Changeset 14552


Ignore:
Timestamp:
2021-02-26T17:18:35+01:00 (4 months ago)
Author:
gsamson
Message:

Merging r14504 through r14551 trunk into branch; ticket #2628

Location:
NEMO/branches/2021/ticket2628_r14502_abl_restart_xios
Files:
19 edited

Legend:

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  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/cfgs/SHARED/field_def_nemo-innerttrc.xml

    r14072 r14552  
    4343    <field id="C14Age"       long_name="Radiocarbon age"                          unit="yr"        grid_ref="grid_T_3D"  /> 
    4444    <field id="RAge"         long_name="Reservoir Age"                            unit="yr"       /> 
    45     <field id="qtr_C14"      long_name="Air-sea flux of C14"                      unit="1/m2/s"   /> 
    46     <field id="qint_C14"     long_name="Cumulative air-sea flux of C14"           unit="1/m2"     /> 
     45    <field id="qtr_c14"      long_name="Air-sea flux of C14"                      unit="1/m2/s"   /> 
     46    <field id="qint_c14"     long_name="Cumulative air-sea flux of C14"           unit="1/m2"     /> 
    4747    <field id="AtmCO2"       long_name="Global atmospheric CO2"                   unit="ppm"      /> 
    4848    <field id="AtmC14"       long_name="Global atmospheric DeltaC14"              unit="permil"   /> 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

    r14375 r14552  
    4242 
    4343\begin{listing} 
    44 %  \nlst{namdom_domcfg} 
    4544  \begin{forlines} 
    4645!----------------------------------------------------------------------- 
     
    409408 
    410409\begin{listing} 
    411 %  \nlst{namzgr_sco_domcfg} 
    412410  \caption{\forcode{&namzgr_sco_domcfg}} 
    413411  \label{lst:namzgr_sco_domcfg} 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/apdx_triads.tex

    r14257 r14552  
    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/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/chap_DIU.tex

    r14257 r14552  
    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/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/chap_LBC.tex

    r14433 r14552  
    168168 
    169169%% ================================================================================================= 
    170 \subsection{Closed, cyclic (\forcode{l\_Iperio,l\_jperio})} 
     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{l\_Iperio,l\_jperio} to true or false 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{l\_Iperio = .false.,l\_jperio = .false.})], 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{l\_Iperio = .true.,l\_jperio = .false.})], 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{l\_Iperio = .false.,l\_jperio = .true.})], 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{l\_Iperio = .true.,l\_jperio = .true.})] 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{l\_NFold = .true.})} 
     209\subsection{North-fold (\forcode{l_NFold = .true.})} 
    210210\label{subsec:LBC_north_fold} 
    211211 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/chap_OBS.tex

    r14257 r14552  
    913913 
    914914\begin{listing} 
    915 %  \nlst{namsao} 
    916915  \begin{forlines} 
    917916!---------------------------------------------------------------------- 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/chap_SBC.tex

    r14375 r14552  
    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 
     
    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/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r14257 r14552  
    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/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/chap_misc.tex

    r14303 r14552  
    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/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r14257 r14552  
    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/2021/ticket2628_r14502_abl_restart_xios/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r14257 r14552  
    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 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/global/document.tex

    r14257 r14552  
    77 
    88%% Layout 
    9 %\documentclass[fontsize=10pt,twoside,abstract,draft]{scrreprt} 
    10 \documentclass[fontsize=10pt,twoside,abstract      ]{scrreprt} 
     9\documentclass[fontsize=10pt,twoside,abstract,draft]{scrreprt} 
     10%\documentclass[fontsize=10pt,twoside,abstract      ]{scrreprt} 
    1111 
    1212%% Overall configuration  
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/global/highlighting.tex

    r14257 r14552  
    3030%% Namelists inclusion 
    3131\newcommand{\nlst}[1]{\forfile{../../../namelists/#1}} 
    32 %\newcommand{\nlst}[1]{ 
    33 %   \begin{listing} 
    34 %      \newmintedfile{fortran}{../../../namelists/#1} 
    35 %      \caption{\forcode{&#1}} 
    36 %      \label{lst:#1} 
    37 %   \end{listing} 
    38 %} 
     32 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/global/latexmk.pl

    r14378 r14552  
    99 
    1010## Custom cmds 
    11 set_tex_cmds('-shell-escape -file-line-error -interaction=batchmode'); 
     11set_tex_cmds('-shell-escape -file-line-error -interaction=nonstopmode'); 
    1212#set_tex_cmds('-shell-escape -file-line-error'); 
    1313$makeindex = 'makeindex %O -s %R.ist -o %D %S'; 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/global/new_cmds.tex

    r14257 r14552  
    5757} 
    5858 
    59 %% Workaround for \listoffigures issue 
    60 \DeclareRobustCommand{\triad}[6]{ 
    61   \ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}} 
    62 } 
     59%% Custom aliases 
     60\newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 
     61\newcommand{\rML}[1][i]{\ensuremath{_{\mathrm{ML}\,#1}}} 
     62\newcommand{\rMLt}[1][i]{\tilde{r}_{\mathrm{ML}\,#1}} 
     63\newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 
     64\newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}} 
     65\newcommand{\triadt}[5]{\ensuremath{{}_{#1}^{#2}{\tilde{\mathbb{#3}}}_{#4}^{\,#5}}} 
     66\newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}} 
     67\newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 
    6368 
    6469%% New command for ToC (?) 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/doc/latex/global/styles.tex

    r14257 r14552  
    1010%% Cover page 
    1111\backgroundsetup{ 
    12    firstpage=true,scale  =1, 
    13    angle    =0   ,opacity=1, 
     12   firstpage=true,scale=1,angle=0,opacity=1, 
    1413   contents ={ 
    1514      \begin{tikzpicture}[remember picture,overlay] 
     
    2221%\pagestyle{scrheadings} 
    2322%\renewcommand{\chapterpagestyle}{empty} 
    24 \renewcommand{\chaptermark}[1]{ \markboth{#1}{}} %% Convert mark to lowercase 
     23\renewcommand{\chaptermark}[1]{\markboth{ #1}{}} %% Convert mark to lowercase 
    2524\renewcommand{\sectionmark}[1]{\markright{#1}{}} %%    "     ""  ""     "   
    2625\ohead{} %% Clear default headings 
     
    3736%% Cross-referencing 
    3837\hypersetup{ 
    39    pdftitle=\hdg                                          , 
    40    pdfauthor=Gurvan Madec and NEMO System Team            , 
    41    pdfsubject=Reference manual of NEMO modelling framework, 
    42    pdfkeywords=ocean circulation modelling                , 
    43    colorlinks                                             , 
    44    allcolors=manclr 
     38   pdftitle=\hdg,pdfauthor=Gurvan Madec and NEMO System Team, 
     39   pdfsubject=Reference manual of NEMO modelling framework,pdfkeywords=ocean circulation modelling, 
     40   colorlinks,allcolors=manclr 
    4541} 
    4642\renewcommand{\appendixautorefname}{appendix}          %% `\autoref` uncapitalization 
     
    6359%% Catcodes (between `\makeatletter` and `\makeatother`) 
    6460\makeatletter 
    65  
    66 %\global\let\tikz@ensure@dollar@catcode=\relax %% Prevent error with tikz and namelist inclusion 
    6761 
    6862%% Apply manual color for chap. headings (original snippets from fncychap.sty) 
     
    9387} 
    9488 
    95 %% Temporary fix? 
    96 %\def\set@curr@file#1{ 
    97 %  \begingroup 
    98 %    \escapechar\m@ne 
    99 %    \xdef\@curr@file{\expandafter\string\csname #1\endcsname} 
    100 %  \endgroup 
    101 %} 
    102 %\def\quote@name#1{"\quote@@name#1\@gobble""} 
    103 %\def\quote@@name#1"{#1\quote@@name} 
    104 %\def\unquote@name#1{\quote@@name#1\@gobble"} 
    105  
    10689\makeatother 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/src/ABL/ablrst.F90

    r14505 r14552  
    175175      IF( lrxios) THEN 
    176176          cr_ablrst_cxt = 'abl_rst' 
    177           IF(lwp) WRITE(numout,*) 'Enable restart reading by XIOS for SI3' 
     177          IF(lwp) WRITE(numout,*) 'Enable restart reading by XIOS for ABL' 
    178178!         IF( TRIM(Agrif_CFixed()) == '0' ) THEN 
    179179!            clpname = cn_ablrst_in 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/src/SAS/sbcssm.F90

    r14072 r14552  
    102102               e3t_m(:,:) = e3t_0(:,:,1)                                 ! vertical scale factor 
    103103            ENDIF 
     104            IF( TRIM(sf_ssm_2d(jf_usp)%clrootname) == 'NOT USED' ) & 
     105               &     sf_ssm_2d(jf_usp)%fnow(:,:,1) = 0._wp 
     106            IF( TRIM(sf_ssm_2d(jf_vsp)%clrootname) == 'NOT USED' ) & 
     107               &     sf_ssm_2d(jf_vsp)%fnow(:,:,1) = 0._wp 
    104108            ssu_m(:,:) = sf_ssm_2d(jf_usp)%fnow(:,:,1) * umask(:,:,1)    ! u-velocity 
    105109            ssv_m(:,:) = sf_ssm_2d(jf_vsp)%fnow(:,:,1) * vmask(:,:,1)    ! v-velocity 
    106110         ENDIF 
    107111         ! 
     112         IF( TRIM(sf_ssm_2d(jf_sal)%clrootname) == 'NOT USED' ) & 
     113            &     sf_ssm_2d(jf_sal)%fnow(:,:,1) = 35._wp 
     114         IF( TRIM(sf_ssm_2d(jf_tem)%clrootname) == 'NOT USED' ) & 
     115            &     CALL eos_fzp( sf_ssm_2d(jf_sal)%fnow(:,:,1), sf_ssm_2d(jf_tem)%fnow(:,:,1) ) 
     116         IF( TRIM(sf_ssm_2d(jf_ssh)%clrootname) == 'NOT USED' ) & 
     117            &     sf_ssm_2d(jf_ssh)%fnow(:,:,1) = 0._wp 
    108118         sst_m(:,:) = sf_ssm_2d(jf_tem)%fnow(:,:,1) * tmask(:,:,1)    ! temperature 
    109119         sss_m(:,:) = sf_ssm_2d(jf_sal)%fnow(:,:,1) * tmask(:,:,1)    ! salinity 
  • NEMO/branches/2021/ticket2628_r14502_abl_restart_xios/src/TOP/TRP/trcadv.F90

    r14433 r14552  
    143143      CASE ( np_MUS )                                 ! MUSCL 
    144144         IF (nn_hls.EQ.2) THEN 
    145             IF (nn_hls.EQ.2) CALL lbc_lnk( 'trcadv', ptr(:,:,:,:,Kbb), 'T', 1.) 
     145            CALL lbc_lnk( 'trcadv', ptr(:,:,:,:,Kbb), 'T', 1.) 
    146146#if defined key_loop_fusion 
    147147            CALL tra_adv_mus_lf( kt, nittrc000,'TRC', rDt_trc, zuu, zvv, zww, Kbb, Kmm, ptr, jptra, Krhs, ln_mus_ups )  
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