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Changeset 3764 for branches/2012/dev_MERGE_2012/DOC/TexFiles – NEMO

Ignore:
Timestamp:
2013-01-23T15:33:04+01:00 (11 years ago)
Author:
smasson
Message:

dev_MERGE_2012: report bugfixes done in the trunk from r3555 to r3763 into dev_MERGE_2012

Location:
branches/2012/dev_MERGE_2012/DOC/TexFiles
Files:
9 edited

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  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Biblio/Biblio.bib

    r3680 r3764  
    14121412} 
    14131413 
    1414 @ARTICLE{Hunke2008, 
     1414@TECHREPORT{Hunke2008, 
    14151415  author = {E.C. Hunke and W.H. Lipscomb}, 
    14161416  title = {CICE: the Los Alamos sea ice model documentation and software user's manual,  
    14171417        Version 4.0}, 
     1418  institution = { Los Alamos National Laboratory, N.M.}, 
    14181419  publisher = {LA-CC-06-012, Los Alamos National Laboratory, N.M.}, 
    14191420  year = {2008} 

  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_CFG.tex

    r3294 r3764  
    3131 
    3232% ================================================================ 
    33 % 1D model functionality 
     33% 1D model configuration 
    3434% ================================================================ 
    3535\section{Water column model: 1D model (C1D) (\key{c1d})} 
    … …  
    4848 
    4949The methodology is based on the use of the zoom functionality over the smallest possible  
    50 domain : a 3 x 3 domain centred on the grid point of interest (see \S\ref{MISC_zoom}),  
     50domain : a 3x3 domain centred on the grid point of interest (see \S\ref{MISC_zoom}),  
    5151with some extra routines. There is no need to define a new mesh, bathymetry,  
    5252initial state or forcing, since the 1D model will use those of the configuration it is a zoom of.  
    53 The chosen grid point is set in par\_oce.F90 module by setting the \jp{jpizoom} and \jp{jpjzoom}  
     53The chosen grid point is set in \mdl{par\_oce} module by setting the \jp{jpizoom} and \jp{jpjzoom}  
    5454parameters to the indices of the location of the chosen grid point. 
    5555 
    56 The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero.  
    57 Therefore a simplified \rou{step} routine is used (\rou{step\_c1d}) in which both lateral tendancy  
    58 terms and lateral physics are not called, and the vertical velocity is zero (so far, no attempt at 
    59 introducing a Ekman pumping velocity has been made). 
    60 Second, the two components of the velocity are moved on a $T$-point.  
    61 This requires a specific treatment of the Coriolis term (see \rou{dyncor\_c1d}) and of the  
    62 dynamic time stepping (\rou{dynnxt\_c1d}). 
    63 All the relevant modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of  
     56The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and 
     57second, the two components of the velocity are moved on a $T$-point.  
     58Therefore, defining \key{c1d} changes five main things in the code behaviour:  
     59\begin{description} 
     60\item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column  
     61of the 3x3 domain is imposed over the whole domain ;  
     62\item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ;  
     63\item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which  
     64both lateral tendancy terms and lateral physics are not called ;  
     65\item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity  
     66has been made) ;  
     67\item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same  
     68(see \mdl{dyncor\_c1d}). 
     69\end{description} 
     70All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of  
    6471the \NEMO distribution. 
    6572 
    … …  
    206213% ------------------------------------------------------------------------------------------------------------- 
    207214\section{GYRE family: double gyre basin (\key{gyre})} 
    208 \label{MISC_config_gyre} 
     215\label{CFG_gyre} 
    209216 
    210217The GYRE configuration \citep{Levy_al_OM10} have been built to simulated  

  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DIA.tex

    r3680 r3764  
    10181018In addition, a series of diagnostics has been added in the \mdl{diaar5}.  
    10191019They corresponds to outputs that are required for AR5 simulations  
    1020 (see Section \ref{MISC_steric} below for one of them).  
     1020(see Section \ref{DIA_steric} below for one of them).  
    10211021Activating those outputs requires to define the \key{diaar5} CPP key. 
    10221022\\ 

  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DOM.tex

    r3680 r3764  
    499499Hybridation of the three main coordinates are available: $s-z$ or $s-zps$ coordinate  
    500500(Fig.~\ref{Fig_z_zps_s_sps}d and \ref{Fig_z_zps_s_sps}e). When using the variable  
    501 volume option \key{vvl}) ($i.e.$ non-linear free surface), the coordinate follow the  
     501volume option \key{vvl} ($i.e.$ non-linear free surface), the coordinate follow the  
    502502time-variation of the free surface so that the transformation is time dependent:  
    503503$z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). This option can be used with full step  

  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DYN.tex

    r3294 r3764  
    127127This is of paramount importance. Replacing $T$ by the number $1$ in the tracer equation and summing 
    128128over the water column must lead to the sea surface height equation otherwise tracer content 
    129 will not be conserved \ref{Griffies_al_MWR01, LeclairMadec2009}. 
     129will not be conserved \citep{Griffies_al_MWR01, Leclair_Madec_OM09}. 
    130130 
    131131The vertical velocity is computed by an upward integration of the horizontal  
    … …  
    189189the relative vorticity term and horizontal kinetic energy for the planetary vorticity  
    190190term (MIX scheme) ; or conserving both the potential enstrophy of horizontally non-divergent  
    191 flow and horizontal kinetic energy (EEN scheme) (see  Appendix~\ref{Apdx_C_vor_zad}). In the  
     191flow and horizontal kinetic energy (EEN scheme) (see  Appendix~\ref{Apdx_C_vorEEN}). In the  
    192192case of ENS, ENE or MIX schemes the land sea mask may be slightly modified to ensure the  
    193193consistency of vorticity term with analytical equations (\textit{ln\_dynvor\_con}=true). 
    … …  
    331331This EEN scheme in fact combines the conservation properties of the ENS and ENE schemes.  
    332332It conserves both total energy and potential enstrophy in the limit of horizontally  
    333 nondivergent flow ($i.e.$ $\chi$=$0$) (see  Appendix~\ref{Apdx_C_vor_zad}).  
     333nondivergent flow ($i.e.$ $\chi$=$0$) (see  Appendix~\ref{Apdx_C_vorEEN}).  
    334334Applied to a realistic ocean configuration, it has been shown that it leads to a significant  
    335335reduction of the noise in the vertical velocity field \citep{Le_Sommer_al_OM09}.  
    … …  
    938938is the \textit{before} velocity in time, except for the pure vertical component  
    939939that appears when a tensor of rotation is used. This latter term is solved  
    940 implicitly together with the vertical diffusion term (see \S\ref{DOM_nxt})  
     940implicitly together with the vertical diffusion term (see \S\ref{STP})  
    941941 
    942942At the lateral boundaries either free slip, no slip or partial slip boundary  
    … …  
    10661066scheme (\np{ln\_zdfexp}=true) using a time splitting technique  
    10671067(\np{nn\_zdfexp} $>$ 1) or $(b)$ a backward (or implicit) time differencing scheme  
    1068 (\np{ln\_zdfexp}=false) (see \S\ref{DOM_nxt}). Note that namelist variables  
     1068(\np{ln\_zdfexp}=false) (see \S\ref{STP}). Note that namelist variables  
    10691069\np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics.  
    10701070 

  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_TRA.tex

    r3308 r3764  
    264264transport) rather than TVD. The TVD scheme is implemented in the \mdl{traadv\_tvd} module. 
    265265 
    266 For stability reasons (see \S\ref{DOM_nxt}), 
     266For stability reasons (see \S\ref{STP}), 
    267267$\tau _u^{cen2}$ is evaluated  in (\ref{Eq_tra_adv_tvd}) using the \textit{now} tracer while $\tau _u^{ups}$  
    268268is evaluated using the \textit{before} tracer. In other words, the advective part of  
    … …  
    337337\np{ln\_traadv\_ubs}=true. 
    338338 
    339 For stability reasons  (see \S\ref{DOM_nxt}), 
     339For stability reasons  (see \S\ref{STP}), 
    340340the first term  in \eqref{Eq_tra_adv_ubs} (which corresponds to a second order centred scheme)  
    341341is evaluated using the \textit{now} tracer (centred in time) while the  
    … …  
    451451except for the pure vertical component that appears when a rotation tensor  
    452452is used. This latter term is solved implicitly together with the  
    453 vertical diffusion term (see \S\ref{DOM_nxt}). 
     453vertical diffusion term (see \S\ref{STP}). 
    454454 
    455455% ------------------------------------------------------------------------------------------------------------- 

  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_ZDF.tex

    r3294 r3764  
    120120\end{equation} 
    121121 
    122 is computed from the wind stress vector $|\tau|$ and the reference dendity $ \rho_o$. 
     122is computed from the wind stress vector $|\tau|$ and the reference density $ \rho_o$. 
    123123The final $h_{e}$ is further constrained by the adjustable bounds \np{rn\_mldmin} and \np{rn\_mldmax}. 
    124124Once $h_{e}$ is computed, the vertical eddy coefficients within $h_{e}$ are set to  
    … …  
    11881188\includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_ZDF_M2_K1_tmx.pdf} 
    11891189\caption{  \label{Fig_ZDF_M2_K1_tmx}  
    1190 (a) M2 and (b) K2 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). } 
     1190(a) M2 and (b) K1 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). } 
    11911191\end{center}   \end{figure} 
    11921192%>>>>>>>>>>>>>>>>>>>>>>>>>>>>  
    … …  
    12051205 
    12061206When \np{ln\_tmx\_itf}=true, the two key parameters $q$ and $F(z)$ are adjusted following  
    1207 the parameterisation developed by \ref{Koch-Larrouy_al_GRL07}: 
     1207the parameterisation developed by \citet{Koch-Larrouy_al_GRL07}: 
    12081208 
    12091209First, the Indonesian archipelago is a complex geographic region  
    … …  
    12191219Second, the vertical structure function, $F(z)$, is no more associated 
    12201220with a bottom intensification of the mixing, but with a maximum of  
    1221 energy available within the thermocline. \ref{Koch-Larrouy_al_GRL07}  
     1221energy available within the thermocline. \citet{Koch-Larrouy_al_GRL07}  
    12221222have suggested that the vertical distribution of the energy dissipation  
    12231223proportional to $N^2$ below the core of the thermocline and to $N$ above.  
    … …  
    12361236and vertical distributions of the mixing are adequately prescribed  
    12371237\citep{Koch-Larrouy_al_GRL07, Koch-Larrouy_al_OD08a, Koch-Larrouy_al_OD08b}. 
    1238 Note also that such a parameterisation has a sugnificant impact on the behaviour  
     1238Note also that such a parameterisation has a significant impact on the behaviour  
    12391239of global coupled GCMs \citep{Koch-Larrouy_al_CD10}. 
    12401240 

  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Namelist/namasm

    r3294 r3764  
    33!----------------------------------------------------------------------- 
    44    ln_bkgwri = .false.    !  Logical switch for writing out background state  
    5     ln_trjwri = .false.    !  Logical switch for writing out state trajectory 
    65    ln_trainc = .false.    !  Logical switch for applying tracer increments 
    76    ln_dyninc = .false.    !  Logical switch for applying velocity increments 
    … …  
    1413    nitiaufin = 15         !  Timestep of end of IAU interval in [0,nitend-nit000-1] 
    1514    niaufn    = 0          !  Type of IAU weighting function 
    16     nittrjfrq = 0          !  Frequency of trajectory output for 4D-VAR 
    1715    ln_salfix = .false.    !  Logical switch for ensuring that the sa > salfixmin 
    1816    salfixmin = -9999      !  Minimum salinity after applying the increments 

  • branches/2012/dev_MERGE_2012/DOC/TexFiles/Namelist/namdyn_vor

    r3294 r3764  
    22&namdyn_vor    !   option of physics/algorithm (not control by CPP keys) 
    33!----------------------------------------------------------------------- 
    4    ln_dynvor_ene = .false. !  enstrophy conserving scheme   
    5    ln_dynvor_ens = .false. !  energy conserving scheme     
     4   ln_dynvor_ene = .false. !  energy    conserving scheme   
     5   ln_dynvor_ens = .false. !  enstrophy conserving scheme     
    66   ln_dynvor_mix = .false. !  mixed scheme                
    77   ln_dynvor_een = .true.  !  energy & enstrophy scheme   
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