 
    861 errors. Setting both \np{ln\_read\_load} and \np{ln\_scal\_load} to 
     767errors. Setting both \np{ln_read_load}{ln\_read\_load} and \np{ln_scal_load}{ln\_scal\_load} to 
    862768\forcode{.false.} removes the SAL contribution. 
    863769 
    864 % ================================================================ 
    865 %        River runoffs 
    866 % ================================================================ 
    867 \section[River runoffs (\textit{sbcrnf.F90})] 
    868 {River runoffs (\protect\mdl{sbcrnf})} 
     770%% ================================================================================================= 
     771\section[River runoffs (\textit{sbcrnf.F90})]{River runoffs (\protect\mdl{sbcrnf})} 
    869772\label{sec:SBC_rnf} 
    870 %------------------------------------------namsbc_rnf---------------------------------------------------- 
    871  
    872 \nlst{namsbc_rnf}  
    873 %------------------------------------------------------------------------------------------------------------- 
    874  
    875 %River runoff generally enters the ocean at a nonzero depth rather than through the surface.  
     773 
     774\begin{listing} 
     775  \nlst{namsbc_rnf} 
     776  \caption{\forcode{&namsbc_rnf}} 
     777  \label{lst:namsbc_rnf} 
     778\end{listing} 
     779 
     780%River runoff generally enters the ocean at a nonzero depth rather than through the surface. 
    876781%Many models, however, have traditionally inserted river runoff to the top model cell. 
    877 %This was the case in \NEMO prior to the version 3.3. The switch toward a input of runoff  
    878 %throughout a nonzero depth has been motivated by the numerical and physical problems  
    879 %that arise when the top grid cells are of the order of one meter. This situation is common in  
    880 %coastal modelling and becomes more and more often open ocean and climate modelling  
     782%This was the case in \NEMO\ prior to the version 3.3. The switch toward a input of runoff 
     783%throughout a nonzero depth has been motivated by the numerical and physical problems 
     784%that arise when the top grid cells are of the order of one meter. This situation is common in 
     785%coastal modelling and becomes more and more often open ocean and climate modelling 
    881786%\footnote{At least a top cells thickness of 1~meter and a 3 hours forcing frequency are 
    882787%required to properly represent the diurnal cycle \citep{bernie.woolnough.ea_JC05}. see also \autoref{fig:SBC_dcy}.}. 
    883788 
    884  
    885 %To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the  
    886 %\mdl{tra\_sbc} module.  We decided to separate them throughout the code, so that the variable  
    887 %\textit{emp} represented solely evaporation minus precipitation fluxes, and a new 2d variable  
    888 %rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with  
    889 %emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use  
     789%To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the 
     790%\mdl{tra\_sbc} module.  We decided to separate them throughout the code, so that the variable 
     791%\textit{emp} represented solely evaporation minus precipitation fluxes, and a new 2d variable 
     792%rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with 
     793%emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use 
    890794%emp or emps and the changes made are below: 
    891  
    892795 
    893796%Rachel: 
    894797River runoff generally enters the ocean at a nonzero depth rather than through the surface. 
    895798Many models, however, have traditionally inserted river runoff to the top model cell. 
    896 This was the case in \NEMO prior to the version 3.3, 
     799This was the case in \NEMO\ prior to the version 3.3, 
    897800and was combined with an option to increase vertical mixing near the river mouth. 
    898801 
    899802However, with this method numerical and physical problems arise when the top grid cells are of the order of one meter. 
    900 This situation is common in coastal modelling and is becoming more common in open ocean and climate modelling  
     803This situation is common in coastal modelling and is becoming more common in open ocean and climate modelling 
    901804\footnote{ 
    902805  At least a top cells thickness of 1~meter and a 3 hours forcing frequency are required to 
    … …  
    909812along with the depth (in metres) which the river should be added to. 
    910813 
    911 Namelist variables in \ngn{namsbc\_rnf}, \np{ln\_rnf\_depth}, \np{ln\_rnf\_sal} and 
    912 \np{ln\_rnf\_temp} control whether the river attributes (depth, salinity and temperature) are read in and used. 
     814Namelist variables in \nam{sbc_rnf}{sbc\_rnf}, \np{ln_rnf_depth}{ln\_rnf\_depth}, \np{ln_rnf_sal}{ln\_rnf\_sal} and 
     815\np{ln_rnf_temp}{ln\_rnf\_temp} control whether the river attributes (depth, salinity and temperature) are read in and used. 
    913816If these are set as false the river is added to the surface box only, assumed to be fresh (0~psu), 
    914817and/or taken as surface temperature respectively. 
    915818 
    916 The runoff value and attributes are read in in sbcrnf.   
     819The runoff value and attributes are read in in sbcrnf. 
    917820For temperature -999 is taken as missing data and the river temperature is taken to 
    918821be the surface temperatue at the river point. 
    919 For the depth parameter a value of -1 means the river is added to the surface box only,  
    920 and a value of -999 means the river is added through the entire water column.  
     822For the depth parameter a value of -1 means the river is added to the surface box only, 
     823and a value of -999 means the river is added through the entire water column. 
    921824After being read in the temperature and salinity variables are multiplied by the amount of runoff 
    922825(converted into m/s) to give the heat and salt content of the river runoff. 
    923826After the user specified depth is read ini, 
    924 the number of grid boxes this corresponds to is calculated and stored in the variable \np{nz\_rnf}. 
     827the number of grid boxes this corresponds to is calculated and stored in the variable \np{nz_rnf}{nz\_rnf}. 
    925828The variable \textit{h\_dep} is then calculated to be the depth (in metres) of 
    926829the bottom of the lowest box the river water is being added to 
    927 (\ie the total depth that river water is being added to in the model). 
     830(\ie\ the total depth that river water is being added to in the model). 
    928831 
    929832The mass/volume addition due to the river runoff is, at each relevant depth level, added to 
    … …  
    931834This increases the diffusion term in the vicinity of the river, thereby simulating a momentum flux. 
    932835The sea surface height is calculated using the sum of the horizontal divergence terms, 
    933 and so the river runoff indirectly forces an increase in sea surface height.  
     836and so the river runoff indirectly forces an increase in sea surface height. 
    934837 
    935838The \textit{hdivn} terms are used in the tracer advection modules to force vertical velocities. 
    … …  
    944847As such the volume of water does not change, but the water is diluted. 
    945848 
    946 For the non-linear free surface case (\key{vvl}), no flux is allowed through the surface. 
     849For the non-linear free surface case, no flux is allowed through the surface. 
    947850Instead in the surface box (as well as water moving up from the boxes below) a volume of runoff water is added with 
    948851no corresponding heat and salt addition and so as happens in the lower boxes there is a dilution effect. 
    … …  
    953856This is done in the same way for both vvl and non-vvl. 
    954857The temperature and salinity are increased through the specified depth according to 
    955 the heat and salt content of the river.  
     858the heat and salt content of the river. 
    956859 
    957860In the non-linear free surface case (vvl), 
    … …  
    962865 
    963866It is also possible for runnoff to be specified as a negative value for modelling flow through straits, 
    964 \ie modelling the Baltic flow in and out of the North Sea. 
     867\ie\ modelling the Baltic flow in and out of the North Sea. 
    965868When the flow is out of the domain there is no change in temperature and salinity, 
    966869regardless of the namelist options used, 
    967 as the ocean water leaving the domain removes heat and salt (at the same concentration) with it.  
    968  
    969  
    970 %\colorbox{yellow}{Nevertheless, Pb of vertical resolution and 3D input : increase vertical mixing near river mouths to mimic a 3D river  
     870as the ocean water leaving the domain removes heat and salt (at the same concentration) with it. 
     871 
     872%\colorbox{yellow}{Nevertheless, Pb of vertical resolution and 3D input : increase vertical mixing near river mouths to mimic a 3D river 
    971873 
    972874%All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface.} 
    … …  
    978880%ENDIF 
    979881 
    980 %\gmcomment{  word doc of runoffs: 
    981 % 
    982 %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. 
    983 %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.   
    984  
    985 %The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between. 
    986  
    987 %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: 
    988  
    989 %} 
    990 % ================================================================ 
    991 %        Ice shelf melting 
    992 % ================================================================ 
    993 \section[Ice shelf melting (\textit{sbcisf.F90})] 
    994 {Ice shelf melting (\protect\mdl{sbcisf})} 
     882\cmtgm{  word doc of runoffs: 
     883In the current \NEMO\ setup river runoff is added to emp fluxes, 
     884these are then applied at just the sea surface as a volume change (in the variable volume case 
     885this is a literal volume change, and in the linear free surface case the free surface is moved) 
     886and a salt flux due to the concentration/dilution effect. 
     887There is also an option to increase vertical mixing near river mouths; 
     888this gives the effect of having a 3d river. 
     889All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and 
     890at the same temperature as the sea surface. 
     891Our aim was to code the option to specify the temperature and salinity of river runoff, 
     892(as well as the amount), along with the depth that the river water will affect. 
     893This would make it possible to model low salinity outflow, such as the Baltic, 
     894and would allow the ocean temperature to be affected by river runoff. 
     895 
     896The depth option makes it possible to have the river water affecting just the surface layer, 
     897throughout depth, or some specified point in between. 
     898 
     899To do this we need to treat evaporation/precipitation fluxes and river runoff differently in 
     900the \mdl{tra_sbc} module. 
     901We decided to separate them throughout the code, 
     902so that the variable emp represented solely evaporation minus precipitation fluxes, 
     903and a new 2d variable rnf was added which represents the volume flux of river runoff 
     904(in $kg/m^2s$ to remain consistent with $emp$). 
     905This meant many uses of emp and emps needed to be changed, 
     906a list of all modules which use $emp$ or $emps$ and the changes made are below:} 
     907 
     908%% ================================================================================================= 
     909\section[Ice shelf melting (\textit{sbcisf.F90})]{Ice shelf melting (\protect\mdl{sbcisf})} 
    995910\label{sec:SBC_isf} 
    996 %------------------------------------------namsbc_isf---------------------------------------------------- 
    997  
    998 \nlst{namsbc_isf} 
    999 %-------------------------------------------------------------------------------------------------------- 
    1000 The namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation. 
    1001 Description and result of sensitivity test to \np{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}.  
     911 
     912\begin{listing} 
     913  \nlst{namsbc_isf} 
     914  \caption{\forcode{&namsbc_isf}} 
     915  \label{lst:namsbc_isf} 
     916\end{listing} 
     917 
     918The namelist variable in \nam{sbc}{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation. 
     919Description and result of sensitivity test to \np{nn_isf}{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}. 
    1002920The different options are illustrated in \autoref{fig:SBC_isf}. 
    1003921 
    1004922\begin{description} 
    1005 \item[\np{nn\_isf}\forcode{ = 1}]: 
    1006   The ice shelf cavity is represented (\np{ln\_isfcav}\forcode{ = .true.} needed). 
     923  \item [{\np[=1]{nn_isf}{nn\_isf}}]: The ice shelf cavity is represented (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    1007924  The fwf and heat flux are depending of the local water properties. 
     925 
    1008926  Two different bulk formulae are available: 
    1009927 
    1010    \begin{description} 
    1011    \item[\np{nn\_isfblk}\forcode{ = 1}]: 
    1012      The melt rate is based on a balance between the upward ocean heat flux and 
    1013      the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
    1014    \item[\np{nn\_isfblk}\forcode{ = 2}]: 
    1015      The melt rate and the heat flux are based on a 3 equations formulation 
    1016      (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation).  
    1017      A complete description is available in \citet{jenkins_JGR91}. 
    1018    \end{description} 
    1019  
    1020      Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}.  
    1021      Its thickness is defined by \np{rn\_hisf\_tbl}. 
    1022      The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn\_hisf\_tbl} m. 
    1023      Then, the fluxes are spread over the same thickness (ie over one or several cells). 
    1024      If \np{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature. 
    1025      This can lead to super-cool temperature in the top cell under melting condition. 
    1026      If \np{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 
    1027  
    1028      Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice.  
    1029      There are 3 different ways to compute the exchange coeficient: 
    1030    \begin{description} 
    1031         \item[\np{nn\_gammablk}\forcode{ = 0}]: 
    1032      The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}.  
    1033 \[ 
    1034   % \label{eq:sbc_isf_gamma_iso} 
    1035 \gamma^{T} = \np{rn\_gammat0} 
    1036 \] 
    1037 \[ 
    1038 \gamma^{S} = \np{rn\_gammas0} 
    1039 \] 
    1040      This is the recommended formulation for ISOMIP. 
    1041    \item[\np{nn\_gammablk}\forcode{ = 1}]: 
    1042      The salt and heat exchange coefficients are velocity dependent and defined as 
    1043 \[ 
    1044 \gamma^{T} = \np{rn\_gammat0} \times u_{*}  
    1045 \] 
    1046 \[ 
    1047 \gamma^{S} = \np{rn\_gammas0} \times u_{*} 
    1048 \] 
    1049      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters). 
    1050      See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
    1051    \item[\np{nn\_gammablk}\forcode{ = 2}]: 
    1052      The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    1053 \[ 
    1054 \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}  
    1055 \] 
    1056      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters), 
    1057      $\Gamma_{Turb}$ the contribution of the ocean stability and 
    1058      $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
    1059      See \citet{holland.jenkins_JPO99} for all the details on this formulation.  
    1060      This formulation has not been extensively tested in NEMO (not recommended). 
    1061    \end{description} 
    1062  \item[\np{nn\_isf}\forcode{ = 2}]: 
    1063    The ice shelf cavity is not represented. 
    1064    The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    1065    The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
    1066    (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
    1067    (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}\forcode{ = 3}). 
    1068    The effective melting length (\np{sn\_Leff\_isf}) is read from a file. 
    1069  \item[\np{nn\_isf}\forcode{ = 3}]: 
    1070    The ice shelf cavity is not represented. 
    1071    The fwf (\np{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
    1072    the depth of the average grounding line (GL) (\np{sn\_depmax\_isf}) and 
    1073    the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}). 
    1074    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    1075  \item[\np{nn\_isf}\forcode{ = 4}]: 
    1076    The ice shelf cavity is opened (\np{ln\_isfcav}\forcode{ = .true.} needed). 
    1077    However, the fwf is not computed but specified from file \np{sn\_fwfisf}). 
    1078    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    1079    As in \np{nn\_isf}\forcode{ = 1}, the fluxes are spread over the top boundary layer thickness (\np{rn\_hisf\_tbl})\\ 
     928  \begin{description} 
     929  \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
     930    the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
     931  \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
     932    (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
     933    A complete description is available in \citet{jenkins_JGR91}. 
     934  \end{description} 
     935 
     936  Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
     937  Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. 
     938  The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m. 
     939  Then, the fluxes are spread over the same thickness (ie over one or several cells). 
     940  If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature. 
     941  This can lead to super-cool temperature in the top cell under melting condition. 
     942  If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 
     943 
     944  Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
     945  There are 3 different ways to compute the exchange coeficient: 
     946  \begin{description} 
     947  \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. 
     948    \begin{gather*} 
     949       % \label{eq:SBC_isf_gamma_iso} 
     950      \gamma^{T} = rn\_gammat0 \\ 
     951      \gamma^{S} = rn\_gammas0 
     952    \end{gather*} 
     953    This is the recommended formulation for ISOMIP. 
     954  \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
     955    \begin{gather*} 
     956      \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
     957      \gamma^{S} = rn\_gammas0 \times u_{*} 
     958    \end{gather*} 
     959    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
     960    See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
     961  \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
     962    \[ 
     963      \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
     964    \] 
     965    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), 
     966    $\Gamma_{Turb}$ the contribution of the ocean stability and 
     967    $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
     968    See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
     969    This formulation has not been extensively tested in \NEMO\ (not recommended). 
     970  \end{description} 
     971\item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
     972  The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
     973  The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
     974  (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
     975  (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
     976  The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
     977\item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
     978  The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
     979  the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
     980  the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
     981  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     982\item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
     983  However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
     984  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     985  As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl}) 
    1080986\end{description} 
    1081987 
    1082 $\bullet$ \np{nn\_isf}\forcode{ = 1} and \np{nn\_isf}\forcode{ = 2} compute a melt rate based on 
     988$\bullet$ \np[=1]{nn_isf}{nn\_isf} and \np[=2]{nn_isf}{nn\_isf} compute a melt rate based on 
    1083989the water mass properties, ocean velocities and depth. 
    1084990This flux is thus highly dependent of the model resolution (horizontal and vertical), 
    1085991realism of the water masses onto the shelf ...\\ 
    1086992 
    1087 $\bullet$ \np{nn\_isf}\forcode{ = 3} and \np{nn\_isf}\forcode{ = 4} read the melt rate from a file. 
     993$\bullet$ \np[=3]{nn_isf}{nn\_isf} and \np[=4]{nn_isf}{nn\_isf} read the melt rate from a file. 
    1088994You have total control of the fwf forcing. 
    1089995This can be useful if the water masses on the shelf are not realistic or 
    1090996the resolution (horizontal/vertical) are too coarse to have realistic melting or 
    1091 for studies where you need to control your heat and fw input.\\  
     997for studies where you need to control your heat and fw input.\\ 
    1092998 
    1093999The ice shelf melt is implemented as a volume flux as for the runoff. 
    … …  
    10961002See the runoff section \autoref{sec:SBC_rnf} for all the details about the divergence correction.\\ 
    10971003 
    1098 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    10991004\begin{figure}[!t] 
    1100   \begin{center} 
    1101     \includegraphics[width=\textwidth]{Fig_SBC_isf} 
    1102     \caption{ 
    1103       \protect\label{fig:SBC_isf} 
    1104       Illustration the location where the fwf is injected and whether or not the fwf is interactif or not depending of \np{nn\_isf}. 
    1105     } 
    1106   \end{center} 
     1005  \centering 
     1006  \includegraphics[width=0.66\textwidth]{SBC_isf} 
     1007  \caption[Ice shelf location and fresh water flux definition]{ 
     1008    Illustration of the location where the fwf is injected and 
     1009    whether or not the fwf is interactif or not depending of \protect\np{nn_isf}{nn\_isf}.} 
     1010  \label{fig:SBC_isf} 
    11071011\end{figure} 
    1108 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    1109  
     1012 
     1013%% ================================================================================================= 
    11101014\section{Ice sheet coupling} 
    11111015\label{sec:SBC_iscpl} 
    1112 %------------------------------------------namsbc_iscpl---------------------------------------------------- 
    1113  
    1114 \nlst{namsbc_iscpl} 
    1115 %-------------------------------------------------------------------------------------------------------- 
     1016 
     1017\begin{listing} 
     1018  \nlst{namsbc_iscpl} 
     1019  \caption{\forcode{&namsbc_iscpl}} 
     1020  \label{lst:namsbc_iscpl} 
     1021\end{listing} 
     1022 
    11161023Ice sheet/ocean coupling is done through file exchange at the restart step. 
    11171024At each restart step: 
    1118 \begin{description} 
    1119 \item[Step 1]: the ice sheet model send a new bathymetry and ice shelf draft netcdf file. 
    1120 \item[Step 2]: a new domcfg.nc file is built using the DOMAINcfg tools. 
    1121 \item[Step 3]: NEMO run for a specific period and output the average melt rate over the period. 
    1122 \item[Step 4]: the ice sheet model run using the melt rate outputed in step 4. 
    1123 \item[Step 5]: go back to 1. 
    1124 \end{description} 
    1125  
    1126 If \np{ln\_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with 
     1025 
     1026\begin{enumerate} 
     1027\item the ice sheet model send a new bathymetry and ice shelf draft netcdf file. 
     1028\item a new domcfg.nc file is built using the DOMAINcfg tools. 
     1029\item \NEMO\ run for a specific period and output the average melt rate over the period. 
     1030\item the ice sheet model run using the melt rate outputed in step 4. 
     1031\item go back to 1. 
     1032\end{enumerate} 
     1033 
     1034If \np[=.true.]{ln_iscpl}{ln\_iscpl}, the isf draft is assume to be different at each restart step with 
    11271035potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics. 
    11281036The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases: 
     1037 
    11291038\begin{description} 
    1130 \item[Thin a cell down]: 
    1131   T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant 
     1039\item [Thin a cell down]: T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant 
    11321040  ($bt_b=bt_n$). 
    1133 \item[Enlarge  a cell]: 
    1134   See case "Thin a cell down" 
    1135 \item[Dry a cell]: 
    1136   mask, T/S, U/V and ssh are set to 0. 
     1041\item [Enlarge  a cell]: See case "Thin a cell down" 
     1042\item [Dry a cell]: mask, T/S, U/V and ssh are set to 0. 
    11371043  Furthermore, U/V into the water column are modified to satisfy ($bt_b=bt_n$). 
    1138 \item[Wet a cell]:  
    1139   mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0. 
    1140   If no neighbours, T/S is extrapolated from old top cell value.  
     1044\item [Wet a cell]: mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0. 
     1045  If no neighbours, T/S is extrapolated from old top cell value. 
    11411046  If no neighbours along i,j and k (both previous test failed), T/S/U/V/ssh and mask are set to 0. 
    1142 \item[Dry a column]: 
    1143    mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0. 
    1144 \item[Wet a column]: 
    1145   set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0. 
     1047\item [Dry a column]: mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0. 
     1048\item [Wet a column]: set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0. 
    11461049  If no neighbour, T/S/U/V and mask set to 0. 
    11471050\end{description} 
    … …  
    11501053the restart time step is prescribed to be an euler time step instead of a leap frog and $fields_b = fields_n$.\\ 
    11511054 
    1152 The horizontal extrapolation to fill new cell with realistic value is called \np{nn\_drown} times. 
    1153 It means that if the grounding line retreat by more than \np{nn\_drown} cells between 2 coupling steps, 
     1055The horizontal extrapolation to fill new cell with realistic value is called \np{nn_drown}{nn\_drown} times. 
     1056It means that if the grounding line retreat by more than \np{nn_drown}{nn\_drown} cells between 2 coupling steps, 
    11541057the code will be unable to fill all the new wet cells properly. 
    11551058The default number is set up for the MISOMIP idealised experiments. 
    11561059This coupling procedure is able to take into account grounding line and calving front migration. 
    1157 However, it is a non-conservative processe.  
     1060However, it is a non-conservative processe. 
    11581061This could lead to a trend in heat/salt content and volume.\\ 
    11591062 
    11601063In order to remove the trend and keep the conservation level as close to 0 as possible, 
    1161 a simple conservation scheme is available with \np{ln\_hsb}\forcode{ = .true.}. 
     1064a simple conservation scheme is available with \np[=.true.]{ln_hsb}{ln\_hsb}. 
    11621065The heat/salt/vol. gain/loss is diagnosed, as well as the location. 
    1163 A correction increment is computed and apply each time step during the next \np{rn\_fiscpl} time steps.  
    1164 For safety, it is advised to set \np{rn\_fiscpl} equal to the coupling period (smallest increment possible). 
     1066A correction increment is computed and apply each time step during the next \np{rn_fiscpl}{rn\_fiscpl} time steps. 
     1067For safety, it is advised to set \np{rn_fiscpl}{rn\_fiscpl} equal to the coupling period (smallest increment possible). 
    11651068The corrective increment is apply into the cell itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry). 
    11661069 
    1167 % 
    1168 % ================================================================ 
    1169 %        Handling of icebergs 
    1170 % ================================================================ 
     1070%% ================================================================================================= 
    11711071\section{Handling of icebergs (ICB)} 
    1172 \label{sec:ICB_icebergs} 
    1173 %------------------------------------------namberg---------------------------------------------------- 
    1174  
    1175 \nlst{namberg} 
    1176 %------------------------------------------------------------------------------------------------------------- 
    1177  
    1178 Icebergs are modelled as lagrangian particles in NEMO \citep{marsh.ivchenko.ea_GMD15}. 
     1072\label{sec:SBC_ICB_icebergs} 
     1073 
     1074\begin{listing} 
     1075  \nlst{namberg} 
     1076  \caption{\forcode{&namberg}} 
     1077  \label{lst:namberg} 
     1078\end{listing} 
     1079 
     1080Icebergs are modelled as lagrangian particles in \NEMO\ \citep{marsh.ivchenko.ea_GMD15}. 
    11791081Their physical behaviour is controlled by equations as described in \citet{martin.adcroft_OM10} ). 
    1180 (Note that the authors kindly provided a copy of their code to act as a basis for implementation in NEMO). 
     1082(Note that the authors kindly provided a copy of their code to act as a basis for implementation in \NEMO). 
    11811083Icebergs are initially spawned into one of ten classes which have specific mass and thickness as 
    1182 described in the \ngn{namberg} namelist: \np{rn\_initial\_mass} and \np{rn\_initial\_thickness}. 
    1183 Each class has an associated scaling (\np{rn\_mass\_scaling}), 
     1084described in the \nam{berg}{berg} namelist: \np{rn_initial_mass}{rn\_initial\_mass} and \np{rn_initial_thickness}{rn\_initial\_thickness}. 
     1085Each class has an associated scaling (\np{rn_mass_scaling}{rn\_mass\_scaling}), 
    11841086which is an integer representing how many icebergs of this class are being described as one lagrangian point 
    11851087(this reduces the numerical problem of tracking every single iceberg). 
    1186 They are enabled by setting \np{ln\_icebergs}\forcode{ = .true.}. 
     1088They are enabled by setting \np[=.true.]{ln_icebergs}{ln\_icebergs}. 
    11871089 
    11881090Two initialisation schemes are possible. 
    11891091\begin{description} 
    1190 \item[\np{nn\_test\_icebergs}~$>$~0] 
    1191   In this scheme, the value of \np{nn\_test\_icebergs} represents the class of iceberg to generate 
    1192   (so between 1 and 10), and \np{nn\_test\_icebergs} provides a lon/lat box in the domain at each grid point of 
     1092\item [{\np{nn_test_icebergs}{nn\_test\_icebergs}~$>$~0}] In this scheme, the value of \np{nn_test_icebergs}{nn\_test\_icebergs} represents the class of iceberg to generate 
     1093  (so between 1 and 10), and \np{nn_test_icebergs}{nn\_test\_icebergs} provides a lon/lat box in the domain at each grid point of 
    11931094  which an iceberg is generated at the beginning of the run. 
    1194   (Note that this happens each time the timestep equals \np{nn\_nit000}.) 
    1195   \np{nn\_test\_icebergs} is defined by four numbers in \np{nn\_test\_box} representing the corners of 
     1095  (Note that this happens each time the timestep equals \np{nn_nit000}{nn\_nit000}.) 
     1096  \np{nn_test_icebergs}{nn\_test\_icebergs} is defined by four numbers in \np{nn_test_box}{nn\_test\_box} representing the corners of 
    11961097  the geographical box: lonmin,lonmax,latmin,latmax 
    1197 \item[\np{nn\_test\_icebergs}\forcode{ = -1}] 
    1198   In this scheme the model reads a calving file supplied in the \np{sn\_icb} parameter. 
     1098\item [{\np[=-1]{nn_test_icebergs}{nn\_test\_icebergs}}] In this scheme, the model reads a calving file supplied in the \np{sn_icb}{sn\_icb} parameter. 
    11991099  This should be a file with a field on the configuration grid (typically ORCA) 
    12001100  representing ice accumulation rate at each model point. 
    … …  
    12041104  At each time step, a test is performed to see if there is enough ice mass to 
    12051105  calve an iceberg of each class in order (1 to 10). 
    1206   Note that this is the initial mass multiplied by the number each particle represents (\ie the scaling). 
     1106  Note that this is the initial mass multiplied by the number each particle represents (\ie\ the scaling). 
    12071107  If there is enough ice, a new iceberg is spawned and the total available ice reduced accordingly. 
    12081108\end{description} 
    … …  
    12111111The latter act to disintegrate the iceberg. 
    12121112This is either all melted freshwater, 
    1213 or (if \np{rn\_bits\_erosion\_fraction}~$>$~0) into melt and additionally small ice bits 
     1113or (if \np{rn_bits_erosion_fraction}{rn\_bits\_erosion\_fraction}~$>$~0) into melt and additionally small ice bits 
    12141114which are assumed to propagate with their larger parent and thus delay fluxing into the ocean. 
    1215 Melt water (and other variables on the configuration grid) are written into the main NEMO model output files. 
     1115Melt water (and other variables on the configuration grid) are written into the main \NEMO\ model output files. 
    12161116 
    12171117Extensive diagnostics can be produced. 
    12181118Separate output files are maintained for human-readable iceberg information. 
    1219 A separate file is produced for each processor (independent of \np{ln\_ctl}). 
     1119A separate file is produced for each processor (independent of \np{ln_ctl}{ln\_ctl}). 
    12201120The amount of information is controlled by two integer parameters: 
    12211121\begin{description} 
    1222 \item[\np{nn\_verbose\_level}] takes a value between one and four and 
     1122\item [{\np{nn_verbose_level}{nn\_verbose\_level}}] takes a value between one and four and 
    12231123  represents an increasing number of points in the code at which variables are written, 
    12241124  and an increasing level of obscurity. 
    1225 \item[\np{nn\_verbose\_write}] is the number of timesteps between writes 
     1125\item [{\np{nn_verbose_write}{nn\_verbose\_write}}] is the number of timesteps between writes 
    12261126\end{description} 
    12271127 
    1228 Iceberg trajectories can also be written out and this is enabled by setting \np{nn\_sample\_rate}~$>$~0. 
     1128Iceberg trajectories can also be written out and this is enabled by setting \np{nn_sample_rate}{nn\_sample\_rate}~$>$~0. 
    12291129A non-zero value represents how many timesteps between writes of information into the output file. 
    12301130These output files are in NETCDF format. 
    … …  
    12341134since its trajectory data may be spread across multiple files. 
    12351135 
    1236 % ------------------------------------------------------------------------------------------------------------- 
    1237 %        Interactions with waves (sbcwave.F90, ln_wave) 
    1238 % ------------------------------------------------------------------------------------------------------------- 
    1239 \section[Interactions with waves (\textit{sbcwave.F90}, \texttt{ln\_wave})] 
    1240 {Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})} 
     1136%% ================================================================================================= 
     1137\section[Interactions with waves (\textit{sbcwave.F90}, \forcode{ln_wave})]{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln_wave}{ln\_wave})} 
    12411138\label{sec:SBC_wave} 
    1242 %------------------------------------------namsbc_wave-------------------------------------------------------- 
    1243  
    1244 \nlst{namsbc_wave} 
    1245 %------------------------------------------------------------------------------------------------------------- 
    1246  
    1247 Ocean waves represent the interface between the ocean and the atmosphere, so NEMO is extended to incorporate  
    1248 physical processes related to ocean surface waves, namely the surface stress modified by growth and  
    1249 dissipation of the oceanic wave field, the Stokes-Coriolis force and the Stokes drift impact on mass and  
    1250 tracer advection; moreover the neutral surface drag coefficient from a wave model can be used to evaluate  
     1139 
     1140\begin{listing} 
     1141  \nlst{namsbc_wave} 
     1142  \caption{\forcode{&namsbc_wave}} 
     1143  \label{lst:namsbc_wave} 
     1144\end{listing} 
     1145 
     1146Ocean waves represent the interface between the ocean and the atmosphere, so \NEMO\ is extended to incorporate 
     1147physical processes related to ocean surface waves, namely the surface stress modified by growth and 
     1148dissipation of the oceanic wave field, the Stokes-Coriolis force and the Stokes drift impact on mass and 
     1149tracer advection; moreover the neutral surface drag coefficient from a wave model can be used to evaluate 
    12511150the wind stress. 
    12521151 
    1253 Physical processes related to ocean surface waves can be accounted by setting the logical variable  
    1254 \np{ln\_wave}\forcode{= .true.} in \ngn{namsbc} namelist. In addition, specific flags accounting for  
    1255 different porcesses should be activated as explained in the following sections. 
     1152Physical processes related to ocean surface waves can be accounted by setting the logical variable 
     1153\np[=.true.]{ln_wave}{ln\_wave} in \nam{sbc}{sbc} namelist. In addition, specific flags accounting for 
     1154different processes should be activated as explained in the following sections. 
    12561155 
    12571156Wave fields can be provided either in forced or coupled mode: 
    12581157\begin{description} 
    1259 \item[forced mode]: wave fields should be defined through the \ngn{namsbc\_wave} namelist  
    1260 for external data names, locations, frequency, interpolation and all the miscellanous options allowed by  
    1261 Input Data generic Interface (see \autoref{sec:SBC_input}).  
    1262 \item[coupled mode]: NEMO and an external wave model can be coupled by setting \np{ln\_cpl} \forcode{= .true.}  
    1263 in \ngn{namsbc} namelist and filling the \ngn{namsbc\_cpl} namelist. 
     1158\item [forced mode]: wave fields should be defined through the \nam{sbc_wave}{sbc\_wave} namelist 
     1159for external data names, locations, frequency, interpolation and all the miscellanous options allowed by 
     1160Input Data generic Interface (see \autoref{sec:SBC_input}). 
     1161\item [coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np[=.true.]{ln_cpl}{ln\_cpl} 
     1162in \nam{sbc}{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist. 
    12641163\end{description} 
    12651164 
    1266  
    1267 % ================================================================ 
    1268 % Neutral drag coefficient from wave model (ln_cdgw) 
    1269  
    1270 % ================================================================ 
    1271 \subsection[Neutral drag coefficient from wave model (\texttt{ln\_cdgw})] 
    1272 {Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})} 
     1165%% ================================================================================================= 
     1166\subsection[Neutral drag coefficient from wave model (\forcode{ln_cdgw})]{Neutral drag coefficient from wave model (\protect\np{ln_cdgw}{ln\_cdgw})} 
    12731167\label{subsec:SBC_wave_cdgw} 
    12741168 
    1275 The neutral surface drag coefficient provided from an external data source (\ie a wave model),  
    1276 can be used by setting the logical variable \np{ln\_cdgw} \forcode{= .true.} in \ngn{namsbc} namelist.  
    1277 Then using the routine \rou{turb\_ncar} and starting from the neutral drag coefficent provided,  
    1278 the drag coefficient is computed according to the stable/unstable conditions of the  
    1279 air-sea interface following \citet{large.yeager_rpt04}.  
    1280  
    1281  
    1282 % ================================================================ 
    1283 % 3D Stokes Drift (ln_sdw, nn_sdrift) 
    1284 % ================================================================ 
    1285 \subsection[3D Stokes Drift (\texttt{ln\_sdw}, \texttt{nn\_sdrift})] 
    1286 {3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})} 
     1169The neutral surface drag coefficient provided from an external data source (\ie\ a wave model), 
     1170can be used by setting the logical variable \np[=.true.]{ln_cdgw}{ln\_cdgw} in \nam{sbc}{sbc} namelist. 
     1171Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided, 
     1172the drag coefficient is computed according to the stable/unstable conditions of the 
     1173air-sea interface following \citet{large.yeager_rpt04}. 
     1174 
     1175%% ================================================================================================= 
     1176\subsection[3D Stokes Drift (\forcode{ln_sdw} \& \forcode{nn_sdrift})]{3D Stokes Drift (\protect\np{ln_sdw}{ln\_sdw} \& \np{nn_sdrift}{nn\_sdrift})} 
    12871177\label{subsec:SBC_wave_sdw} 
    12881178 
    1289 The Stokes drift is a wave driven mechanism of mass and momentum transport \citep{stokes_ibk09}.  
    1290 It is defined as the difference between the average velocity of a fluid parcel (Lagrangian velocity)  
    1291 and the current measured at a fixed point (Eulerian velocity).  
    1292 As waves travel, the water particles that make up the waves travel in orbital motions but  
    1293 without a closed path. Their movement is enhanced at the top of the orbit and slowed slightly  
    1294 at the bottom so the result is a net forward motion of water particles, referred to as the Stokes drift.  
    1295 An accurate evaluation of the Stokes drift and the inclusion of related processes may lead to improved  
    1296 representation of surface physics in ocean general circulation models. 
    1297 The Stokes drift velocity $\mathbf{U}_{st}$ in deep water can be computed from the wave spectrum and may be written as:  
     1179The Stokes drift is a wave driven mechanism of mass and momentum transport \citep{stokes_ibk09}. 
     1180It is defined as the difference between the average velocity of a fluid parcel (Lagrangian velocity) 
     1181and the current measured at a fixed point (Eulerian velocity). 
     1182As waves travel, the water particles that make up the waves travel in orbital motions but 
     1183without a closed path. Their movement is enhanced at the top of the orbit and slowed slightly 
     1184at the bottom, so the result is a net forward motion of water particles, referred to as the Stokes drift. 
     1185An accurate evaluation of the Stokes drift and the inclusion of related processes may lead to improved 
     1186representation of surface physics in ocean general circulation models. %GS: reference needed 
     1187The Stokes drift velocity $\mathbf{U}_{st}$ in deep water can be computed from the wave spectrum and may be written as: 
    12981188 
    12991189\[ 
    1300   % \label{eq:sbc_wave_sdw} 
     1190  % \label{eq:SBC_wave_sdw} 
    13011191  \mathbf{U}_{st} = \frac{16{\pi^3}} {g} 
    13021192  \int_0^\infty \int_{-\pi}^{\pi} (cos{\theta},sin{\theta}) {f^3} 
    … …  
    13041194\] 
    13051195 
    1306 where: ${\theta}$ is the wave direction, $f$ is the wave intrinsic frequency,  
    1307 $\mathrm{S}($f$,\theta)$ is the 2D frequency-direction spectrum,  
    1308 $k$ is the mean wavenumber defined as:  
     1196where: ${\theta}$ is the wave direction, $f$ is the wave intrinsic frequency, 
     1197$\mathrm{S}($f$,\theta)$ is the 2D frequency-direction spectrum, 
     1198$k$ is the mean wavenumber defined as: 
    13091199$k=\frac{2\pi}{\lambda}$ (being $\lambda$ the wavelength). \\ 
    13101200 
    1311 In order to evaluate the Stokes drift in a realistic ocean wave field the wave spectral shape is required  
    1312 and its computation quickly becomes expensive as the 2D spectrum must be integrated for each vertical level.  
     1201In order to evaluate the Stokes drift in a realistic ocean wave field, the wave spectral shape is required 
     1202and its computation quickly becomes expensive as the 2D spectrum must be integrated for each vertical level. 
    13131203To simplify, it is customary to use approximations to the full Stokes profile. 
    1314 Three possible parameterizations for the calculation for the approximate Stokes drift velocity profile  
    1315 are included in the code through the \np{nn\_sdrift} parameter once provided the surface Stokes drift  
    1316 $\mathbf{U}_{st |_{z=0}}$ which is evaluated by an external wave model that accurately reproduces the wave spectra  
    1317 and makes possible the estimation of the surface Stokes drift for random directional waves in  
     1204Three possible parameterizations for the calculation for the approximate Stokes drift velocity profile 
     1205are included in the code through the \np{nn_sdrift}{nn\_sdrift} parameter once provided the surface Stokes drift 
     1206$\mathbf{U}_{st |_{z=0}}$ which is evaluated by an external wave model that accurately reproduces the wave spectra 
     1207and makes possible the estimation of the surface Stokes drift for random directional waves in 
    13181208realistic wave conditions: 
    13191209 
    13201210\begin{description} 
    1321 \item[\np{nn\_sdrift} = 0]: exponential integral profile parameterization proposed by  
     1211\item [{\np{nn_sdrift}{nn\_sdrift} = 0}]: exponential integral profile parameterization proposed by 
    13221212\citet{breivik.janssen.ea_JPO14}: 
    13231213 
    13241214\[ 
    1325   % \label{eq:sbc_wave_sdw_0a} 
    1326   \mathbf{U}_{st} \cong \mathbf{U}_{st |_{z=0}} \frac{\mathrm{e}^{-2k_ez}} {1-8k_ez}  
     1215  % \label{eq:SBC_wave_sdw_0a} 
     1216  \mathbf{U}_{st} \cong \mathbf{U}_{st |_{z=0}} \frac{\mathrm{e}^{-2k_ez}} {1-8k_ez} 
    13271217\] 
    13281218 
    … …  
    13301220 
    13311221\[ 
    1332   % \label{eq:sbc_wave_sdw_0b} 
     1222  % \label{eq:SBC_wave_sdw_0b} 
    13331223  k_e = \frac{|\mathbf{U}_{\left.st\right|_{z=0}}|} {|T_{st}|} 
    13341224  \quad \text{and }\ 
    1335   T_{st} = \frac{1}{16} \bar{\omega} H_s^2  
     1225  T_{st} = \frac{1}{16} \bar{\omega} H_s^2 
    13361226\] 
    13371227 
    13381228where $H_s$ is the significant wave height and $\omega$ is the wave frequency. 
    13391229 
    1340 \item[\np{nn\_sdrift} = 1]: velocity profile based on the Phillips spectrum which is considered to be a  
    1341 reasonable estimate of the part of the spectrum most contributing to the Stokes drift velocity near the surface 
     1230\item [{\np{nn_sdrift}{nn\_sdrift} = 1}]: velocity profile based on the Phillips spectrum which is considered to be a 
     1231reasonable estimate of the part of the spectrum mostly contributing to the Stokes drift velocity near the surface 
    13421232\citep{breivik.bidlot.ea_OM16}: 
    13431233 
    13441234\[ 
    1345   % \label{eq:sbc_wave_sdw_1} 
     1235  % \label{eq:SBC_wave_sdw_1} 
    13461236  \mathbf{U}_{st} \cong \mathbf{U}_{st |_{z=0}} \Big[exp(2k_pz)-\beta \sqrt{-2 \pi k_pz} 
    13471237  \textit{ erf } \Big(\sqrt{-2 k_pz}\Big)\Big] 
    … …  
    13501240where $erf$ is the complementary error function and $k_p$ is the peak wavenumber. 
    13511241 
    1352 \item[\np{nn\_sdrift} = 2]: velocity profile based on the Phillips spectrum as for \np{nn\_sdrift} = 1  
     1242\item [{\np{nn_sdrift}{nn\_sdrift} = 2}]: velocity profile based on the Phillips spectrum as for \np{nn_sdrift}{nn\_sdrift} = 1 
    13531243but using the wave frequency from a wave model. 
    13541244 
    13551245\end{description} 
    13561246 
    1357 The Stokes drift enters the wave-averaged momentum equation, as well as the tracer advection equations  
    1358 and its effect on the evolution of the sea-surface height ${\eta}$ is considered as follows:  
     1247The Stokes drift enters the wave-averaged momentum equation, as well as the tracer advection equations 
     1248and its effect on the evolution of the sea-surface height ${\eta}$ is considered as follows: 
    13591249 
    13601250\[ 
    1361   % \label{eq:sbc_wave_eta_sdw} 
     1251  % \label{eq:SBC_wave_eta_sdw} 
    13621252  \frac{\partial{\eta}}{\partial{t}} = 
    13631253  -\nabla_h \int_{-H}^{\eta} (\mathbf{U} + \mathbf{U}_{st}) dz 
    13641254\] 
    13651255 
    1366 The tracer advection equation is also modified in order for Eulerian ocean models to properly account  
    1367 for unresolved wave effect. The divergence of the wave tracer flux equals the mean tracer advection  
    1368 that is induced by the three-dimensional Stokes velocity.  
    1369 The advective equation for a tracer $c$ combining the effects of the mean current and sea surface waves  
    1370 can be formulated as follows:  
     1256The tracer advection equation is also modified in order for Eulerian ocean models to properly account 
     1257for unresolved wave effect. The divergence of the wave tracer flux equals the mean tracer advection 
     1258that is induced by the three-dimensional Stokes velocity. 
     1259The advective equation for a tracer $c$ combining the effects of the mean current and sea surface waves 
     1260can be formulated as follows: 
    13711261 
    13721262\[ 
    1373   % \label{eq:sbc_wave_tra_sdw} 
     1263  % \label{eq:SBC_wave_tra_sdw} 
    13741264  \frac{\partial{c}}{\partial{t}} = 
    13751265  - (\mathbf{U} + \mathbf{U}_{st}) \cdot \nabla{c} 
    13761266\] 
    13771267 
    1378  
    1379 % ================================================================ 
    1380 % Stokes-Coriolis term (ln_stcor) 
    1381 % ================================================================ 
    1382 \subsection[Stokes-Coriolis term (\texttt{ln\_stcor})] 
    1383 {Stokes-Coriolis term (\protect\np{ln\_stcor})} 
     1268%% ================================================================================================= 
     1269\subsection[Stokes-Coriolis term (\forcode{ln_stcor})]{Stokes-Coriolis term (\protect\np{ln_stcor}{ln\_stcor})} 
    13841270\label{subsec:SBC_wave_stcor} 
    13851271 
    1386 In a rotating ocean, waves exert a wave-induced stress on the mean ocean circulation which results  
    1387 in a force equal to $\mathbf{U}_{st}$×$f$, where $f$ is the Coriolis parameter.  
    1388 This additional force may have impact on the Ekman turning of the surface current.  
    1389 In order to include this term, once evaluated the Stokes drift (using one of the 3 possible  
    1390 approximations described in \autoref{subsec:SBC_wave_sdw}),  
    1391 \np{ln\_stcor}\forcode{ = .true.} has to be set. 
    1392  
    1393  
    1394 % ================================================================ 
    1395 % Waves modified stress (ln_tauwoc, ln_tauw) 
    1396 % ================================================================ 
    1397 \subsection[Wave modified sress (\texttt{ln\_tauwoc}, \texttt{ln\_tauw})] 
    1398 {Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})} 
     1272In a rotating ocean, waves exert a wave-induced stress on the mean ocean circulation which results 
     1273in a force equal to $\mathbf{U}_{st}$×$f$, where $f$ is the Coriolis parameter. 
     1274This additional force may have impact on the Ekman turning of the surface current. 
     1275In order to include this term, once evaluated the Stokes drift (using one of the 3 possible 
     1276approximations described in \autoref{subsec:SBC_wave_sdw}), 
     1277\np[=.true.]{ln_stcor}{ln\_stcor} has to be set. 
     1278 
     1279%% ================================================================================================= 
     1280\subsection[Wave modified stress (\forcode{ln_tauwoc} \& \forcode{ln_tauw})]{Wave modified sress (\protect\np{ln_tauwoc}{ln\_tauwoc} \& \np{ln_tauw}{ln\_tauw})} 
    13991281\label{subsec:SBC_wave_tauw} 
    14001282 
    1401 The surface stress felt by the ocean is the atmospheric stress minus the net stress going  
    1402 into the waves \citep{janssen.breivik.ea_rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not  
    1403 available for forcing the mean circulation, while in the opposite case of a decaying sea  
    1404 state more momentum is available for forcing the ocean.  
    1405 Only when the sea state is in equilibrium the ocean is forced by the atmospheric stress,  
    1406 but in practice an equilibrium sea state is a fairly rare event.  
    1407 So the atmospheric stress felt by the ocean circulation $\tau_{oc,a}$ can be expressed as:  
     1283The surface stress felt by the ocean is the atmospheric stress minus the net stress going 
     1284into the waves \citep{janssen.breivik.ea_rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not 
     1285available for forcing the mean circulation, while in the opposite case of a decaying sea 
     1286state, more momentum is available for forcing the ocean. 
     1287Only when the sea state is in equilibrium, the ocean is forced by the atmospheric stress, 
     1288but in practice, an equilibrium sea state is a fairly rare event. 
     1289So the atmospheric stress felt by the ocean circulation $\tau_{oc,a}$ can be expressed as: 
    14081290 
    14091291\[ 
    1410   % \label{eq:sbc_wave_tauoc} 
     1292  % \label{eq:SBC_wave_tauoc} 
    14111293  \tau_{oc,a} = \tau_a - \tau_w 
    14121294\] 
    … …  
    14161298 
    14171299\[ 
    1418   % \label{eq:sbc_wave_tauw} 
     1300  % \label{eq:SBC_wave_tauw} 
    14191301  \tau_w = \rho g \int {\frac{dk}{c_p} (S_{in}+S_{nl}+S_{diss})} 
    14201302\] 
    14211303 
    14221304where: $c_p$ is the phase speed of the gravity waves, 
    1423 $S_{in}$, $S_{nl}$ and $S_{diss}$ are three source terms that represent  
    1424 the physics of ocean waves. The first one, $S_{in}$, describes the generation  
    1425 of ocean waves by wind and therefore represents the momentum and energy transfer  
    1426 from air to ocean waves; the second term $S_{nl}$ denotes  
    1427 the nonlinear transfer by resonant four-wave interactions; while the third term $S_{diss}$  
    1428 describes the dissipation of waves by processes such as white-capping, large scale breaking  
     1305$S_{in}$, $S_{nl}$ and $S_{diss}$ are three source terms that represent 
     1306the physics of ocean waves. The first one, $S_{in}$, describes the generation 
     1307of ocean waves by wind and therefore represents the momentum and energy transfer 
     1308from air to ocean waves; the second term $S_{nl}$ denotes 
     1309the nonlinear transfer by resonant four-wave interactions; while the third term $S_{diss}$ 
     1310describes the dissipation of waves by processes such as white-capping, large scale breaking 
    14291311eddy-induced damping. 
    14301312 
    1431 The wave stress derived from an external wave model can be provided either through the normalized  
    1432 wave stress into the ocean by setting \np{ln\_tauwoc}\forcode{ = .true.}, or through the zonal and  
    1433 meridional stress components by setting \np{ln\_tauw}\forcode{ = .true.}. 
    1434  
    1435  
    1436 % ================================================================ 
    1437 % Miscellanea options 
    1438 % ================================================================ 
     1313The wave stress derived from an external wave model can be provided either through the normalized 
     1314wave stress into the ocean by setting \np[=.true.]{ln_tauwoc}{ln\_tauwoc}, or through the zonal and 
     1315meridional stress components by setting \np[=.true.]{ln_tauw}{ln\_tauw}. 
     1316 
     1317%% ================================================================================================= 
    14391318\section{Miscellaneous options} 
    14401319\label{sec:SBC_misc} 
    14411320 
    1442 % ------------------------------------------------------------------------------------------------------------- 
    1443 %        Diurnal cycle 
    1444 % ------------------------------------------------------------------------------------------------------------- 
    1445 \subsection[Diurnal cycle (\textit{sbcdcy.F90})] 
    1446 {Diurnal cycle (\protect\mdl{sbcdcy})} 
     1321%% ================================================================================================= 
     1322\subsection[Diurnal cycle (\textit{sbcdcy.F90})]{Diurnal cycle (\protect\mdl{sbcdcy})} 
    14471323\label{subsec:SBC_dcy} 
    1448 %------------------------------------------namsbc_rnf---------------------------------------------------- 
    1449 % 
    1450 \nlst{namsbc}  
    1451 %------------------------------------------------------------------------------------------------------------- 
    1452  
    1453 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     1324 
    14541325\begin{figure}[!t] 
    1455   \begin{center} 
    1456     \includegraphics[width=\textwidth]{Fig_SBC_diurnal} 
    1457     \caption{ 
    1458       \protect\label{fig:SBC_diurnal} 
    1459       Example of recontruction of the diurnal cycle variation of short wave flux from daily mean values. 
    1460       The reconstructed diurnal cycle (black line) is chosen as 
    1461       the mean value of the analytical cycle (blue line) over a time step, 
    1462       not as the mid time step value of the analytically cycle (red square). 
    1463       From \citet{bernie.guilyardi.ea_CD07}. 
    1464     } 
    1465   \end{center} 
     1326  \centering 
     1327  \includegraphics[width=0.66\textwidth]{SBC_diurnal} 
     1328  \caption[Reconstruction of the diurnal cycle variation of short wave flux]{ 
     1329    Example of reconstruction of the diurnal cycle variation of short wave flux from 
     1330    daily mean values. 
     1331    The reconstructed diurnal cycle (black line) is chosen as 
     1332    the mean value of the analytical cycle (blue line) over a time step, 
     1333    not as the mid time step value of the analytically cycle (red square). 
     1334    From \citet{bernie.guilyardi.ea_CD07}.} 
     1335  \label{fig:SBC_diurnal} 
    14661336\end{figure} 
    1467 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14681337 
    14691338\cite{bernie.woolnough.ea_JC05} have shown that to capture 90$\%$ of the diurnal variability of SST requires a vertical resolution in upper ocean of 1~m or better and a temporal resolution of the surface fluxes of 3~h or less. 
    1470 Unfortunately high frequency forcing fields are rare, not to say inexistent. 
    1471 Nevertheless, it is possible to obtain a reasonable diurnal cycle of the SST knowning only short wave flux (SWF) at 
    1472 high frequency \citep{bernie.guilyardi.ea_CD07}. 
     1339%Unfortunately high frequency forcing fields are rare, not to say inexistent. GS: not true anymore ! 
     1340Nevertheless, it is possible to obtain a reasonable diurnal cycle of the SST knowning only short wave flux (SWF) at high frequency \citep{bernie.guilyardi.ea_CD07}. 
    14731341Furthermore, only the knowledge of daily mean value of SWF is needed, 
    14741342as higher frequency variations can be reconstructed from them, 
    14751343assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF. 
    1476 The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO by 
    1477 setting \np{ln\_dm2dc}\forcode{ = .true.} (a \textit{\ngn{namsbc}} namelist variable) when 
    1478 using CORE bulk formulea (\np{ln\_blk\_core}\forcode{ = .true.}) or 
    1479 the flux formulation (\np{ln\_flx}\forcode{ = .true.}). 
     1344The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO\ by 
     1345setting \np[=.true.]{ln_dm2dc}{ln\_dm2dc} (a \textit{\nam{sbc}{sbc}} namelist variable) when 
     1346using a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk}) or 
     1347the flux formulation (\np[=.true.]{ln_flx}{ln\_flx}). 
    14801348The reconstruction is performed in the \mdl{sbcdcy} module. 
    14811349The detail of the algoritm used can be found in the appendix~A of \cite{bernie.guilyardi.ea_CD07}. 
    1482 The algorithm preserve the daily mean incoming SWF as the reconstructed SWF at 
     1350The algorithm preserves the daily mean incoming SWF as the reconstructed SWF at 
    14831351a given time step is the mean value of the analytical cycle over this time step (\autoref{fig:SBC_diurnal}). 
    14841352The use of diurnal cycle reconstruction requires the input SWF to be daily 
    1485 (\ie a frequency of 24 and a time interpolation set to true in \np{sn\_qsr} namelist parameter). 
    1486 Furthermore, it is recommended to have a least 8 surface module time step per day, 
     1353(\ie\ a frequency of 24 hours and a time interpolation set to true in \np{sn_qsr}{sn\_qsr} namelist parameter). 
     1354Furthermore, it is recommended to have a least 8 surface module time steps per day, 
    14871355that is  $\rdt \ nn\_fsbc < 10,800~s = 3~h$. 
    14881356An example of recontructed SWF is given in \autoref{fig:SBC_dcy} for a 12 reconstructed diurnal cycle, 
    14891357one every 2~hours (from 1am to 11pm). 
    14901358 
    1491 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14921359\begin{figure}[!t] 
    1493   \begin{center} 
    1494     \includegraphics[width=\textwidth]{Fig_SBC_dcy} 
    1495     \caption{ 
    1496       \protect\label{fig:SBC_dcy} 
    1497       Example of recontruction of the diurnal cycle variation of short wave flux from 
    1498       daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm). 
    1499       The display is on (i,j) plane. 
    1500     } 
    1501   \end{center} 
     1360  \centering 
     1361  \includegraphics[width=0.66\textwidth]{SBC_dcy} 
     1362  \caption[Reconstruction of the diurnal cycle variation of short wave flux on an ORCA2 grid]{ 
     1363    Example of reconstruction of the diurnal cycle variation of short wave flux from 
     1364    daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm). 
     1365    The display is on (i,j) plane.} 
     1366  \label{fig:SBC_dcy} 
    15021367\end{figure} 
    1503 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    15041368 
    15051369Note also that the setting a diurnal cycle in SWF is highly recommended when 
    … …  
    15071371an inconsistency between the scale of the vertical resolution and the forcing acting on that scale. 
    15081372 
    1509 % ------------------------------------------------------------------------------------------------------------- 
    1510 %        Rotation of vector pairs onto the model grid directions 
    1511 % ------------------------------------------------------------------------------------------------------------- 
     1373%% ================================================================================================= 
    15121374\subsection{Rotation of vector pairs onto the model grid directions} 
    15131375\label{subsec:SBC_rotation} 
    15141376 
    1515 When using a flux (\np{ln\_flx}\forcode{ = .true.}) or 
    1516 bulk (\np{ln\_clio}\forcode{ = .true.} or \np{ln\_core}\forcode{ = .true.}) formulation, 
     1377When using a flux (\np[=.true.]{ln_flx}{ln\_flx}) or bulk (\np[=.true.]{ln_blk}{ln\_blk}) formulation, 
    15171378pairs of vector components can be rotated from east-north directions onto the local grid directions. 
    15181379This is particularly useful when interpolation on the fly is used since here any vectors are likely to 
    15191380be defined relative to a rectilinear grid. 
    1520 To activate this option a non-empty string is supplied in the rotation pair column of the relevant namelist. 
    1521 The eastward component must start with "U" and the northward component with "V".   
     1381To activate this option, a non-empty string is supplied in the rotation pair column of the relevant namelist. 
     1382The eastward component must start with "U" and the northward component with "V". 
    15221383The remaining characters in the strings are used to identify which pair of components go together. 
    15231384So for example, strings "U1" and "V1" next to "utau" and "vtau" would pair the wind stress components together and 
    … …  
    15271388The rot\_rep routine from the \mdl{geo2ocean} module is used to perform the rotation. 
    15281389 
    1529 % ------------------------------------------------------------------------------------------------------------- 
    1530 %        Surface restoring to observed SST and/or SSS 
    1531 % ------------------------------------------------------------------------------------------------------------- 
    1532 \subsection[Surface restoring to observed SST and/or SSS (\textit{sbcssr.F90})] 
    1533 {Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})} 
     1390%% ================================================================================================= 
     1391\subsection[Surface restoring to observed SST and/or SSS (\textit{sbcssr.F90})]{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})} 
    15341392\label{subsec:SBC_ssr} 
    1535 %------------------------------------------namsbc_ssr---------------------------------------------------- 
    1536  
    1537 \nlst{namsbc_ssr}  
    1538 %------------------------------------------------------------------------------------------------------------- 
    1539  
    1540 IOptions are defined through the \ngn{namsbc\_ssr} namelist variables. 
    1541 On forced mode using a flux formulation (\np{ln\_flx}\forcode{ = .true.}), 
     1393 
     1394\begin{listing} 
     1395  \nlst{namsbc_ssr} 
     1396  \caption{\forcode{&namsbc_ssr}} 
     1397  \label{lst:namsbc_ssr} 
     1398\end{listing} 
     1399 
     1400Options are defined through the \nam{sbc_ssr}{sbc\_ssr} namelist variables. 
     1401On forced mode using a flux formulation (\np[=.true.]{ln_flx}{ln\_flx}), 
    15421402a feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$: 
    15431403\[ 
    1544   % \label{eq:sbc_dmp_q} 
     1404  % \label{eq:SBC_dmp_q} 
    15451405  Q_{ns} = Q_{ns}^o + \frac{dQ}{dT} \left( \left. T \right|_{k=1} - SST_{Obs} \right) 
    15461406\] 
    … …  
    15481408$T$ is the model surface layer temperature and 
    15491409$\frac{dQ}{dT}$ is a negative feedback coefficient usually taken equal to $-40~W/m^2/K$. 
    1550 For a $50~m$ mixed-layer depth, this value corresponds to a relaxation time scale of two months.  
    1551 This term ensures that if $T$ perfectly matches the supplied SST, then $Q$ is equal to $Q_o$.  
     1410For a $50~m$ mixed-layer depth, this value corresponds to a relaxation time scale of two months. 
     1411This term ensures that if $T$ perfectly matches the supplied SST, then $Q$ is equal to $Q_o$. 
    15521412 
    15531413In the fresh water budget, a feedback term can also be added. 
    … …  
    15551415 
    15561416\begin{equation} 
    1557   \label{eq:sbc_dmp_emp} 
     1417  \label{eq:SBC_dmp_emp} 
    15581418  \textit{emp} = \textit{emp}_o + \gamma_s^{-1} e_{3t}  \frac{  \left(\left.S\right|_{k=1}-SSS_{Obs}\right)} 
    15591419  {\left.S\right|_{k=1}} 
    … …  
    15661426$\left.S\right|_{k=1}$ is the model surface layer salinity and 
    15671427$\gamma_s$ is a negative feedback coefficient which is provided as a namelist parameter. 
    1568 Unlike heat flux, there is no physical justification for the feedback term in \autoref{eq:sbc_dmp_emp} as 
     1428Unlike heat flux, there is no physical justification for the feedback term in \autoref{eq:SBC_dmp_emp} as 
    15691429the atmosphere does not care about ocean surface salinity \citep{madec.delecluse_IWN97}. 
    15701430The SSS restoring term should be viewed as a flux correction on freshwater fluxes to 
    15711431reduce the uncertainties we have on the observed freshwater budget. 
    15721432 
    1573 % ------------------------------------------------------------------------------------------------------------- 
    1574 %        Handling of ice-covered area 
    1575 % ------------------------------------------------------------------------------------------------------------- 
     1433%% ================================================================================================= 
    15761434\subsection{Handling of ice-covered area  (\textit{sbcice\_...})} 
    15771435\label{subsec:SBC_ice-cover} 
    … …  
    15791437The presence at the sea surface of an ice covered area modifies all the fluxes transmitted to the ocean. 
    15801438There are several way to handle sea-ice in the system depending on 
    1581 the value of the \np{nn\_ice} namelist parameter found in \ngn{namsbc} namelist. 
     1439the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc}{sbc} namelist. 
    15821440\begin{description} 
    1583 \item[nn{\_}ice = 0] 
    1584   there will never be sea-ice in the computational domain. 
     1441\item [nn\_ice = 0] there will never be sea-ice in the computational domain. 
    15851442  This is a typical namelist value used for tropical ocean domain. 
    15861443  The surface fluxes are simply specified for an ice-free ocean. 
    15871444  No specific things is done for sea-ice. 
    1588 \item[nn{\_}ice = 1] 
    1589   sea-ice can exist in the computational domain, but no sea-ice model is used. 
     1445\item [nn\_ice = 1] sea-ice can exist in the computational domain, but no sea-ice model is used. 
    15901446  An observed ice covered area is read in a file. 
    15911447  Below this area, the SST is restored to the freezing point and 
    … …  
    15951451  This prevents deep convection to occur when trying to reach the freezing point 
    15961452  (and so ice covered area condition) while the SSS is too large. 
    1597   This manner of managing sea-ice area, just by using si IF case, 
     1453  This manner of managing sea-ice area, just by using a IF case, 
    15981454  is usually referred as the \textit{ice-if} model. 
    1599   It can be found in the \mdl{sbcice{\_}if} module. 
    1600 \item[nn{\_}ice = 2 or more] 
    1601   A full sea ice model is used. 
     1455  It can be found in the \mdl{sbcice\_if} module. 
     1456\item [nn\_ice = 2 or more] A full sea ice model is used. 
    16021457  This model computes the ice-ocean fluxes, 
    16031458  that are combined with the air-sea fluxes using the ice fraction of each model cell to 
    1604   provide the surface ocean fluxes. 
    1605   Note that the activation of a sea-ice model is is done by defining a CPP key (\key{lim3} or \key{cice}). 
    1606   The activation automatically overwrites the read value of nn{\_}ice to its appropriate value 
    1607   (\ie $2$ for LIM-3 or $3$ for CICE). 
     1459  provide the surface averaged ocean fluxes. 
     1460  Note that the activation of a sea-ice model is done by defining a CPP key (\key{si3} or \key{cice}). 
     1461  The activation automatically overwrites the read value of nn\_ice to its appropriate value 
     1462  (\ie\ $2$ for SI3 or $3$ for CICE). 
    16081463\end{description} 
    16091464 
    16101465% {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?} 
    1611  
    1612 \subsection[Interface to CICE (\textit{sbcice\_cice.F90})] 
    1613 {Interface to CICE (\protect\mdl{sbcice\_cice})} 
     1466%GS: ocean-ice (SI3) interface is not located in SBC directory anymore, so it should be included in SI3 doc 
     1467 
     1468%% ================================================================================================= 
     1469\subsection[Interface to CICE (\textit{sbcice\_cice.F90})]{Interface to CICE (\protect\mdl{sbcice\_cice})} 
    16141470\label{subsec:SBC_cice} 
    16151471 
    1616 It is now possible to couple a regional or global NEMO configuration (without AGRIF) 
     1472It is possible to couple a regional or global \NEMO\ configuration (without AGRIF) 
    16171473to the CICE sea-ice model by using \key{cice}. 
    16181474The CICE code can be obtained from \href{http://oceans11.lanl.gov/trac/CICE/}{LANL} and 
    16191475the additional 'hadgem3' drivers will be required, even with the latest code release. 
    1620 Input grid files consistent with those used in NEMO will also be needed, 
     1476Input grid files consistent with those used in \NEMO\ will also be needed, 
    16211477and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used 
    16221478(seek advice from UKMO if necessary). 
    1623 Currently the code is only designed to work when using the CORE forcing option for NEMO 
    1624 (with \textit{calc\_strair}\forcode{ = .true.} and \textit{calc\_Tsfc}\forcode{ = .true.} in the CICE name-list), 
    1625 or alternatively when NEMO is coupled to the HadGAM3 atmosphere model 
    1626 (with \textit{calc\_strair}\forcode{ = .false.} and \textit{calc\_Tsfc}\forcode{ = false}). 
    1627 The code is intended to be used with \np{nn\_fsbc} set to 1 
     1479Currently, the code is only designed to work when using the NCAR forcing option for \NEMO\ %GS: still true ? 
     1480(with \textit{calc\_strair}\forcode{=.true.} and \textit{calc\_Tsfc}\forcode{=.true.} in the CICE name-list), 
     1481or alternatively when \NEMO\ is coupled to the HadGAM3 atmosphere model 
     1482(with \textit{calc\_strair}\forcode{=.false.} and \textit{calc\_Tsfc}\forcode{=false}). 
     1483The code is intended to be used with \np{nn_fsbc}{nn\_fsbc} set to 1 
    16281484(although coupling ocean and ice less frequently should work, 
    16291485it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly - 
    16301486the user should check that results are not significantly different to the standard case). 
    16311487 
    1632 There are two options for the technical coupling between NEMO and CICE. 
     1488There are two options for the technical coupling between \NEMO\ and CICE. 
    16331489The standard version allows complete flexibility for the domain decompositions in the individual models, 
    16341490but this is at the expense of global gather and scatter operations in the coupling which 
    16351491become very expensive on larger numbers of processors. 
    1636 The alternative option (using \key{nemocice\_decomp} for both NEMO and CICE) ensures that 
     1492The alternative option (using \key{nemocice\_decomp} for both \NEMO\ and CICE) ensures that 
    16371493the domain decomposition is identical in both models (provided domain parameters are set appropriately, 
    16381494and \textit{processor\_shape~=~square-ice} and \textit{distribution\_wght~=~block} in the CICE name-list) and 
    … …  
    16411497there is no sea ice. 
    16421498 
    1643 % ------------------------------------------------------------------------------------------------------------- 
    1644 %        Freshwater budget control  
    1645 % ------------------------------------------------------------------------------------------------------------- 
    1646 \subsection[Freshwater budget control (\textit{sbcfwb.F90})] 
    1647 {Freshwater budget control (\protect\mdl{sbcfwb})} 
     1499%% ================================================================================================= 
     1500\subsection[Freshwater budget control (\textit{sbcfwb.F90})]{Freshwater budget control (\protect\mdl{sbcfwb})} 
    16481501\label{subsec:SBC_fwb} 
    16491502 
    1650 For global ocean simulation it can be useful to introduce a control of the mean sea level in order to 
     1503For global ocean simulation, it can be useful to introduce a control of the mean sea level in order to 
    16511504prevent unrealistic drift of the sea surface height due to inaccuracy in the freshwater fluxes. 
    1652 In \NEMO, two way of controlling the the freshwater budget.  
     1505In \NEMO, two way of controlling the freshwater budget are proposed: 
     1506 
    16531507\begin{description} 
    1654 \item[\np{nn\_fwb}\forcode{ = 0}] 
    1655   no control at all. 
     1508\item [{\np[=0]{nn_fwb}{nn\_fwb}}] no control at all. 
    16561509  The mean sea level is free to drift, and will certainly do so. 
    1657 \item[\np{nn\_fwb}\forcode{ = 1}] 
    1658   global mean \textit{emp} set to zero at each model time step.  
    1659 %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).  
    1660 \item[\np{nn\_fwb}\forcode{ = 2}] 
    1661   freshwater budget is adjusted from the previous year annual mean budget which 
     1510\item [{\np[=1]{nn_fwb}{nn\_fwb}}] global mean \textit{emp} set to zero at each model time step. 
     1511  %GS: comment below still relevant ? 
     1512  %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling). 
     1513\item [{\np[=2]{nn_fwb}{nn\_fwb}}] freshwater budget is adjusted from the previous year annual mean budget which 
    16621514  is read in the \textit{EMPave\_old.dat} file. 
    16631515  As the model uses the Boussinesq approximation, the annual mean fresh water budget is simply evaluated from 
    1664   the change in the mean sea level at January the first and saved in the \textit{EMPav.dat} file.  
     1516  the change in the mean sea level at January the first and saved in the \textit{EMPav.dat} file. 
    16651517\end{description} 
    16661518 
    1667  
    1668  
    16691519% Griffies doc: 
    1670 % When running ocean-ice simulations, we are not explicitly representing land processes,  
    1671 % such as rivers, catchment areas, snow accumulation, etc. However, to reduce model drift,  
    1672 % it is important to balance the hydrological cycle in ocean-ice models.  
    1673 % We thus need to prescribe some form of global normalization to the precipitation minus evaporation plus river runoff.  
    1674 % The result of the normalization should be a global integrated zero net water input to the ocean-ice system over  
    1675 % a chosen time scale.  
    1676 %How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step,  
    1677 % so that there is always a zero net input of water to the ocean-ice system.  
    1678 % Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used  
    1679 % to alter the subsequent year�s water budget in an attempt to damp the annual water imbalance.  
    1680 % Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing.  
    1681 % When running ocean-ice coupled models, it is incorrect to include the water transport between the ocean  
    1682 % and ice models when aiming to balance the hydrological cycle.  
    1683 % 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,  
    1684 % not the water in any one sub-component. As an extreme example to illustrate the issue,  
    1685 % consider an ocean-ice model with zero initial sea ice. As the ocean-ice model spins up,  
    1686 % there should be a net accumulation of water in the growing sea ice, and thus a net loss of water from the ocean.  
    1687 % The total water contained in the ocean plus ice system is constant, but there is an exchange of water between  
    1688 % the subcomponents. This exchange should not be part of the normalization used to balance the hydrological cycle  
    1689 % in ocean-ice models.  
    1690  
    1691 \biblio 
    1692  
    1693 \pindex 
     1520% When running ocean-ice simulations, we are not explicitly representing land processes, 
     1521% such as rivers, catchment areas, snow accumulation, etc. However, to reduce model drift, 
     1522% it is important to balance the hydrological cycle in ocean-ice models. 
     1523% We thus need to prescribe some form of global normalization to the precipitation minus evaporation plus river runoff. 
     1524% The result of the normalization should be a global integrated zero net water input to the ocean-ice system over 
     1525% a chosen time scale. 
     1526% How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step, 
     1527% so that there is always a zero net input of water to the ocean-ice system. 
     1528% Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used 
     1529% to alter the subsequent year�s water budget in an attempt to damp the annual water imbalance. 
     1530% Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing. 
     1531% When running ocean-ice coupled models, it is incorrect to include the water transport between the ocean 
     1532% and ice models when aiming to balance the hydrological cycle. 
     1533% 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, 
     1534% not the water in any one sub-component. As an extreme example to illustrate the issue, 
     1535% consider an ocean-ice model with zero initial sea ice. As the ocean-ice model spins up, 
     1536% there should be a net accumulation of water in the growing sea ice, and thus a net loss of water from the ocean. 
     1537% The total water contained in the ocean plus ice system is constant, but there is an exchange of water between 
     1538% the subcomponents. This exchange should not be part of the normalization used to balance the hydrological cycle 
     1539% in ocean-ice models. 
     1540 
     1541\subinc{\input{../../global/epilogue}} 
    16941542 
    16951543\end{document} 
Note: See TracChangeset for help on using the changeset viewer.