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Changeset 14676 for NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles – NEMO

Ignore:
Timestamp:
2021-04-07T15:48:38+02:00 (3 years ago)
Author:
ayoung
Message:

Updating SEAMOUNT test case to trunk at revision 14675. 2021 ticket #2651. 2020 ticket #2480.

Location:
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles
Files:
13 edited

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  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles

    • Property svn:ignore

      •  

        old new  
         1*.aux 
         2*.bbl 
         3*.blg 
         4*.fdb* 
         5*.fls 
         6*.idx 
         7*.ilg 
        18*.ind 
        2 *.ilg 
         9*.lo* 
         10*.out 
         11*.pdf 
         12*.pyg 
         13*.tdo 
         14*.toc 
         15*.xdv 
         16cache* 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

    r14328 r14676  
    66\label{apdx:DOMCFG} 
    77 
    8 %    {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains }  \\ 
    9  
    108\chaptertoc 
    119 
    … …  
    1412{\footnotesize 
    1513  \begin{tabularx}{\textwidth}{l||X|X} 
    16     Release & Author(s) & Modifications \\ 
    17     \hline 
    18     {\em   next}& {\em Pierre Mathiot} & {\em add ice shelf and closed sea option description } \\ 
    19     {\em   4.0} & {\em Andrew Coward}  & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains }  \\ 
    20     {\em   3.6} & {\em ...} & {\em ...} \\ 
    21     {\em   3.4} & {\em ...} & {\em ...} \\ 
    22     {\em <=3.4} & {\em ...} & {\em ...} 
     14    Release     & Author(s)            & Modifications                                                 \\ 
     15    \hline 
     16    {\em  next} & {\em Pierre Mathiot} & {\em Add ice shelf and closed sea option description        } \\ 
     17    {\em   4.0} & {\em  Andrew Coward} & {\em Creation from materials removed from \autoref{chap:DOM} 
     18                                              that are still relevant to the DOMAINcfg tool 
     19                                              when setting up new domains                            } 
    2320  \end{tabularx} 
    2421} 
    … …  
    4542 
    4643\begin{listing} 
    47 %  \nlst{namdom_domcfg} 
    4844  \begin{forlines} 
    4945!----------------------------------------------------------------------- 
    … …  
    412408 
    413409\begin{listing} 
    414 %  \nlst{namzgr_sco_domcfg} 
    415410  \caption{\forcode{&namzgr_sco_domcfg}} 
    416411  \label{lst:namzgr_sco_domcfg} 
    … …  
    592587  the \textit{isfdraft\_meter} file (Netcdf format). This file need to include the \textit{isf\_draft} variable.  
    593588  A positive value will mean ice shelf/ocean or ice shelf bedrock interface below the reference 0m ssh.  
    594   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{zgr_isf}{zgr_isf}. 
     589  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{zgr_isf}{zgr\_isf}. 
    595590 
    596591\begin{listing} 
    … …  
    616611\end{listing} 
    617612 
    618    The options available to define the shape of the under ice shelf cavities are listed in \nam{zgr_isf}{zgr_isf} (\texttt{DOMAINcfg} only, \autoref{lst:namzgr_isf}). 
    619  
    620    \subsection{Model ice shelf draft definition} 
    621    \label{subsec:zgrisf_isfd} 
    622  
    623    First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry. 
    624    There are 3 compulsory steps to achieve this: 
    625  
    626    \begin{description} 
    627    \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 $e3t\_1d(1)$.  
    628    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}. 
    629  
    630    \item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position. 
    631    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).  
    632    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, ...). 
    633  
    634    \item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is the minimum water column thickness in the cavity.  
    635    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.  
    636    If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked. 
    637    \end{description} 
    638  
    639    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}.   
     613   The options available to define the shape of the under ice shelf cavities are listed in \nam{zgr_isf}{zgr\_isf} (\texttt{DOMAINcfg} only, \autoref{lst:namzgr_isf}). 
     614 
     615\subsection{Model ice shelf draft definition} 
     616\label{subsec:zgrisf_isfd} 
     617 
     618First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry. 
     619There are 3 compulsory steps to achieve this: 
     620 
     621\begin{description} 
     622\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 $e3t\_1d(1)$.  
     623  Where $h_{isf} < MAX(e3t\_1d(1),rn\_isfdep\_min)$, $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}. 
     624 
     625\item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position. 
     626  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).  
     627  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, ...). 
     628 
     629\item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is the minimum water column thickness in the cavity.  
     630  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.  
     631  If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked. 
     632\end{description} 
     633 
     634Once 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}.   
    640635  
    641    \subsection{Model top level definition} 
    642    After the definition of the ice shelf draft, the tool defines the top level.  
    643    The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points. 
    644    To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\ 
    645  
    646    The process is the following: 
    647    \begin{description} 
    648    \item{step 1:} The top level is defined in the same way as the bottom level is defined. 
    649    \item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf) 
    650    \item{step 3:} The tools make sure, the top level is above or equal to the bottom level 
    651    \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 
    652    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. 
    653    \end{description} 
    654  
    655    In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourging ice shelf draft).  
    656    The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells. 
    657    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}). 
    658    This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels. 
    659  
    660    \subsection{Subglacial lakes} 
    661    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. 
    662    For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling,  
    663    you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded).  
    664    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:  
    665    one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\ 
    666  
    667    The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes. 
    668    This may be useful for esthetical reason or for stability reasons: 
    669  
    670    \begin{description} 
    671    \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.  
    672          This will lead to constant freezing until water reaches -20C.  
    673          This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}). 
    674    \item $\bullet$ In case of coupling with an ice sheet model,  
    675          the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example),  
    676          and so if for any reason both a connected at some point, the model is likely to fall over.\\ 
    677    \end{description} 
     636\subsection{Model top level definition} 
     637After the definition of the ice shelf draft, the tool defines the top level.  
     638The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points. 
     639To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\ 
     640 
     641The process is the following: 
     642\begin{description} 
     643\item{step 1:} The top level is defined in the same way as the bottom level is defined. 
     644\item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf) 
     645\item{step 3:} The tools make sure, the top level is above or equal to the bottom level 
     646\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 
     647  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. 
     648\end{description} 
     649 
     650In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourging ice shelf draft).  
     651The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells. 
     652Some 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}). 
     653This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels. 
     654 
     655\subsection{Subglacial lakes} 
     656Despite 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. 
     657For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling,  
     658you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded).  
     659If 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:  
     660one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\ 
     661 
     662The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes. 
     663This may be useful for esthetical reason or for stability reasons: 
     664 
     665\begin{description} 
     666\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.  
     667  This will lead to constant freezing until water reaches -20C.  
     668  This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}). 
     669\item $\bullet$ In case of coupling with an ice sheet model,  
     670  the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example),  
     671  and so if for any reason both a connected at some point, the model is likely to fall over.\\ 
     672\end{description} 
    678673 
    679674\section{Closed sea definition} 
    … …  
    707702\end{listing} 
    708703 
    709 The 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}{dom_clo} (\texttt{DOMAINcfg} only). 
     704The options available to define the closed seas and how closed sea net fresh water input will be redistributed by NEMO are listed in \nam{dom_clo}{dom\_clo} (\texttt{DOMAINcfg} only). 
    710705The individual definition of each closed sea is managed by \np{sn_lake}{sn\_lake}. In this fields the user needs to define:\\ 
    711706   \begin{description} 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/apdx_triads.tex

    r14328 r14676  
    22 
    33\begin{document} 
    4  
    5 %% Local cmds 
    6 \newcommand{\rML}[1][i]{\ensuremath{_{\mathrm{ML}\,#1}}} 
    7 \newcommand{\rMLt}[1][i]{\tilde{r}_{\mathrm{ML}\,#1}} 
    8 %% Move to ../../global/new_cmds.tex to avoid error with \listoffigures 
    9 %\newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}} 
    10 \newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}} 
    11 \newcommand{\triadt}[5]{\ensuremath{{}_{#1}^{#2}{\tilde{\mathbb{#3}}}_{#4}^{\,#5}}} 
    12 \newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}} 
    13 \newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 
    144 
    155\chapter{Iso-Neutral Diffusion and Eddy Advection using Triads} 
    … …  
    3424 
    3525%% ================================================================================================= 
    36 \section[Choice of \forcode{namtra\_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters} 
     26\section[Choice of \forcode{namtra_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters} 
    3727 
    3828Two scheme are available to perform the iso-neutral diffusion. 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_DIU.tex

    r14328 r14676  
    5050 
    5151This namelist contains only two variables: 
     52 
    5253\begin{description} 
    5354\item [{\np{ln_diurnal}{ln\_diurnal}}] A logical switch for turning on/off both the cool skin and warm layer. 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_DOM.tex

    r14328 r14676  
    377377in which case \np{cn_cfg}{cn\_cfg} and \np{nn_cfg}{nn\_cfg} are set from these values accordingly). 
    378378 
    379 The global lateral boundary condition type is selected from 8 options using parameter \texttt{jperio}. 
     379The global lateral boundary condition type is selected from 8 options using parameters \texttt{l\_Iperio}, \texttt{l\_Jperio}, \texttt{l\_NFold} and \texttt{c\_NFtype}. 
    380380See \autoref{sec:LBC_jperio} for details on the available options and 
    381 the corresponding values for \texttt{jperio}. 
     381the corresponding values for \texttt{l\_Iperio}, \texttt{l\_Jperio}, \texttt{l\_NFold} and \texttt{c\_NFtype}. 
    382382 
    383383%% ================================================================================================= 
    … …  
    394394 
    395395\begin{clines} 
    396 int    jpiglo, jpjglo, jpkglo     /* global domain sizes                                    */ 
    397 int    jperio                     /* lateral global domain b.c.                             */ 
    398 double glamt, glamu, glamv, glamf /* geographic longitude (t,u,v and f points respectively) */ 
    399 double gphit, gphiu, gphiv, gphif /* geographic latitude                                    */ 
    400 double e1t, e1u, e1v, e1f         /* horizontal scale factors                               */ 
    401 double e2t, e2u, e2v, e2f         /* horizontal scale factors                               */ 
     396integer   Ni0glo, NjOglo, jpkglo       /* global domain sizes (without MPI halos)                */ 
     397logical   l\_Iperio, l\_Jperio         /* lateral global domain b.c.: i- j-periodicity           */ 
     398logical   l\_NFold                     /* lateral global domain b.c.: North Pole folding         */ 
     399char(1)   c\_NFtype                    /*    type of North pole Folding: T or F point            */ 
     400real      glamt, glamu, glamv, glamf   /* geographic longitude (t,u,v and f points respectively) */ 
     401real      gphit, gphiu, gphiv, gphif   /* geographic latitude                                    */ 
     402real      e1t, e1u, e1v, e1f           /* horizontal scale factors                               */ 
     403real      e2t, e2u, e2v, e2f           /* horizontal scale factors                               */ 
    402404\end{clines} 
    403405 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_LBC.tex

    r14328 r14676  
    159159 
    160160%% ================================================================================================= 
    161 \section{Model domain boundary condition (\forcode{jperio})} 
     161\section{Model domain boundary condition} 
    162162\label{sec:LBC_jperio} 
    163163 
    … …  
    168168 
    169169%% ================================================================================================= 
    170 \subsection{Closed, cyclic (\forcode{jperio={0,1,2,7}})} 
     170\subsection{Closed, cyclic (\forcode{l_Iperio,l_jperio})} 
    171171\label{subsec:LBC_jperio012} 
    172172 
    173173The choice of closed or cyclic model domain boundary condition is made by 
    174 setting \forcode{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}. 
     174setting \forcode{l_Iperio,l_jperio} to true or false in namelist \nam{cfg}{cfg}. 
    175175Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}. 
    176176The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$, 
    … …  
    181181\begin{description} 
    182182 
    183 \item [For closed boundary (\forcode{jperio=0})], solid walls are imposed at all model boundaries: 
     183\item [For closed boundary (\forcode{l_Iperio = .false.,l_jperio = .false.})], solid walls are imposed at all model boundaries: 
    184184  first and last rows and columns are set to zero. 
    185185 
    186 \item [For cyclic east-west boundary (\forcode{jperio=1})], first and last rows are set to zero (closed) whilst the first column is set to 
     186\item [For cyclic east-west boundary (\forcode{l_Iperio = .true.,l_jperio = .false.})], first and last rows are set to zero (closed) whilst the first column is set to 
    187187  the value of the last-but-one column and the last column to the value of the second one 
    188188  (\autoref{fig:LBC_jperio}-a). 
    189189  Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end. 
    190190 
    191 \item [For cyclic north-south boundary (\forcode{jperio=2})], first and last columns are set to zero (closed) whilst the first row is set to 
     191\item [For cyclic north-south boundary (\forcode{l_Iperio = .false.,l_jperio = .true.})], first and last columns are set to zero (closed) whilst the first row is set to 
    192192  the value of the last-but-one row and the last row to the value of the second one 
    193193  (\autoref{fig:LBC_jperio}-a). 
    194194  Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end. 
    195195 
    196 \item [Bi-cyclic east-west and north-south boundary (\forcode{jperio=7})] combines cases 1 and 2. 
     196\item [Bi-cyclic east-west and north-south boundary (\forcode{l_Iperio = .true.,l_jperio = .true.})] combines cases 1 and 2. 
    197197 
    198198\end{description} 
    … …  
    207207 
    208208%% ================================================================================================= 
    209 \subsection{North-fold (\forcode{jperio={3,6}})} 
     209\subsection{North-fold (\forcode{l_NFold = .true.})} 
    210210\label{subsec:LBC_north_fold} 
    211211 
    … …  
    220220  \includegraphics[width=0.66\textwidth]{LBC_North_Fold_T} 
    221221  \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{ 
    222     North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$), 
     222    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($c\_NFtype='T'$), 
    223223    as used in ORCA 2\deg, 1/4\deg and 1/12\deg. 
    224224    Pink shaded area corresponds to the inner domain mask (see text).} 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_OBS.tex

    r14328 r14676  
    913913 
    914914\begin{listing} 
    915 %  \nlst{namsao} 
    916915  \begin{forlines} 
    917916!---------------------------------------------------------------------- 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_SBC.tex

    r14328 r14676  
    975975M2, S2, N2, K2, nu2, mu2, 2N2, L2, T2, eps2, lam2, R2, M3, MKS2, MN4, MS4, M4, 
    976976N4, S4, M6, and M8; see file \textit{tide.h90} and \mdl{tide\_mod} for further 
    977 information and references\footnote{As a legacy option \np{ln_tide_var} can be 
     977information and references\footnote{As a legacy option \np{ln_tide_var}{ln\_tide\_var} can be 
    978978  set to \forcode{0}, in which case the 19 tidal constituents (M2, N2, 2N2, S2, 
    979979  K2, K1, O1, Q1, P1, M4, Mf, Mm, Msqm, Mtm, S1, MU2, NU2, L2, and T2; see file 
    … …  
    11791179%% ================================================================================================= 
    11801180\section[Ice Shelf (ISF)]{Interaction with ice shelves (ISF)} 
    1181 \label{sec:isf} 
     1181\label{sec:SBC_isf} 
    11821182 
    11831183\begin{listing} 
    … …  
    11971197 
    11981198     \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .true.} activates the ocean/ice shelf thermodynamics interactions at the ice shelf/ocean interface.  
    1199      If \np{ln_isfcav_mlt}\forcode{ = .false.}, thermodynamics interactions are desctivated but the ocean dynamics inside the cavity is still active. 
     1199     If \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .false.}, thermodynamics interactions are desctivated but the ocean dynamics inside the cavity is still active. 
    12001200     The logical flag \np{ln_isfcav}{ln\_isfcav} control whether 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.\\ 
    12011201 
    12021202     3 options are available to represent to ice-shelf/ocean fluxes at the interface: 
    12031203     \begin{description} 
    1204         \item[\np{cn_isfcav_mlt}\forcode{ = 'spe'}]: 
     1204        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'spe'}]: 
    12051205        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). 
    12061206        The latent heat fluxes is derived from the fresh water flux.  
    12071207        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}) 
    12081208 
    1209         \item[\np{cn_isfcav_mlt}\forcode{ = 'oasis'}]: 
     1209        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'oasis'}]: 
    12101210        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.  
    12111211        It has not been tested and therefore the model will stop if you try to use it.  
    12121212        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. 
    12131213 
    1214         \item[\np{cn_isfcav_mlt}\forcode{ = '2eq'}]: 
     1214        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}]: 
    12151215        The heat flux and the fresh water flux (negative for melting) resulting from ice shelf melting/freezing are parameterized following \citet{Grosfeld1997}.  
    12161216        This formulation is based on a balance between the vertical diffusive heat flux across the ocean top boundary layer (\autoref{eq:ISOMIP1})  
    … …  
    12311231        and $\gamma$ the thermal exchange coefficient. 
    12321232 
    1233         \item[\np{cn_isfcav_mlt}\forcode{ = '3eq'}]: 
     1233        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'}]: 
    12341234        For realistic studies, the heat and freshwater fluxes are parameterized following \citep{Jenkins2001}. This formulation is based on three equations:  
    12351235        a balance between the vertical diffusive heat flux across the boundary layer  
    … …  
    12871287     If \np{rn_htbl}{rn\_htbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 
    12881288 
    1289      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. 
     1289     Each melt formula (\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'} or \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}) depends on an exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
    12901290     Below, the exchange coeficient $\Gamma^{T}$ and $\Gamma^{S}$ are respectively defined by \np{rn_gammat0}{rn\_gammat0} and \np{rn_gammas0}{rn\_gammas0}.  
    12911291     There are 3 different ways to compute the exchange velocity: 
    12921292 
    12931293     \begin{description} 
    1294         \item[\np{cn_gammablk}\forcode{='spe'}]: 
     1294        \item[\np{cn_gammablk}{cn\_gammablk}\forcode{='spe'}]: 
    12951295        The salt and heat exchange coefficients are constant and defined by: 
    12961296\[ 
    … …  
    13021302        This is the recommended formulation for ISOMIP. 
    13031303 
    1304    \item[\np{cn_gammablk}\forcode{='vel'}]: 
     1304   \item[\np{cn_gammablk}{cn\_gammablk}\forcode{='vel'}]: 
    13051305        The salt and heat exchange coefficients are velocity dependent and defined as 
    13061306\[ 
    … …  
    13131313        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. 
    13141314 
    1315    \item[\np{cn_gammablk}\forcode{'vel\_stab'}]: 
     1315   \item[\np{cn_gammablk}{cn\_gammablk}\forcode{'vel\_stab'}]: 
    13161316        The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    13171317\[ 
    … …  
    13291329  \begin{description} 
    13301330 
    1331      \item[\np{cn_isfpar_mlt}\forcode{ = 'bg03'}]: 
     1331     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'bg03'}]: 
    13321332     The ice shelf cavities are not represented. 
    13331333     The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    13341334     The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
    13351335     (\np{sn_isfpar_zmax}{sn\_isfpar\_zmax}) and the base of the ice shelf along the calving front 
    1336      (\np{sn_isfpar_zmin}{sn\_isfpar\_zmin}) as in (\np{cn_isfpar_mlt}\forcode{ = 'spe'}). 
     1336     (\np{sn_isfpar_zmin}{sn\_isfpar\_zmin}) as in (\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'}). 
    13371337     The effective melting length (\np{sn_isfpar_Leff}{sn\_isfpar\_Leff}) is read from a file. 
    13381338     This parametrisation has not been tested since a while and based on \citet{Favier2019},  
    13391339     this parametrisation should probably not be used. 
    13401340 
    1341      \item[\np{cn_isfpar_mlt}\forcode{ = 'spe'}]: 
     1341     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'}]: 
    13421342     The ice shelf cavity is not represented. 
    13431343     The fwf (\np{sn_isfpar_fwf}{sn\_isfpar\_fwf}) is prescribed and distributed along the ice shelf edge between 
    … …  
    13461346     The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    13471347 
    1348      \item[\np{cn_isfpar_mlt}\forcode{ = 'oasis'}]: 
     1348     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'oasis'}]: 
    13491349     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.  
    13501350     It has not been tested and therefore the model will stop if you try to use it.  
    … …  
    13531353  \end{description} 
    13541354 
    1355 \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 
     1355\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}, \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'} and \np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'bg03'} compute a melt rate based on 
    13561356the water mass properties, ocean velocities and depth. 
    13571357The resulting fluxes are thus highly dependent of the model resolution (horizontal and vertical) and  
    13581358realism of the water masses onto the shelf.\\ 
    13591359 
    1360 \np{cn_isfcav_mlt}\forcode{ = 'spe'} and \np{cn_isfpar_mlt}\forcode{ = 'spe'} read the melt rate from a file. 
     1360\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'spe'} and \np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'} read the melt rate from a file. 
    13611361You have total control of the fwf forcing. 
    13621362This can be useful if the water masses on the shelf are not realistic or 
    … …  
    14371437\end{description} 
    14381438 
    1439 If \np{ln_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with 
     1439If \np{ln_iscpl}{ln\_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with 
    14401440potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics. 
    14411441The wetting and drying scheme, applied on the restart, is very simple. The 6 different possible cases for the tracer and ssh are: 
    … …  
    14821482 
    14831483In order to remove the trend and keep the conservation level as close to 0 as possible, 
    1484 a simple conservation scheme is available with \np{ln_isfcpl_cons}\forcode{ = .true.}. 
     1484a simple conservation scheme is available with \np{ln_isfcpl_cons}{ln\_isfcpl\_cons}\forcode{ = .true.}. 
    14851485The heat/salt/vol. gain/loss are diagnosed, as well as the location. 
    14861486A correction increment is computed and applied each time step during the model run. 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_TRA.tex

    r14328 r14676  
    733733  (see \autoref{sec:SBC_rnf} for further detail of how it acts on temperature and salinity tendencies) 
    734734\item [\textit{fwfisf}] The mass flux associated with ice shelf melt, 
    735   (see \autoref{sec:isf} for further details on how the ice shelf melt is computed and applied). 
     735  (see \autoref{sec:SBC_isf} for further details on how the ice shelf melt is computed and applied). 
    736736\end{labeling} 
    737737 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r14328 r14676  
    22 
    33\begin{document} 
    4  
    5 %% Custom aliases 
    6 \newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 
    74 
    85\chapter{Vertical Ocean Physics (ZDF)} 
    … …  
    10831080  \label{lst:namdrg} 
    10841081\end{listing} 
     1082 
    10851083\begin{listing} 
    10861084  \nlst{namdrg_top} 
    … …  
    10881086  \label{lst:namdrg_top} 
    10891087\end{listing} 
     1088 
    10901089\begin{listing} 
    10911090  \nlst{namdrg_bot} 
    … …  
    15621561by only a few extra physics choices namely: 
    15631562 
    1564 \begin{verbatim} 
     1563\begin{forlines} 
    15651564     ln_dynldf_OFF = .false. 
    15661565     ln_dynldf_lap = .true. 
    … …  
    15701569        nn_fct_h   =  2 
    15711570        nn_fct_v   =  2 
    1572 \end{verbatim} 
     1571\end{forlines} 
    15731572 
    15741573\noindent which were chosen to provide a slightly more stable and less noisy solution. The 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_misc.tex

    r14328 r14676  
    1212{\footnotesize 
    1313  \begin{tabularx}{\textwidth}{l||X|X} 
    14     Release & Author(s) & Modifications \\ 
     14    Release     & Author(s)            & Modifications                      \\ 
    1515    \hline 
    16     {\em   X.X} & {\em Pierre Mathiot} & {update of the closed sea section} 
    17     {\em   4.0} & {\em ...} & {\em ...} \\ 
    18     {\em   3.6} & {\em ...} & {\em ...} \\ 
    19     {\em   3.4} & {\em ...} & {\em ...} \\ 
    20     {\em <=3.4} & {\em ...} & {\em ...} 
     16    {\em   X.X} & {\em Pierre Mathiot} & {Update of the closed sea section} \\ 
     17    {\em   4.0} & {\em ...           } & {\em ...                         } \\ 
     18    {\em   3.6} & {\em ...           } & {\em ...                         } \\ 
     19    {\em   3.4} & {\em ...           } & {\em ...                         } \\ 
     20    {\em <=3.4} & {\em ...           } & {\em ...                         } 
    2121  \end{tabularx} 
    2222} 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r14328 r14676  
    8383 
    8484%\nlst{nam_dynspg} 
     85 
    8586Options are defined through the \nam{_dynspg}{\_dynspg} namelist variables. 
    8687The surface pressure gradient term is related to the representation of the free surface (\autoref{sec:MB_hor_pg}). 

  • NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r14328 r14676  
    1212{\footnotesize 
    1313  \begin{tabularx}{0.5\textwidth}{l||X|X} 
    14     Release          & Author(s)                                       & 
     14    Release          & Author(s)                                       &  
    1515    Modifications                                                      \\ 
    1616    \hline 
    17     {\em        4.0} & {\em J\'{e}r\^{o}me Chanut \newline Tim Graham} & 
     17    {\em        4.0} & {\em J\'{e}r\^{o}me Chanut \newline Tim Graham} &  
    1818    {\em Review \newline Update                                      } \\ 
    19     {\em        3.6} & {\em Christian \'{E}th\'{e}                   } & 
     19    {\em        3.6} & {\em Christian \'{E}th\'{e}                   } &  
    2020    {\em Update                                                      } \\ 
    21     {\em $\leq$ 3.4} & {\em Gurvan Madec                             } & 
     21    {\em $\leq$ 3.4} & {\em Gurvan Madec                             } &  
    2222    {\em First version                                               } \\ 
    2323  \end{tabularx} 
    … …  
    4444 
    4545The time stepping used in \NEMO\ is a three level scheme that can be represented as follows: 
     46 
    4647\begin{equation} 
    4748  \label{eq:TD} 
    4849  x^{t + \rdt} = x^{t - \rdt} + 2 \, \rdt \ \text{RHS}_x^{t - \rdt, \, t, \, t + \rdt} 
    4950\end{equation} 
     51 
    5052where $x$ stands for $u$, $v$, $T$ or $S$; 
    5153RHS is the \textbf{R}ight-\textbf{H}and-\textbf{S}ide of the corresponding time evolution equation; 
    … …  
    9799first designed by \citet{robert_JMSJ66} and more comprehensively studied by \citet{asselin_MWR72}, 
    98100is a kind of laplacian diffusion in time that mixes odd and even time steps: 
     101 
    99102\begin{equation} 
    100103  \label{eq:TD_asselin} 
    101104  x_F^t = x^t + \gamma \, \lt[ x_F^{t - \rdt} - 2 x^t + x^{t + \rdt} \rt] 
    102105\end{equation} 
     106 
    103107where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient. 
    104108$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp} (namelist parameter). 
    … …  
    132136The conditions for stability of second and fourth order horizontal diffusion schemes are 
    133137\citep{griffies_bk04}: 
     138 
    134139\begin{equation} 
    135140  \label{eq:TD_euler_stability} 
    … …  
    140145  \end{cases} 
    141146\end{equation} 
     147 
    142148where $e$ is the smallest grid size in the two horizontal directions and 
    143149$A^h$ is the mixing coefficient. 
    … …  
    151157To overcome the stability constraint, a backward (or implicit) time differencing scheme is used. 
    152158This scheme is unconditionally stable but diffusive and can be written as follows: 
     159 
    153160\begin{equation} 
    154161  \label{eq:TD_imp} 
    … …  
    168175where RHS is the right hand side of the equation except for the vertical diffusion term. 
    169176We rewrite \autoref{eq:TD_imp} as: 
     177 
    170178\begin{equation} 
    171179  \label{eq:TD_imp_mat} 
    172180  -c(k + 1) \; T^{t + 1}(k + 1) + d(k) \; T^{t + 1}(k) - \; c(k) \; T^{t + 1}(k - 1) \equiv b(k) 
    173181\end{equation} 
     182 
    174183where 
     184 
    175185\[ 
    176186  c(k) = A_w^{vT} (k) \, / \, e_{3w} (k) \text{,} \quad 
    … …  
    239249$Q$ is redistributed over several time step. 
    240250In the modified LF-RA environment, these two formulations have been replaced by: 
     251 
    241252\begin{gather} 
    242253  \label{eq:TD_forcing} 
    … …  
    246257                    - \gamma \, \rdt \, \lt( Q^{t + \rdt / 2} - Q^{t - \rdt / 2} \rt) 
    247258\end{gather} 
     259 
    248260The change in the forcing formulation given by \autoref{eq:TD_forcing} 
    249261(see \autoref{fig:TD_MLF_forcing}) has a significant effect: 
    … …  
    375387  % 
    376388\end{flalign*} 
     389 
    377390\begin{flalign*} 
    378391  \allowdisplaybreaks 
    … …  
    387400  % 
    388401\end{flalign*} 
     402 
    389403\begin{flalign*} 
    390404  \allowdisplaybreaks 
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