Changeset 12769


Ignore:
Timestamp:
2020-04-17T17:06:11+02:00 (8 months ago)
Author:
mathiot
Message:

#2444: update of the documentation (prior to changes suggested by Dave)

Location:
NEMO/branches/2020/ticket_2444/doc
Files:
1 added
1 deleted
4 edited

Legend:

Unmodified
Added
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  • NEMO/branches/2020/ticket_2444/doc/latex/NEMO/main/bibliography.bib

    r12377 r12769  
    119119  issn          = "0148-0227", 
    120120  doi           = "10.1029/2001jc000922" 
     121} 
     122 
     123@Article{         Asaydavis2016, 
     124  author        = {Asay-Davis, X. S. and Cornford, S. L. and Durand, G. and Galton-Fenzi, B. K. and Gladstone, R. M. and Gudmundsson, G. H. and Hattermann, T. and Holland, D. M. and Holland, D. and Holland, P. R. and Martin, D. F. and Mathiot, P. and Pattyn, F. and Seroussi, H.}, 
     125  title         = {Experimental design for three interrelated marine ice sheet and ocean model intercomparison projects: MISMIP v. 3 (MISMIP$+$), ISOMIP v. 2 (ISOMIP$+$) and MISOMIP v. 1 (MISOMIP1)}, 
     126  journal       = {Geoscientific Model Development}, 
     127  volume        = {9}, 
     128  year          = {2016}, 
     129  number        = {7}, 
     130  pages         = {2471--2497}, 
     131  url           = {https://www.geosci-model-dev.net/9/2471/2016/}, 
     132  doi           = {10.5194/gmd-9-2471-2016} 
    121133} 
    122134 
     
    899911} 
    900912 
     913@Article{         favier2019, 
     914  author        = {Favier, L. and Jourdain, N. C. and Jenkins, A. and Merino, N. and Durand, G. and Gagliardini, O. and Gillet-Chaulet, F. and Mathiot, P.}, 
     915  title         = {Assessment of sub-shelf melting parameterisations using the ocean--ice-sheet coupled model NEMO(v3.6)--Elmer/Ice(v8.3)}, 
     916  journal       = {Geoscientific Model Development}, 
     917  volume        = {12}, 
     918  year          = {2019}, 
     919  number        = {6}, 
     920  pages         = {2255--2283}, 
     921  url           = {https://www.geosci-model-dev.net/12/2255/2019/}, 
     922  doi           = {10.5194/gmd-12-2255-2019} 
     923} 
     924 
    901925@article{         flather_JPO94, 
    902926  title         = "A storm surge prediction model for the northern Bay of 
     
    12221246} 
    12231247 
     1248@article{         grosfeld1997, 
     1249author          = {Grosfeld, K. and Gerdes, R. and Determann, J.}, 
     1250title           = {Thermohaline circulation and interaction between ice shelf cavities and the adjacent open ocean}, 
     1251journal         = {Journal of Geophysical Research: Oceans}, 
     1252 
     1253volume          = {102}, 
     1254number          = {C7}, 
     1255pages           = {15595-15610}, 
     1256doi             = {10.1029/97JC00891}, 
     1257url             = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/97JC00891}, 
     1258year            = {1997} 
     1259} 
     1260 
    12241261@article{         guilyardi.madec.ea_CD01, 
    12251262  title         = "The role of lateral ocean physics in the upper ocean 
     
    14511488  doi           = "10.1029/91jc01842" 
    14521489} 
     1490 
     1491@article{         jenkins2001, 
     1492  author        = {Jenkins, Adrian and Hellmer, Hartmut H. and Holland, David M.}, 
     1493  title         = {The Role of Meltwater Advection in the Formulation of Conservative Boundary Conditions at an Ice–Ocean Interface}, 
     1494  journal       = {Journal of Physical Oceanography}, 
     1495  volume        = {31}, 
     1496  number        = {1}, 
     1497  pages         = {285-296}, 
     1498  year          = {2001}, 
     1499  doi           = {10.1175/1520-0485(2001)031<0285:TROMAI>2.0.CO;2}, 
     1500  url           = {https://doi.org/10.1175/1520-0485(2001)031<0285:TROMAI>2.0.CO;2} 
     1501} 
     1502 
     1503@article{         jourdain2017, 
     1504  author        = {Jourdain, Nicolas C. and Mathiot, Pierre and Merino, Nacho and Durand, Gaël and Le Sommer, Julien and Spence, Paul and Dutrieux, Pierre and Madec, Gurvan}, 
     1505  title         = {Ocean circulation and sea-ice thinning induced by melting ice shelves in the Amundsen Sea}, 
     1506  journal       = {Journal of Geophysical Research: Oceans}, 
     1507  volume        = {122}, 
     1508  number        = {3}, 
     1509  pages         = {2550-2573}, 
     1510  keywords      = {Amundsen Sea, ice shelf, efficiency, circumpolar deep water, ocean circulation, sea ice}, 
     1511  doi           = {10.1002/2016JC012509}, 
     1512  url           = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016JC012509}, 
     1513  year          = {2017} 
     1514} 
     1515 
    14531516 
    14541517@article{         kantha.carniel_JMR03, 
  • NEMO/branches/2020/ticket_2444/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

    r11693 r12769  
    319319  Defining the bathymetry also defines the coastline: where the bathymetry is zero, 
    320320  no wet levels are defined (all levels are masked). 
    321  
    322   The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 
    323   each grid point of the model grid. 
    324   This file is only needed if \np[=.true.]{ln_isfcav}{ln\_isfcav}. 
    325   Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. 
    326321\end{description} 
    327322 
     
    530525This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. 
    531526 
     527\section{Ice shelf cavity definition} 
     528\label{subsec:zgrisf} 
     529 
     530  If the under ice shelf seas are opened (\np{ln_isfcav}{ln\_isfcav}), the depth of the ice shelf/ocean interface has to be include in  
     531  the \ifile{isfdraft\_meter} file (Netcdf format). This file need to include the \ifile{isf\_draft} variable.  
     532  A positive value will me an ice shelf/ocean or ice shelf bedrock interface below the reference 0m ssh.  
     533  The exact shape of the ice shelf cavity (grounding line position and minimum thickness of the water column under an ice shelf, ...) can be specify in \nam{lst:namzgr_isf}. 
     534 
     535 
     536\begin{listing} 
     537  \nlst{namzgr_isf_domcfg} 
     538  \caption{\forcode{&namzgr_isf}} 
     539  \label{lst:namzgr_isf} 
     540\end{listing} 
     541 
     542   The options available to define the shape of the under ice shelf cavities are listed in \nam{namzgr_isf}{namzgr\_isf} (\texttt{DOMAINcfg} only, \autoref{lst:namzgr_isf}). 
     543 
     544   \subsection{Model ice shelf draft definition} 
     545   \label{subsec:zgrisf_isfd} 
     546 
     547   First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry. 
     548   There are 3 compulsory steps to achieve this: 
     549 
     550   \begin{description} 
     551   \item{\np{rn_isfdep_min}{rn\_isfdep\_min}:} this is the minimum ice shelf draft. This is to make sure there is no ridiculous thin ice shelf. If \np{rn_isfdep_min}{rn\_isfdep\_min} is smaller than the surface level, \np{rn_isfdep_min}{rn\_isfdep\_min} is set to $e3t\_1d(1)$.  
     552   Where $h_{isf} < MAX(e3t\_1d(1),\np{rn_isfdep_min}{rn\_isfdep\_min}$), $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}. 
     553 
     554   \item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position. 
     555   Where the difference between the bathymetry and the ice shelf draft is smaller than \np{rn_glhw_min}{rn\_glhw\_min}, the cell are grounded (ie masked).  
     556   This step is needed to take into account possible small mismatch between ice shelf draft value and bathymetry value (sources are coming from different grid, different data processes, rounding error, ...). 
     557 
     558   \item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is minimum water column thickness in the cavity.  
     559   Where the water column thickness is lower than \np{rn_isfhw_min}{rn\_isfhw\_min}, the ice shelf draft is adjusted to match this criterion.  
     560   If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked. 
     561   \end{description} 
     562 
     563   Once all these adjustements are made, if the water column thickness contains one cell wide channels, these channels can be closed using \np{ln_isfchannel}{ln\_isfchannel}.   
     564  
     565   \subsection{Model top level definition} 
     566   After the definition of the ice shelf draft, the tool defines the top level.  
     567   The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points. 
     568   To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\ 
     569 
     570   The process is the following: 
     571   \begin{description} 
     572   \item{step 1:} The top level is defined in the same way as the bottom level is defined. 
     573   \item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf) 
     574   \item{step 3:} The tools make sure, the top level is above or equal to the bottom level 
     575   \item{step 4:} If the water column at a U- or V- point is one wet cell wide, the ice shelf draft is adjusted. So the actual top cell become fully open and the new 
     576   top cell thickness is set to the minimum cell thickness allowed (following the same logic as for the bottom partial cell). This step is iterated 4 times to ensure the condition is fullfill along the 4 sides of the cell. 
     577   \end{description} 
     578 
     579   In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourg ice shelf draft).  
     580   The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells. 
     581   Some limiters in meter or levels on the digging allowed by the tool are available (respectively, \np{rn_zisfmax}{rn\_zisfmax} or \np{rn_kisfmax}{rn\_kisfmax}). 
     582   This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels. 
     583 
     584   \subsection{Subglacial lakes} 
     585   Despite careful setting of your ice shelf draft and bathymetry input file as well as setting described in \autoref{subsec:zgrisf_isfd}, some situation are unavoidable. 
     586   For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling,  
     587   you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded).  
     588   If you do so, the subglacial lakes will show up (Vostock for example). An other possibility is with coarse vertical resolution, some ice shelves could be cut in 2 parts:  
     589   one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\ 
     590 
     591   The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes. 
     592   This may be useful for esthetical reason or for stability reasons: 
     593 
     594   \begin{description} 
     595   \item $\bullet$ In a subglacial lakes, in case of very weak circulation (often the case), the only heat flux is the conductive heat flux through the ice sheet.  
     596         This will lead to constant freezing until water reaches -20C.  
     597         This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}). 
     598   \item $\bullet$ In case of coupling with an ice sheet model,  
     599         the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example),  
     600         and so if for any reason both a connected at some point, the model is likely to fall over.\\ 
     601   \end{description} 
     602 
     603\section{Closed sea definition} 
     604\label{sec:clocfg} 
     605 
     606\begin{listing} 
     607  \nlst{namclo_domcfg} 
     608  \caption{\forcode{&namclo}} 
     609  \label{lst:namclo} 
     610\end{listing} 
     611 
     612The options available to define the closed seas and how closed sea net fresh water input will be redistributed by NEMO are listed in \nam{clo} (\texttt{DOMAINcfg} only, \autoref{lst:namclo}). 
     613The individual definition of each closed sea is managed by \np{sn_lake}{sn\_lake}. In this fields the user needs to defined:\\ 
     614   \begin{description} 
     615   \item $\bullet$    the name of the closed sea (print output purposes). 
     616   \item $\bullet$    the seed location to define the area of the closed sea (if seed on land because not present in this configuration, this closed sea will be ignored).\\ 
     617   \item $\bullet$    the seed location for the target area. 
     618   \item $\bullet$    the type of target area ('local','coast' or 'global'). See point 6 for definition of these cases. 
     619   \item $\bullet$    the type of redistribution scheme for the net fresh water flux over the closed sea (as a runoff in a target area, as emp in a target area, as emp globally). For the runoff case, if the net fwf is negative, it will be redistribut globally. 
     620   \item $\bullet$    the radius of the target area (not used for the 'global' case). So the target defined by a 'local' target area of a radius of 100km, for example, correspond to all the wet points within this radius. The coastal case will return only the coastal point within the specifid radius. 
     621   \item $\bullet$    the target id. This target id is used to group multiple lakes into the same river ouflow (Great Lakes for example). 
     622   \end{description} 
     623 
     624The closed sea module defines a number of masks in the \ifile{domain\_cfg} output: 
     625   \begin{description} 
     626   \item[\textit{mask\_opensea}:] a mask of the main ocean without all the closed seas closed. This mask is defined by a flood filling algorithm with an initial seed (localisation defined by \np{rn_lon_opnsea}{rn\_lon\_opnsea} and \np{rn_lat_opnsea}{rn\_lat\_opnsea}). 
     627   \item[\textit{mask\_csglo}, \textit{mask\_csrnf}, \textit{mask\_csemp}:] a mask of all the closed seas defined in the namelist by \np{sn_lake}{sn\_lake} for each redistribution scheme. The total number of defined closed seas has to be defined in \np{nn_closea}{nn\_closea}. 
     628   \item[\textit{mask\_csgrpglo}, \textit{mask\_csgrprnf}, \textit{mask\_csgrpemp}:] a mask of all the closed seas and targets grouped by target id for each type of redistribution scheme. 
     629   \item[\textit{mask\_csundef}:] a mask of all the closed sea not defined in \np{sn_lake}{sn\_lake}. This will allows NEMO to mask them if needed or to inform the user of potential minor issues in its bathymetry. 
     630   \end{description} 
     631    
    532632\subinc{\input{../../global/epilogue}} 
    533633 
  • NEMO/branches/2020/ticket_2444/doc/latex/NEMO/subfiles/chap_SBC.tex

    r12377 r12769  
    1818    Release & Author(s) & Modifications \\ 
    1919    \hline 
     20    {\em   X.X} & {\em Pierre Mathiot} & {\em update of the ice shelf section (2019 development)} \\ 
    2021    {\em   4.0} & {\em ...} & {\em ...} \\ 
    2122    {\em   3.6} & {\em ...} & {\em ...} \\ 
     
    7576  (\np[=0..3]{nn_ice}{nn\_ice}), 
    7677\item the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np[=.true.]{ln_rnf}{ln\_rnf}), 
    77 \item the addition of ice-shelf melting as lateral inflow (parameterisation) or 
    78   as fluxes applied at the land-ice ocean interface (\np[=.true.]{ln_isf}{ln\_isf}), 
    7978\item the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift 
    8079  (\np[=0..2]{nn_fwb}{nn\_fwb}), 
     
    10099One of these is modification by icebergs (see \autoref{sec:SBC_ICB_icebergs}), 
    101100which act as drifting sources of fresh water. 
    102 Another example of modification is that due to the ice shelf melting/freezing (see \autoref{sec:SBC_isf}), 
    103 which provides additional sources of fresh water. 
    104101 
    105102%% ================================================================================================= 
     
    12011198 
    12021199%% ================================================================================================= 
    1203 \section[Ice shelf melting (\textit{sbcisf.F90})]{Ice shelf melting (\protect\mdl{sbcisf})} 
    1204 \label{sec:SBC_isf} 
     1200\section[Ice Shelf (ISF)]{Interaction with ice shelves (ISF)} 
     1201\label{sec:isf} 
    12051202 
    12061203\begin{listing} 
    1207   \nlst{namsbc_isf} 
    1208   \caption{\forcode{&namsbc_isf}} 
    1209   \label{lst:namsbc_isf} 
     1204  \nlst{namisf} 
     1205  \caption{\forcode{&namisf}} 
     1206  \label{lst:namisf} 
    12101207\end{listing} 
    12111208 
    1212 The namelist variable in \nam{sbc}{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation. 
    1213 Description and result of sensitivity test to \np{nn_isf}{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}. 
    1214 The different options are illustrated in \autoref{fig:SBC_isf}. 
    1215  
     1209The namelist variable in \ngn{namisf}, \np{ln_isf}{ln\_isf}, controls the ice shelf interactions: 
    12161210\begin{description} 
    1217   \item [{\np[=1]{nn_isf}{nn\_isf}}]: The ice shelf cavity is represented (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    1218   The fwf and heat flux are depending of the local water properties. 
    1219  
    1220   Two different bulk formulae are available: 
     1211   \item $\bullet$ representation of the ice shelf/ocean melting/freezing for opened cavity (cav, \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}). 
     1212   \item $\bullet$ parametrisation of the ice shelf/ocean melting/freezing for closed cavities (par, \np{ln_isfpar_mlt}{ln\_isfpar\_mlt}). 
     1213   \item $\bullet$ coupling with an ice sheet model (\np{ln_isfcpl}{ln\_isfcpl}). 
     1214\end{description} 
     1215 
     1216  \subsection{Ocean/Ice shelf fluxes in opened cavities} 
     1217 
     1218     \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .true.} activates the ocean/ice shelf thermodynamics interactions at the ice shelf/ocean interface.  
     1219     If \np{ln_isfcav_mlt}\forcode{ = .false.}, thermodynamics interactions are desctivated but the ocean dynamics inside the cavity is still active. 
     1220     The logical flag \np{ln_isfcav}{ln\_isfcav} control wether or not the ice shelf cavities are closed. \np{ln_isfcav}{ln\_isfcav} is not defined in the namelist but in the domcfg.nc input file.\\ 
     1221 
     1222     3 options are available to represent to ice-shelf/ocean fluxes at the interface: 
     1223     \begin{description} 
     1224        \item[\np{cn_isfcav_mlt}\forcode{ = 'spe'}]: 
     1225        The fresh water flux is specified by a forcing fields \np{sn_isfcav_fwf}{sn\_isfcav\_fwf}. Convention of the input file is: positive toward the ocean (i.e. positive for melting and negative for freezing). 
     1226        The latent heat fluxes is derived from the fresh water flux.  
     1227        The heat content flux is derived from the fwf flux assuming a temperature set to the freezing point in the top boundary layer (\np{rn_htbl}{rn\_htbl}) 
     1228 
     1229        \item[\np{cn_isfcav_mlt}\forcode{ = 'oasis'}]: 
     1230        The \forcode{'oasis'} is a prototype of what could be a method to spread precipitation on Antarctic ice sheet as ice shelf melt inside the cavity when a coupled model Atmosphere/Ocean is used.  
     1231        It has not been tested and therefore the model will stop if you try to use it.  
     1232        Actions will be undertake in 2020 to build a comprehensive interface to do so for Greenland, Antarctic and ice shelf (cav), ice shelf (par), icebergs, subglacial runoff and runoff. 
     1233 
     1234        \item[\np{cn_isfcav_mlt}\forcode{ = '2eq'}]: 
     1235        The heat flux and the fresh water flux (negative for melting) resulting from ice shelf melting/freezing are parameterized following \citet{Grosfeld1997}.  
     1236        This formulation is based on a balance between the vertical diffusive heat flux across the ocean top boundary layer (\autoref{eq:ISOMIP1})  
     1237        and the latent heat due to melting/freezing (\autoref{eq:ISOMIP2}): 
     1238 
     1239        \begin{equation} 
     1240        \label{eq:ISOMIP1} 
     1241        \mathcal{Q}_h = \rho c_p \gamma (T_w - T_f) 
     1242        \end{equation} 
     1243        \begin{equation} 
     1244        \label{eq:ISOMIP2} 
     1245        q = \frac{-\mathcal{Q}_h}{L_f} 
     1246        \end{equation} 
     1247         
     1248        where $\mathcal{Q}_h$($W.m^{-2}$) is the heat flux,q($kg.s^{-1}m^{-2}$) the fresh-water flux,  
     1249        $L_f$ the specific latent heat, $T_w$ the temperature averaged over a boundary layer below the ice shelf (explained below),  
     1250        $T_f$ the freezing point using  the  pressure  at  the  ice  shelf  base  and  the  salinity  of the water in the boundary layer,  
     1251        and $\gamma$ the thermal exchange coefficient. 
     1252 
     1253        \item[\np{cn_isfcav_mlt}\forcode{ = '3eq'}]: 
     1254        For realistic studies, the heat and freshwater fluxes are parameterized following \citep{Jenkins2001}. This formulation is based on three equations:  
     1255        a balance between the vertical diffusive heat flux across the boundary layer  
     1256        , the latent heat due to melting/freezing of ice and the vertical diffusive heat flux into the ice shelf (\autoref{eq:3eq1});  
     1257        a balance between the vertical diffusive salt flux across the boundary layer and the salt source or sink represented by the melting/freezing (\autoref{eq:3eq2});  
     1258        and a linear equation for the freezing temperature of sea water (\autoref{eq:3eq3}, detailed of the linearisation coefficient in \citet{AsayDavis2016}): 
     1259 
     1260        \begin{equation} 
     1261        \label{eq:3eq1} 
     1262        c_p \rho \gamma_T (T_w-T_b) = -L_f q - \rho_i c_{p,i} \kappa \frac{T_s - T_b}{h_{isf}} 
     1263        \end{equation} 
     1264        \begin{equation} 
     1265        \label{eq:3eq2} 
     1266        \rho \gamma_S (S_w - S_b) = (S_i - S_b)q 
     1267        \end{equation} 
     1268        \begin{equation} 
     1269        \label{eq:3eq3} 
     1270        T_b = \lambda_1 S_b + \lambda_2 +\lamda_3 zisf 
     1271        \end{equation} 
     1272 
     1273        where $T_b$ is the temperature at the interface, $S_b$ the salinity at the interface, $\gamma_T$ and $\gamma_S$ the exchange coefficients for temperature and salt, respectively,  
     1274        $S_i$ the salinity of the ice (assumedto be 0), $h_{isf}$ the ice shelf thickness, $\rho_i$ the density of the iceshelf,  
     1275        $c_{p,i}$ the specific heat capacity of the ice, $\kappa$ the thermal diffusivity of the ice  
     1276        and $T_s$ the atmospheric surface temperature (at the ice/air interface, assumed to be -20C).  
     1277        The Liquidus slope ($\lambda_1$), the liquidus intercept ($\lambda_2$) and the Liquidus pressure coefficient ($\lambda_3$)  
     1278        for TEOS80 and TEOS10 are described in \citep{AsayDavis2016} and in \citep{Jourdain2017}. 
     1279        The linear system formed by \autoref{eq:3eq1}, \autoref{eq:3eq2} and the linearised equation for the freezing temperature of sea water (\autoref{eq:3eq3}) can be solved for $S_b$ or $T_b$.  
     1280        Afterward, the freshwater flux ($q$) and the heat flux ($\mathcal{Q}_h$) can be computed. 
     1281 
     1282     \end{description} 
     1283 
     1284     \begin{table}[h] 
     1285        \centering 
     1286        \caption{Description of the parameters hard coded into the ISF module} 
     1287        \label{tab:isf} 
     1288        \begin{tabular}{|l|l|l|l|} 
     1289        \hline 
     1290        Symbol    & Description               & Value              & Unit               \\ 
     1291        \hline 
     1292        $C_p$     & Ocean specific heat       & 3992               & $J.kg^{-1}.K^{-1}$ \\ 
     1293        $L_f$     & Ice latent heat of fusion & $3.34 \times 10^5$ & $J.kg^{-1}$        \\ 
     1294        $C_{p,i}$ & Ice specific heat         & 2000               & $J.kg^{-1}.K^{-1}$ \\ 
     1295        $\kappa$  & Heat diffusivity          & $1.54 \times 10^{-6}$& $m^2.s^{-1}$     \\ 
     1296        $\rho_i$  & Ice density               & 920                & $kg.m^3$           \\ 
     1297        \hline 
     1298        \end{tabular} 
     1299     \end{table} 
     1300 
     1301     Temperature and salinity used to compute the fluxes in \autoref{eq:ISOMIP1}, \autoref{eq:3eq1} and \autoref{eq:3eq2} are the average temperature in the top boundary layer \citep{losch_JGR08}.  
     1302     Its thickness is defined by \np{rn_htbl}{rn\_htbl}. 
     1303     The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the first \np{rn_htbl}{rn\_htbl} m. 
     1304     Then, the fluxes are spread over the same thickness (ie over one or several cells). 
     1305     If \np{rn_htbl}{rn\_htbl} larger than top $e_{3}t$, there is no more direct feedback between the freezing point at the interface and the top cell temperature. 
     1306     This can lead to super-cool temperature in the top cell under melting condition. 
     1307     If \np{rn_htbl}{rn\_htbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 
     1308 
     1309     Each melt formula (\np{cn_isfcav_mlt}\forcode{ = '3eq'} or \np{cn_isfcav_mlt}\forcode{ = '2eq'}) depends on an exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
     1310     Below, the exchange coeficient $\Gamma^{T}$ and $\Gamma^{S}$ are respectively defined by \np{rn_gammat0}{rn\_gammat0} and \np{rn_gammas0}{rn\_gammas0}.  
     1311     There are 3 different ways to compute the exchange velocity: 
     1312 
     1313     \begin{description} 
     1314        \item[\np{cn_gammablk}\forcode{='spe'}]: 
     1315        The salt and heat exchange coefficients are constant and defined by: 
     1316\[ 
     1317\gamma^{T} = \Gamma^{T} 
     1318\] 
     1319\[ 
     1320\gamma^{S} = \Gamma^{S} 
     1321\]  
     1322        This is the recommended formulation for ISOMIP. 
     1323 
     1324   \item[\np{cn_gammablk}\forcode{='vel'}]: 
     1325        The salt and heat exchange coefficients are velocity dependent and defined as 
     1326\[ 
     1327\gamma^{T} = \Gamma^{T} \times u_{*}  
     1328\] 
     1329\[ 
     1330\gamma^{S} = \Gamma^{S} \times u_{*} 
     1331\] 
     1332        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_htbl}{rn\_htbl} meters). 
     1333        See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application and ISOMIP+/MISOMIP configuration. 
     1334 
     1335   \item[\np{cn_gammablk}\forcode{'vel\_stab'}]: 
     1336        The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
     1337\[ 
     1338\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}  
     1339\] 
     1340        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_tbl}{rn\_htbl} meters), 
     1341        $\Gamma_{Turb}$ the contribution of the ocean stability and 
     1342        $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
     1343        See \citet{holland.jenkins_JPO99} for all the details on this formulation.  
     1344        This formulation has not been extensively tested in NEMO (not recommended). 
     1345     \end{description} 
     1346 
     1347\subsection{Ocean/Ice shelf fluxes in parametrised cavities} 
    12211348 
    12221349  \begin{description} 
    1223   \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
    1224     the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
    1225   \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
    1226     (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
    1227     A complete description is available in \citet{jenkins_JGR91}. 
     1350 
     1351     \item[\np{cn_isfpar_mlt}\forcode{ = 'bg03'}]: 
     1352     The ice shelf cavities are not represented. 
     1353     The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
     1354     The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
     1355     (\np{sn_isfpar_zmax}{sn\_isfpar\_zmax}) and the base of the ice shelf along the calving front 
     1356     (\np{sn_isfpar_zmin}{sn\_isfpar\_zmin}) as in (\np{cn_isfpar_mlt}\forcode{ = 'spe'}). 
     1357     The effective melting length (\np{sn_isfpar_Leff}{sn\_isfpar\_Leff}) is read from a file. 
     1358     This parametrisation has not been tested since a while and based on \citet{Favier2019},  
     1359     this parametrisation should probably not be used. 
     1360 
     1361     \item[\np{cn_isfpar_mlt}\forcode{ = 'spe'}]: 
     1362     The ice shelf cavity is not represented. 
     1363     The fwf (\np{sn_isfpar_fwf}{sn\_isfpar\_fwf}) is prescribed and distributed along the ice shelf edge between 
     1364     the depth of the average grounding line (GL) (\np{sn_isfpar_zmax}{sn\_isfpar\_zmax}) and 
     1365     the base of the ice shelf along the calving front (\np{sn_isfpar_zmin}{sn\_isfpar\_min}). Convention of the input file is positive toward the ocean (i.e. positive for melting and negative for freezing). 
     1366     The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     1367 
     1368     \item[\np{cn_isfpar_mlt}\forcode{ = 'oasis'}]: 
     1369     The \forcode{'oasis'} is a prototype of what could be a method to spread precipitation on Antarctic ice sheet as ice shelf melt inside the cavity when a coupled model Atmosphere/Ocean is used.  
     1370     It has not been tested and therefore the model will stop if you try to use it.  
     1371     Action will be undertake in 2020 to build a comprehensive interface to do so for Greenland, Antarctic and ice shelf (cav), ice shelf (par), icebergs, subglacial runoff and runoff. 
     1372 
    12281373  \end{description} 
    12291374 
    1230   Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
    1231   Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. 
    1232   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. 
    1233   Then, the fluxes are spread over the same thickness (ie over one or several cells). 
    1234   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. 
    1235   This can lead to super-cool temperature in the top cell under melting condition. 
    1236   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.\\ 
    1237  
    1238   Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
    1239   There are 3 different ways to compute the exchange coeficient: 
    1240   \begin{description} 
    1241   \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}. 
    1242     \begin{gather*} 
    1243        % \label{eq:SBC_isf_gamma_iso} 
    1244       \gamma^{T} = rn\_gammat0 \\ 
    1245       \gamma^{S} = rn\_gammas0 
    1246     \end{gather*} 
    1247     This is the recommended formulation for ISOMIP. 
    1248   \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
    1249     \begin{gather*} 
    1250       \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
    1251       \gamma^{S} = rn\_gammas0 \times u_{*} 
    1252     \end{gather*} 
    1253     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
    1254     See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
    1255   \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    1256     \[ 
    1257       \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
    1258     \] 
    1259     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), 
    1260     $\Gamma_{Turb}$ the contribution of the ocean stability and 
    1261     $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
    1262     See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
    1263     This formulation has not been extensively tested in \NEMO\ (not recommended). 
    1264   \end{description} 
    1265 \item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    1266   The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    1267   The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
    1268   (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
    1269   (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
    1270   The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
    1271 \item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    1272   The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
    1273   the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
    1274   the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
    1275   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    1276 \item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    1277   However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
    1278   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    1279   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}) 
    1280 \end{description} 
    1281  
    1282 $\bullet$ \np[=1]{nn_isf}{nn\_isf} and \np[=2]{nn_isf}{nn\_isf} compute a melt rate based on 
     1375\np{cn_isfcav_mlt}\forcode{ = '2eq'}, \np{cn_isfcav_mlt}\forcode{ = '3eq'} and \np{cn_isfpar_mlt}\forcode{ = 'bg03'} compute a melt rate based on 
    12831376the water mass properties, ocean velocities and depth. 
    1284 This flux is thus highly dependent of the model resolution (horizontal and vertical), 
    1285 realism of the water masses onto the shelf ...\\ 
    1286  
    1287 $\bullet$ \np[=3]{nn_isf}{nn\_isf} and \np[=4]{nn_isf}{nn\_isf} read the melt rate from a file. 
     1377The resulting fluxes are thus highly dependent of the model resolution (horizontal and vertical) and  
     1378realism of the water masses onto the shelf.\\ 
     1379 
     1380\np{cn_isfcav_mlt}\forcode{ = 'spe'} and \np{cn_isfpar_mlt}\forcode{ = 'spe'} read the melt rate from a file. 
    12881381You have total control of the fwf forcing. 
    12891382This can be useful if the water masses on the shelf are not realistic or 
    12901383the resolution (horizontal/vertical) are too coarse to have realistic melting or 
    1291 for studies where you need to control your heat and fw input.\\ 
    1292  
    1293 The ice shelf melt is implemented as a volume flux as for the runoff. 
    1294 The fw addition due to the ice shelf melting is, at each relevant depth level, added to 
    1295 the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divhor}. 
     1384for studies where you need to control your heat and fw input.  
     1385However, if your forcing is not consistent with the dynamics below you can reach unrealistic low water temperature.\\ 
     1386 
     1387The ice shelf fwf is implemented as a volume flux as for the runoff. 
     1388The fwf addition due to the ice shelf melting is, at each relevant depth level, added to 
     1389the horizontal divergence (\textit{hdivn}) in the subroutine \rou{isf\_hdiv}, called from \mdl{divhor}. 
    12961390See the runoff section \autoref{sec:SBC_rnf} for all the details about the divergence correction.\\ 
     1391 
     1392Description and result of sensitivity tests to \np{ln_isfcav_mlt}{ln\_isfcav\_mlt} and \np{ln_isfpar_mlt}{ln\_isfpar\_mlt} are presented in \citet{mathiot.jenkins.ea_GMD17}.  
     1393The different options are illustrated in \autoref{fig:ISF}. 
    12971394 
    12981395\begin{figure}[!t] 
    12991396  \centering 
    1300   \includegraphics[width=0.66\textwidth]{SBC_isf} 
     1397  \includegraphics[width=0.66\textwidth]{SBC_isf_v4.2} 
    13011398  \caption[Ice shelf location and fresh water flux definition]{ 
    13021399    Illustration of the location where the fwf is injected and 
    1303     whether or not the fwf is interactif or not depending of \protect\np{nn_isf}{nn\_isf}.} 
    1304   \label{fig:SBC_isf} 
     1400    whether or not the fwf is interactif or not.} 
     1401  \label{fig:ISF} 
    13051402\end{figure} 
    13061403 
    1307 %% ================================================================================================= 
    1308 \section{Ice sheet coupling} 
    1309 \label{sec:SBC_iscpl} 
    1310  
    1311 \begin{listing} 
    1312   \nlst{namsbc_iscpl} 
    1313   \caption{\forcode{&namsbc_iscpl}} 
    1314   \label{lst:namsbc_iscpl} 
    1315 \end{listing} 
     1404\subsection{Available outputs} 
     1405The following outputs are availables via XIOS: 
     1406\begin{description} 
     1407   \item[for parametrised cavities]: 
     1408      \begin{xmllines} 
     1409 <field id="isftfrz_par"     long_name="freezing point temperature in the parametrization boundary layer" unit="degC"     /> 
     1410 <field id="fwfisf_par"      long_name="Ice shelf melt rate"                           unit="kg/m2/s"  /> 
     1411 <field id="qoceisf_par"     long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     /> 
     1412 <field id="qlatisf_par"     long_name="Ice shelf latent heat flux"                    unit="W/m2"     /> 
     1413 <field id="qhcisf_par"      long_name="Ice shelf heat content flux of injected water" unit="W/m2"     /> 
     1414 <field id="fwfisf3d_par"    long_name="Ice shelf melt rate"                           unit="kg/m2/s"  grid_ref="grid_T_3D" /> 
     1415 <field id="qoceisf3d_par"   long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" /> 
     1416 <field id="qlatisf3d_par"   long_name="Ice shelf latent heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" /> 
     1417 <field id="qhcisf3d_par"    long_name="Ice shelf heat content flux of injected water" unit="W/m2"     grid_ref="grid_T_3D" /> 
     1418 <field id="ttbl_par"        long_name="temperature in the parametrisation boundary layer" unit="degC" /> 
     1419 <field id="isfthermald_par" long_name="thermal driving of ice shelf melting"          unit="degC"     /> 
     1420      \end{xmllines} 
     1421   \item[for open cavities]: 
     1422      \begin{xmllines} 
     1423 <field id="isftfrz_cav"     long_name="freezing point temperature at ocean/isf interface"                unit="degC"     /> 
     1424 <field id="fwfisf_cav"      long_name="Ice shelf melt rate"                           unit="kg/m2/s"  /> 
     1425 <field id="qoceisf_cav"     long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     /> 
     1426 <field id="qlatisf_cav"     long_name="Ice shelf latent heat flux"                    unit="W/m2"     /> 
     1427 <field id="qhcisf_cav"      long_name="Ice shelf heat content flux of injected water" unit="W/m2"     /> 
     1428 <field id="fwfisf3d_cav"    long_name="Ice shelf melt rate"                           unit="kg/m2/s"  grid_ref="grid_T_3D" /> 
     1429 <field id="qoceisf3d_cav"   long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" /> 
     1430 <field id="qlatisf3d_cav"   long_name="Ice shelf latent heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" /> 
     1431 <field id="qhcisf3d_cav"    long_name="Ice shelf heat content flux of injected water" unit="W/m2"     grid_ref="grid_T_3D" /> 
     1432 <field id="ttbl_cav"        long_name="temperature in Losch tbl"                      unit="degC"     /> 
     1433 <field id="isfthermald_cav" long_name="thermal driving of ice shelf melting"          unit="degC"     /> 
     1434 <field id="isfgammat"       long_name="Ice shelf heat-transfert velocity"             unit="m/s"      /> 
     1435 <field id="isfgammas"       long_name="Ice shelf salt-transfert velocity"             unit="m/s"      /> 
     1436 <field id="stbl"            long_name="salinity in the Losh tbl"                      unit="1e-3"     /> 
     1437 <field id="utbl"            long_name="zonal current in the Losh tbl at T point"      unit="m/s"      /> 
     1438 <field id="vtbl"            long_name="merid current in the Losh tbl at T point"      unit="m/s"      /> 
     1439 <field id="isfustar"        long_name="ustar at T point used in ice shelf melting"    unit="m/s"      /> 
     1440 <field id="qconisf"         long_name="Conductive heat flux through the ice shelf"    unit="W/m2"     /> 
     1441      \end{xmllines} 
     1442\end{description} 
     1443 
     1444%% ================================================================================================= 
     1445\subsection{Ice sheet coupling} 
     1446\label{subsec:ISF_iscpl} 
    13161447 
    13171448Ice sheet/ocean coupling is done through file exchange at the restart step. 
    1318 At each restart step: 
    1319  
    1320 \begin{enumerate} 
    1321 \item the ice sheet model send a new bathymetry and ice shelf draft netcdf file. 
    1322 \item a new domcfg.nc file is built using the DOMAINcfg tools. 
    1323 \item \NEMO\ run for a specific period and output the average melt rate over the period. 
    1324 \item the ice sheet model run using the melt rate outputed in step 4. 
    1325 \item go back to 1. 
    1326 \end{enumerate} 
    1327  
    1328 If \np[=.true.]{ln_iscpl}{ln\_iscpl}, the isf draft is assume to be different at each restart step with 
     1449At each restart step, the procedure is this one: 
     1450 
     1451\begin{description} 
     1452\item[Step 1]: the ice sheet model send a new bathymetry and ice shelf draft netcdf file. 
     1453\item[Step 2]: a new domcfg.nc file is built using the DOMAINcfg tools. 
     1454\item[Step 3]: NEMO run for a specific period and output the average melt rate over the period. 
     1455\item[Step 4]: the ice sheet model run using the melt rate outputed in step 4. 
     1456\item[Step 5]: go back to 1. 
     1457\end{description} 
     1458 
     1459If \np{ln_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with 
    13291460potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics. 
    1330 The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases: 
     1461The wetting and drying scheme, applied on the restart, is very simple. The 6 different possible cases for the tracer and ssh are: 
    13311462 
    13321463\begin{description} 
    1333 \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 
    1334   ($bt_b=bt_n$). 
    1335 \item [Enlarge  a cell]: See case "Thin a cell down" 
    1336 \item [Dry a cell]: mask, T/S, U/V and ssh are set to 0. 
    1337   Furthermore, U/V into the water column are modified to satisfy ($bt_b=bt_n$). 
    1338 \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. 
    1339   If no neighbours, T/S is extrapolated from old top cell value. 
    1340   If no neighbours along i,j and k (both previous test failed), T/S/U/V/ssh and mask are set to 0. 
    1341 \item [Dry a column]: mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0. 
    1342 \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. 
    1343   If no neighbour, T/S/U/V and mask set to 0. 
     1464   \item[Thin a cell]: 
     1465   T/S/ssh are unchanged. 
     1466 
     1467   \item[Enlarge  a cell]: 
     1468   See case "Thin a cell down" 
     1469 
     1470   \item[Dry a cell]: 
     1471   Mask, T/S, U/V and ssh are set to 0. 
     1472 
     1473   \item[Wet a cell]:  
     1474   Mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$. 
     1475   If no neighbours, T/S is extrapolated from old top cell value.  
     1476   If no neighbours along i,j and k (both previous tests failed), T/S/ssh and mask are set to 0. 
     1477 
     1478   \item[Dry a column]: 
     1479   mask, T/S and ssh are set to 0. 
     1480 
     1481   \item[Wet a column]: 
     1482   set mask to 1, T/S/ssh are extrapolated from neighbours. 
     1483   If no neighbour, T/S/ssh and mask set to 0. 
    13441484\end{description} 
     1485 
     1486The method described above will strongly affect the barotropic transport under an ice shelf when the geometry change. 
     1487In order to keep the model stable, an adjustment of the dynamics at the initialisation after the coupling step is needed.  
     1488The idea behind this is to keep $\pd[\eta]{t}$ as it should be without change in geometry at the initialisation.  
     1489This will prevent any strong velocity due to large pressure gradient.  
     1490To do so, we correct the horizontal divergence before $\pd[\eta]{t}$ is computed in the first time step.\\ 
    13451491 
    13461492Furthermore, as the before and now fields are not compatible (modification of the geometry), 
     
    13491495The horizontal extrapolation to fill new cell with realistic value is called \np{nn_drown}{nn\_drown} times. 
    13501496It means that if the grounding line retreat by more than \np{nn_drown}{nn\_drown} cells between 2 coupling steps, 
    1351 the code will be unable to fill all the new wet cells properly. 
     1497the code will be unable to fill all the new wet cells properly and the model is likely to blow up at the initialisation. 
    13521498The default number is set up for the MISOMIP idealised experiments. 
    13531499This coupling procedure is able to take into account grounding line and calving front migration. 
    1354 However, it is a non-conservative processe. 
     1500However, it is a non-conservative proccess.  
    13551501This could lead to a trend in heat/salt content and volume.\\ 
    13561502 
    13571503In order to remove the trend and keep the conservation level as close to 0 as possible, 
    1358 a simple conservation scheme is available with \np[=.true.]{ln_hsb}{ln\_hsb}. 
    1359 The heat/salt/vol. gain/loss is diagnosed, as well as the location. 
    1360 A correction increment is computed and apply each time step during the next \np{rn_fiscpl}{rn\_fiscpl} time steps. 
    1361 For safety, it is advised to set \np{rn_fiscpl}{rn\_fiscpl} equal to the coupling period (smallest increment possible). 
    1362 The 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). 
     1504a simple conservation scheme is available with \np{ln_isfcpl_cons}\forcode{ = .true.}. 
     1505The heat/salt/vol. gain/loss are diagnosed, as well as the location. 
     1506A correction increment is computed and applied each time step during the model run. 
     1507The corrective increment are applied into the cells itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry). 
    13631508 
    13641509%% ================================================================================================= 
     
    18111956\end{description} 
    18121957 
     1958\subsection[Closed sea freshwater budget control (\textit{sbcclo.F90})]{Closed sea freswater budget control (\protect\mdl{sbcclo})} 
     1959\label{subsec:SBC_clo} 
     1960 
     1961Some configurations include inland seas and lakes as ocean 
     1962points. This is particularly the case for configurations that are 
     1963coupled to an atmosphere model where one might want to include inland 
     1964seas and lakes as ocean model points in order to provide a better 
     1965bottom boundary condition for the atmosphere. However there is no 
     1966route for freshwater to run off from the lakes to the ocean and this 
     1967can lead to large drifts in the sea surface height over the lakes. The 
     1968closea module provides options to either fill in closed seas and lakes 
     1969at run time, or to set the net surface freshwater flux for each lake 
     1970to zero and put the residual flux into the ocean.  
     1971Full details on the usage on the closed sea module are available in \autoref{sec:MISC_closea}  
     1972 
     1973The following outputs are availables via XIOS: 
     1974\begin{xmllines} 
     1975   <field id="wclosea"  long_name="closed sea empmr correction"   standard_name="closea_empmr"                          unit="kg/m2/s"   /> 
     1976   <field id="qclosea"  long_name="closed sea heat content flux"  standard_name="closea_heat_content_downward_flux"     unit="W/m2"      /> 
     1977\end{xmllines} 
     1978 
     1979 
    18131980% Griffies doc: 
    18141981% When running ocean-ice simulations, we are not explicitly representing land processes, 
  • NEMO/branches/2020/ticket_2444/doc/latex/NEMO/subfiles/chap_misc.tex

    r12377 r12769  
    1616    Release & Author(s) & Modifications \\ 
    1717    \hline 
     18    {\em   X.X} & {\em Pierre Mathiot} & {update of the closed sea section} 
    1819    {\em   4.0} & {\em ...} & {\em ...} \\ 
    1920    {\em   3.6} & {\em ...} & {\em ...} \\ 
     
    109110\end{figure} 
    110111 
    111 \begin{figure}[!tbp] 
    112   \centering 
    113   \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example} 
    114   \caption[Mask fields for the \protect\mdl{closea} module]{ 
    115     Example of mask fields for the \protect\mdl{closea} module. 
    116     \textit{Left}: a closea\_mask field; 
    117     \textit{Right}: a closea\_mask\_rnf field. 
    118     In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.}, 
    119     the mean freshwater flux over each of the American Great Lakes will be set to zero, 
    120     and the total residual for all the lakes, if negative, will be put into 
    121     the St Laurence Seaway in the area shown.} 
    122   \label{fig:MISC_closea_mask_example} 
    123 \end{figure} 
    124  
    125112%% ================================================================================================= 
    126113\section[Closed seas (\textit{closea.F90})]{Closed seas (\protect\mdl{closea})} 
    127114\label{sec:MISC_closea} 
     115 
     116\begin{listing} 
     117  \nlst{namclo} 
     118  \caption{\forcode{&namclo}} 
     119  \label{lst:namclo} 
     120\end{listing} 
    128121 
    129122Some configurations include inland seas and lakes as ocean 
     
    138131to zero and put the residual flux into the ocean. 
    139132 
    140 Prior to \NEMO\ 4 the locations of inland seas and lakes was set via 
    141 hardcoded indices for various ORCA configurations. From \NEMO\ 4 onwards 
    142 the inland seas and lakes are defined using mask fields in the 
    143 domain configuration file. The options are as follows. 
    144  
    145 \begin{enumerate} 
    146 \item {{\bfseries No ``closea\_mask'' field is included in domain configuration 
    147   file.} In this case the closea module does nothing.} 
    148  
    149 \item {{\bfseries A field called closea\_mask is included in the domain 
    150 configuration file and ln\_closea=.false. in namelist namcfg.} In this 
    151 case the inland seas defined by the closea\_mask field are filled in 
    152 (turned to land points) at run time. That is every point in 
    153 closea\_mask that is nonzero is set to be a land point.} 
    154  
    155 \item {{\bfseries A field called closea\_mask is included in the domain 
    156 configuration file and ln\_closea=.true. in namelist namcfg.} Each 
    157 inland sea or group of inland seas is set to a positive integer value 
    158 in the closea\_mask field (see \autoref{fig:MISC_closea_mask_example} 
    159 for an example). The net surface flux over each inland sea or group of 
     133The inland seas and lakes are defined using mask fields in the 
     134domain configuration file. Special treatment of the closed sea (redistribution of net freshwater or mask those), are defined in \autoref{lst:namclo} and 
     135can be trigger by \np{ln_closea}{ln\_closea}\forcode{=.true.} in namelist namcfg. 
     136 
     137The options available are the following: 
     138\begin{description} 
     139\item[\np{ln_maskcs}{ln\_maskcs}\forcode{ = .true.}] All the closed seas are masked using \textit{mask\_opensea} variable. 
     140\item[\np{ln_maskcs}{ln\_maskcs}\forcode{ = .false.}] The net surface flux over each inland sea or group of 
    160141inland seas is set to zero each timestep and the residual flux is 
    161 distributed over the global ocean (ie. all ocean points where 
    162 closea\_mask is zero).} 
    163  
    164 \item {{\bfseries Fields called closea\_mask and closea\_mask\_rnf are 
    165 included in the domain configuration file and ln\_closea=.true. in 
    166 namelist namcfg.} This option works as for option 3, except that if 
    167 the net surface flux over an inland sea is negative (net 
    168 precipitation) it is put into the ocean at specified runoff points. A 
    169 net positive surface flux (net evaporation) is still spread over the 
    170 global ocean. The mapping from inland seas to runoff points is defined 
    171 by the closea\_mask\_rnf field. Each mapping is defined by a positive 
    172 integer value for the inland sea(s) and the corresponding runoff 
    173 points. An example is given in 
    174 \autoref{fig:MISC_closea_mask_example}. If no mapping is provided for a 
    175 particular inland sea then the residual is spread over the global 
    176 ocean.} 
    177  
    178 \item {{\bfseries Fields called closea\_mask and closea\_mask\_emp are 
    179 included in the domain configuration file and ln\_closea=.true. in 
    180 namelist namcfg.} This option works the same as option 4 except that 
    181 the nonzero net surface flux is sent to the ocean at the specified 
    182 runoff points regardless of whether it is positive or negative. The 
    183 mapping from inland seas to runoff points in this case is defined by 
    184 the closea\_mask\_emp field.} 
    185 \end{enumerate} 
    186  
    187 There is a python routine to create the closea\_mask fields and append 
    188 them to the domain configuration file in the utils/tools/DOMAINcfg directory. 
     142distributed over a target area. 
     143\end{description} 
     144 
     145When \np{ln_maskcs}{ln\_maskcs}\forcode{ = .false.},  
     1463 options are available for the redistribution (set up of these options is done in the tool DOMAINcfg): 
     147\begin{description}[font=$\bullet$ ] 
     148\item[ glo]: The residual flux is redistributed globally. 
     149\item[ emp]: The residual flux is redistributed as emp in a river outflow. 
     150\item[ rnf]: The residual flux is redistributed as rnf in a river outflow if negative. If there is a net evaporation, the residual flux is redistributed globally. 
     151\end{description} 
     152 
     153For each case, 2 masks are needed (\autoref{fig:MISC_closea_mask_example}):  
     154\begin{description} 
     155\item $\bullet$ one describing the 'sources' (ie the closed seas concerned by each options) called \textit{mask\_csglo}, \textit{mask\_csrnf}, \textit{mask\_csemp}.  
     156\item $\bullet$ one describing each group of inland seas (the Great Lakes for example) and the target area (river outflow or world ocean) for each group of inland seas (St Laurence for the Great Lakes for example) called 
     157\textit{mask\_csgrpglo}, \textit{mask\_csgrprnf}, \textit{mask\_csgrpemp}. 
     158\end{description} 
     159 
     160\begin{figure}[!tbp] 
     161  \centering 
     162  \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example} 
     163  \caption[Mask fields for the \protect\mdl{closea} module]{ 
     164    Example of mask fields for the \protect\mdl{closea} module. 
     165    \textit{Left}: a \textit{mask\_csrnf} field; 
     166    \textit{Right}: a \textit{mask\_csgrprnf} field. 
     167    In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.}, 
     168    the mean freshwater flux over each of the American Great Lakes will be set to zero, 
     169    and the total residual for all the lakes, if negative, will be put into 
     170    the St Laurence Seaway in the area shown.} 
     171  \label{fig:MISC_closea_mask_example} 
     172\end{figure} 
     173 
     174Closed sea not defined (because too small, issue in the bathymetry definition ...) are defined in \textit{mask\_csundef}. 
     175These points can be masked using the namelist option \np{ln_mask_csundef}{ln\_mask\_csundef}\forcode{= .true.} or used to correct the bathymetry input file.\\ 
     176 
     177The masks needed for the closed sea can be created using the DOMAINcfg tool in the utils/tools/DOMAINcfg directory. 
     178See \autoref{sec:clocfg} for details on the usage of definition of the closed sea masks. 
    189179 
    190180%% ================================================================================================= 
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