Changeset 11693


Ignore:
Timestamp:
2019-10-14T14:53:52+02:00 (12 months ago)
Author:
nicolasmartin
Message:

Macros renaming

Location:
NEMO/trunk/doc/latex
Files:
27 edited

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

    r11690 r11693  
    530530This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. 
    531531 
    532 \onlyinsubfile{\input{../../global/epilogue}} 
     532\subinc{\input{../../global/epilogue}} 
    533533 
    534534\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex

    r11690 r11693  
    311311\begin{figure}[!ht] 
    312312  \centering 
    313   \includegraphics[width=0.66\textwidth]{ALGOS_ISO_triad} 
     313  %\includegraphics[width=0.66\textwidth]{ALGOS_ISO_triad} 
    314314  \caption[Triads used in the Griffies's like iso-neutral diffision scheme for 
    315315    $u$- and $w$-components)]{ 
     
    461461where $A_{e}$ is the eddy induced velocity coefficient, 
    462462and $r_i$ and $r_j$ the slopes between the iso-neutral and the geopotential surfaces. 
    463 %%gm wrong: to be modified with 2 2D streamfunctions 
     463\cmtgm{Wrong: to be modified with 2 2D streamfunctions} 
    464464In other words, the eddy induced velocity can be derived from a vector streamfuntion, $\phi$, 
    465465which is given by $\phi = A_e\,\textbf{r}$ as $\textbf{U}^*  = \textbf{k} \times \nabla \phi$. 
    466 %%end gm 
    467466 
    468467A traditional way to implement this additional advection is to add it to the eulerian velocity prior to 
     
    822821\ie\ the variance of the tracer is preserved by the discretisation of the skew fluxes. 
    823822 
    824 \onlyinsubfile{\input{../../global/epilogue}} 
     823\subinc{\input{../../global/epilogue}} 
    825824 
    826825\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

    r11598 r11693  
    421421that is a Laplacian diffusion is applied on momentum along the coordinate directions. 
    422422 
    423 \onlyinsubfile{\input{../../global/epilogue}} 
     423\subinc{\input{../../global/epilogue}} 
    424424 
    425425\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex

    r11599 r11693  
    2525\clearpage 
    2626 
    27 %%%  Appendix put in gmcomment as it has not been updated for \zstar and s coordinate 
     27%%%  Appendix put in cmtgm as it has not been updated for \zstar and s coordinate 
    2828%I'm writting this appendix. It will be available in a forthcoming release of the documentation 
    2929 
    30 %\gmcomment{ 
     30%\cmtgm{ 
    3131 
    3232%% ================================================================================================= 
     
    270270 
    271271%gm comment 
    272 \gmcomment{ 
     272\cmtgm{ 
    273273The last equality comes from the following equation, 
    274274\begin{flalign*} 
     
    583583\label{subsec:INVARIANTS_2.6} 
    584584 
    585 \gmcomment{ 
     585\cmtgm{ 
    586586  A pressure gradient has no contribution to the evolution of the vorticity as the curl of a gradient is zero. 
    587587  In the $z$-coordinate, this property is satisfied locally on a C-grid with 2nd order finite differences 
     
    694694 
    695695%gm comment 
    696 \gmcomment{ 
     696\cmtgm{ 
    697697  \begin{flalign*} 
    698698    \sum\limits_{i,j,k} \biggl\{   p_t\;\partial_t b_t   \biggr\}                                &&&\\ 
     
    14791479%} 
    14801480 
    1481 \onlyinsubfile{\input{../../global/epilogue}} 
     1481\subinc{\input{../../global/epilogue}} 
    14821482 
    14831483\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex

    r11599 r11693  
    584584the expression of the 3D divergence in the $s-$coordinates established above. 
    585585 
    586 \onlyinsubfile{\input{../../global/epilogue}} 
     586\subinc{\input{../../global/epilogue}} 
    587587 
    588588\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex

    r11690 r11693  
    11771177\] 
    11781178 
    1179 \onlyinsubfile{\input{../../global/epilogue}} 
     1179\subinc{\input{../../global/epilogue}} 
    11801180 
    11811181\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

    r11599 r11693  
    194194\end{clines} 
    195195 
    196 \onlyinsubfile{\input{../../global/epilogue}} 
     196\subinc{\input{../../global/epilogue}} 
    197197 
    198198\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

    r11690 r11693  
    5555A complete description of the use of this I/O server is presented in the next section. 
    5656 
    57 %\gmcomment{                    % start of gmcomment 
     57%\cmtgm{                    % start of gmcomment 
    5858 
    5959%% ================================================================================================= 
     
    20612061The maximum values from the run are also copied to the ocean.output file. 
    20622062 
    2063 \onlyinsubfile{\input{../../global/epilogue}} 
     2063\subinc{\input{../../global/epilogue}} 
    20642064 
    20652065\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

    r11599 r11693  
    160160\] 
    161161 
    162 \onlyinsubfile{\input{../../global/epilogue}} 
     162\subinc{\input{../../global/epilogue}} 
    163163 
    164164\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11690 r11693  
    695695\end{description} 
    696696 
    697 \onlyinsubfile{\input{../../global/epilogue}} 
     697\subinc{\input{../../global/epilogue}} 
    698698 
    699699\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11690 r11693  
    6767Furthermore, the tendency terms associated with the 2D barotropic vorticity balance (when \texttt{trdvor?} is defined) 
    6868can be derived from the 3D terms. 
    69 \gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does 
    70 MISC correspond to "extracting tendency terms" or "vorticity balance"?} 
     69\cmtgm{STEVEN: not quite sure I've got the sense of the last sentence. 
     70  Does MISC correspond to "extracting tendency terms" or "vorticity balance"?} 
    7171 
    7272%% ================================================================================================= 
     
    153153as changes in the divergence of the barotropic transport are absorbed into the change of the level thicknesses, 
    154154re-orientated downward. 
    155 \gmcomment{not sure of this...  to be modified with the change in emp setting} 
     155\cmtgm{not sure of this...  to be modified with the change in emp setting} 
    156156In the case of a linear free surface, the time derivative in \autoref{eq:DYN_wzv} disappears. 
    157157The upper boundary condition applies at a fixed level $z=0$. 
     
    287287$u$ and $v$ are located at different grid points, 
    288288a price worth paying to avoid a double averaging in the pressure gradient term as in the $B$-grid. 
    289 \gmcomment{ To circumvent this, Adcroft (ADD REF HERE) 
     289\cmtgm{ To circumvent this, Adcroft (ADD REF HERE) 
    290290Nevertheless, this technique strongly distort the phase and group velocity of Rossby waves....} 
    291291 
     
    516516In the vertical, the centred $2^{nd}$ order evaluation of the advection is preferred, \ie\ $u_{uw}^{ubs}$ and 
    517517$u_{vw}^{ubs}$ in \autoref{eq:DYN_adv_cen2} are used. 
    518 UBS is diffusive and is associated with vertical mixing of momentum. \gmcomment{ gm  pursue the 
     518UBS is diffusive and is associated with vertical mixing of momentum. \cmtgm{ gm  pursue the 
    519519sentence:Since vertical mixing of momentum is a source term of the TKE equation...  } 
    520520 
     
    534534there is also the possibility of using a $4^{th}$ order evaluation of the advective velocity as in ROMS. 
    535535This is an error and should be suppressed soon. 
    536 \gmcomment{action :  this have to be done} 
     536\cmtgm{action :  this have to be done} 
    537537 
    538538%% ================================================================================================= 
     
    915915it is still significant as shown by \citet{levier.treguier.ea_rpt07} in the case of an analytical barotropic Kelvin wave. 
    916916 
    917 \gmcomment{               %%% copy from griffies Book 
     917\cmtgm{               %%% copy from griffies Book 
    918918 
    919919\textbf{title: Time stepping the barotropic system } 
     
    10431043 
    10441044%% gm %%======>>>>   given here the discrete eqs provided to the solver 
    1045 \gmcomment{               %%% copy from chap-model basics 
     1045\cmtgm{               %%% copy from chap-model basics 
    10461046  \[ 
    10471047    % \label{eq:DYN_spg_flt} 
     
    10541054  and $\mathrm {\mathbf M}$ represents the collected contributions of the Coriolis, hydrostatic pressure gradient, 
    10551055  non-linear and viscous terms in \autoref{eq:MB_dyn}. 
    1056 }   %end gmcomment 
     1056}   %end cmtgm 
    10571057 
    10581058Note that in the linear free surface formulation (\texttt{vvl?} not defined), 
     
    10821082no slip or partial slip boundary conditions are applied according to the user's choice (see \autoref{chap:LBC}). 
    10831083 
    1084 \gmcomment{ 
     1084\cmtgm{ 
    10851085  Hyperviscous operators are frequently used in the simulation of turbulent flows to 
    10861086  control the dissipation of unresolved small scale features. 
     
    11831183the first derivative term normal to the coast depends on the free or no-slip lateral boundary conditions chosen, 
    11841184while the third derivative terms normal to the coast are set to zero (see \autoref{chap:LBC}). 
    1185 \gmcomment{add a remark on the the change in the position of the coefficient} 
     1185\cmtgm{add a remark on the the change in the position of the coefficient} 
    11861186 
    11871187%% ================================================================================================= 
     
    12521252the snow-ice mass is taken into account when computing the surface pressure gradient. 
    12531253 
    1254 \gmcomment{ missing : the lateral boundary condition !!!   another external forcing 
     1254\cmtgm{ missing : the lateral boundary condition !!!   another external forcing 
    12551255 } 
    12561256 
     
    15961596and only array swapping and Asselin filtering is done in \mdl{dynnxt}. 
    15971597 
    1598 \onlyinsubfile{\input{../../global/epilogue}} 
     1598\subinc{\input{../../global/epilogue}} 
    15991599 
    16001600\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11690 r11693  
    2525\clearpage 
    2626 
    27 %gm% add here introduction to this chapter 
     27\cmtgm{Add here introduction to this chapter} 
    2828 
    2929%% ================================================================================================= 
     
    708708direction of rotation). %, e.g. anticlockwise or clockwise. 
    709709 
    710 \onlyinsubfile{\input{../../global/epilogue}} 
     710\subinc{\input{../../global/epilogue}} 
    711711 
    712712\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11690 r11693  
    6868\label{sec:LDF_slp} 
    6969 
    70 \gmcomment{ 
     70\cmtgm{ 
    7171  we should emphasize here that the implementation is a rather old one. 
    7272  Better work can be achieved by using \citet{griffies.gnanadesikan.ea_JPO98, griffies_bk04} iso-neutral scheme. 
     
    8484$r_{1f}$, $r_{1vw}$, $r_{2t}$, $r_{2vw}$ for $v$. 
    8585 
    86 %gm% add here afigure of the slope in i-direction 
     86\cmtgm{Add here afigure of the slope in i-direction} 
    8787 
    8888%% ================================================================================================= 
     
    9494the diffusive fluxes in the three directions are set to zero and $T$ is assumed to be horizontally uniform, 
    9595\ie\ a linear function of $z_T$, the depth of a $T$-point. 
    96 %gm { Steven : My version is obviously wrong since I'm left with an arbitrary constant which is the local vertical temperature gradient} 
     96\cmtgm{Steven : My version is obviously wrong since 
     97  I'm left with an arbitrary constant which is the local vertical temperature gradient} 
    9798 
    9899\begin{equation} 
     
    112113\end{equation} 
    113114 
    114 %gm%  caution I'm not sure the simplification was a good idea! 
     115\cmtgm{Caution I'm not sure the simplification was a good idea!} 
    115116 
    116117These slopes are computed once in \rou{ldf\_slp\_init} when \np[=.true.]{ln_sco}{ln\_sco}, 
     
    144145\end{equation} 
    145146 
    146 %gm% rewrite this as the explanation is not very clear !!! 
     147\cmtgm{rewrite this as the explanation is not very clear !!!} 
    147148%In practice, \autoref{eq:LDF_slp_iso} is of little help in evaluating the neutral surface slopes. Indeed, for an unsimplified equation of state, the density has a strong dependancy on pressure (here approximated as the depth), therefore applying \autoref{eq:LDF_slp_iso} using the $in situ$ density, $\rho$, computed at T-points leads to a flattening of slopes as the depth increases. This is due to the strong increase of the $in situ$ density with depth. 
    148149 
     
    173174  will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes. 
    174175 
    175 %gm% 
    176176  Note: The solution for $s$-coordinate passes trough the use of different (and better) expression for 
    177177  the constraint on iso-neutral fluxes. 
     
    182182    \alpha \ \textbf{F}(T) = \beta \ \textbf{F}(S) 
    183183  \] 
    184   % gm{  where vector F is ....} 
     184  \cmtgm{where vector F is ....} 
    185185 
    186186This constraint leads to the following definition for the slopes: 
     
    229229This allows an iso-neutral diffusion scheme without additional background horizontal mixing. 
    230230This technique can be viewed as a diffusion operator that acts along large-scale 
    231 (2~$\Delta$x) \gmcomment{2deltax doesnt seem very large scale} iso-neutral surfaces. 
     231(2~$\Delta$x) \cmtgm{2deltax doesnt seem very large scale} iso-neutral surfaces. 
    232232The diapycnal diffusion required for numerical stability is thus minimized and its net effect on the flow is quite small when compared to the effect of an horizontal background mixing. 
    233233 
     
    478478 
    479479%%gm  from Triad appendix  : to be incorporated.... 
    480 \gmcomment{ 
     480\cmtgm{ 
    481481  Values of iso-neutral diffusivity and GM coefficient are set as described in \autoref{sec:LDF_coef}. 
    482482  If none of the keys \key{traldf\_cNd}, N=1,2,3 is set (the default), spatially constant iso-neutral $A_l$ and 
     
    544544\colorbox{yellow}{TBC} 
    545545 
    546 \onlyinsubfile{\input{../../global/epilogue}} 
     546\subinc{\input{../../global/epilogue}} 
    547547 
    548548\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11690 r11693  
    11801180\end{figure} 
    11811181 
    1182 \onlyinsubfile{\input{../../global/epilogue}} 
     1182\subinc{\input{../../global/epilogue}} 
    11831183 
    11841184\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11690 r11693  
    880880%ENDIF 
    881881 
    882 %\gmcomment{  word doc of runoffs: 
    883 %In the current \NEMO\ setup river runoff is added to emp fluxes, these are then applied at just the sea surface as a volume change (in the variable volume case this is a literal volume change, and in the linear free surface case the free surface is moved) and a salt flux due to the concentration/dilution effect.  There is also an option to increase vertical mixing near river mouths; this gives the effect of having a 3d river.  All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface. 
    884 %Our aim was to code the option to specify the temperature and salinity of river runoff, (as well as the amount), along with the depth that the river water will affect.  This would make it possible to model low salinity outflow, such as the Baltic, and would allow the ocean temperature to be affected by river runoff. 
    885  
    886 %The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between. 
    887  
    888 %To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the tra_sbc module.  We decided to separate them throughout the code, so that the variable emp represented solely evaporation minus precipitation fluxes, and a new 2d variable rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use emp or emps and the changes made are below: 
     882\cmtgm{  word doc of runoffs: 
     883In the current \NEMO\ setup river runoff is added to emp fluxes, 
     884these are then applied at just the sea surface as a volume change (in the variable volume case 
     885this is a literal volume change, and in the linear free surface case the free surface is moved) 
     886and a salt flux due to the concentration/dilution effect. 
     887There is also an option to increase vertical mixing near river mouths; 
     888this gives the effect of having a 3d river. 
     889All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and 
     890at the same temperature as the sea surface. 
     891Our aim was to code the option to specify the temperature and salinity of river runoff, 
     892(as well as the amount), along with the depth that the river water will affect. 
     893This would make it possible to model low salinity outflow, such as the Baltic, 
     894and would allow the ocean temperature to be affected by river runoff. 
     895 
     896The depth option makes it possible to have the river water affecting just the surface layer, 
     897throughout depth, or some specified point in between. 
     898 
     899To do this we need to treat evaporation/precipitation fluxes and river runoff differently in 
     900the \mdl{tra_sbc} module. 
     901We decided to separate them throughout the code, 
     902so that the variable emp represented solely evaporation minus precipitation fluxes, 
     903and a new 2d variable rnf was added which represents the volume flux of river runoff 
     904(in $kg/m^2s$ to remain consistent with $emp$). 
     905This meant many uses of emp and emps needed to be changed, 
     906a list of all modules which use $emp$ or $emps$ and the changes made are below:} 
    889907 
    890908%% ================================================================================================= 
     
    908926  Two different bulk formulae are available: 
    909927 
    910    \begin{description} 
    911    \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
    912      the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
    913    \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
    914      (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
    915      A complete description is available in \citet{jenkins_JGR91}. 
    916    \end{description} 
    917  
    918      Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
    919      Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. 
    920      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. 
    921      Then, the fluxes are spread over the same thickness (ie over one or several cells). 
    922      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. 
    923      This can lead to super-cool temperature in the top cell under melting condition. 
    924      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.\\ 
    925  
    926      Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
    927      There are 3 different ways to compute the exchange coeficient: 
    928    \begin{description} 
    929         \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}. 
    930      \begin{gather*} 
     928  \begin{description} 
     929  \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
     930    the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
     931  \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
     932    (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
     933    A complete description is available in \citet{jenkins_JGR91}. 
     934  \end{description} 
     935 
     936  Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
     937  Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. 
     938  The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m. 
     939  Then, the fluxes are spread over the same thickness (ie over one or several cells). 
     940  If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature. 
     941  This can lead to super-cool temperature in the top cell under melting condition. 
     942  If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 
     943 
     944  Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
     945  There are 3 different ways to compute the exchange coeficient: 
     946  \begin{description} 
     947  \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. 
     948    \begin{gather*} 
    931949       % \label{eq:SBC_isf_gamma_iso} 
    932        \gamma^{T} = rn\_gammat0 \\ 
    933        \gamma^{S} = rn\_gammas0 
    934      \end{gather*} 
    935      This is the recommended formulation for ISOMIP. 
    936    \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
    937      \begin{gather*} 
    938        \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
    939        \gamma^{S} = rn\_gammas0 \times u_{*} 
    940      \end{gather*} 
    941      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
    942      See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
    943    \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    944 \[ 
    945 \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
    946 \] 
    947      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), 
    948      $\Gamma_{Turb}$ the contribution of the ocean stability and 
    949      $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
    950      See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
    951      This formulation has not been extensively tested in \NEMO\ (not recommended). 
    952    \end{description} 
    953   \item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    954    The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    955    The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
    956    (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
    957    (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
    958    The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
    959   \item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    960    The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
    961    the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
    962    the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
    963    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    964   \item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    965    However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
    966    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    967    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})\\ 
     950      \gamma^{T} = rn\_gammat0 \\ 
     951      \gamma^{S} = rn\_gammas0 
     952    \end{gather*} 
     953    This is the recommended formulation for ISOMIP. 
     954  \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
     955    \begin{gather*} 
     956      \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
     957      \gamma^{S} = rn\_gammas0 \times u_{*} 
     958    \end{gather*} 
     959    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
     960    See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
     961  \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
     962    \[ 
     963      \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
     964    \] 
     965    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), 
     966    $\Gamma_{Turb}$ the contribution of the ocean stability and 
     967    $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
     968    See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
     969    This formulation has not been extensively tested in \NEMO\ (not recommended). 
     970  \end{description} 
     971\item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
     972  The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
     973  The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
     974  (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
     975  (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
     976  The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
     977\item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
     978  The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
     979  the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
     980  the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
     981  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     982\item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
     983  However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
     984  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     985  As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl}) 
    968986\end{description} 
    969987 
     
    15211539% in ocean-ice models. 
    15221540 
    1523 \onlyinsubfile{\input{../../global/epilogue}} 
     1541\subinc{\input{../../global/epilogue}} 
    15241542 
    15251543\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

    r11598 r11693  
    205205The first four parameters define the stochastic part of equation of state. 
    206206 
    207 \onlyinsubfile{\input{../../global/epilogue}} 
     207\subinc{\input{../../global/epilogue}} 
    208208 
    209209\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11690 r11693  
    452452restore this property. 
    453453 
    454 %%%gmcomment   :  Cross term are missing in the current implementation.... 
     454\cmtgm{Cross term are missing in the current implementation....} 
    455455 
    456456%% ================================================================================================= 
     
    10371037%!!        i.e. transport proportional to the along-slope density gradient 
    10381038 
    1039 %%%gmcomment   :  this section has to be really written 
     1039\cmtgm{This section has to be really written} 
    10401040 
    10411041When applying an advective BBL (\np[=1..2]{nn_bbl_adv}{nn\_bbl\_adv}), 
     
    13741374\label{sec:TRA_zpshde} 
    13751375 
    1376 \gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, 
     1376\cmtgm{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, 
    13771377I've changed "derivative" to "difference" and "mean" to "average"} 
    13781378 
     
    14641464Sensitivity of the advection schemes to the way horizontal averages are performed in 
    14651465the vicinity of partial cells should be further investigated in the near future. 
    1466 \gmcomment{gm :   this last remark has to be done} 
    1467  
    1468 \onlyinsubfile{\input{../../global/epilogue}} 
     1466\cmtgm{gm :   this last remark has to be done} 
     1467 
     1468\subinc{\input{../../global/epilogue}} 
    14691469 
    14701470\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r11690 r11693  
    2828\clearpage 
    2929 
    30 %gm% Add here a small introduction to ZDF and naming of the different physics (similar to what have been written for TRA and DYN. 
     30\cmtgm{ Add here a small introduction to ZDF and naming of the different physics 
     31(similar to what have been written for TRA and DYN).} 
    3132 
    3233%% ================================================================================================= 
     
    16421643\end{figure} 
    16431644 
    1644 \onlyinsubfile{\input{../../global/epilogue}} 
     1645\subinc{\input{../../global/epilogue}} 
    16451646 
    16461647\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r11690 r11693  
    292292Unlike ordinary river points the Baltic inputs also include salinity and temperature data. 
    293293 
    294 \onlyinsubfile{\input{../../global/epilogue}} 
     294\subinc{\input{../../global/epilogue}} 
    295295 
    296296\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex

    r11598 r11693  
    334334It has not been implemented. 
    335335 
    336 \onlyinsubfile{\input{../../global/epilogue}} 
     336\subinc{\input{../../global/epilogue}} 
    337337 
    338338\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r11690 r11693  
    415415increment also applies to the time.step file which is otherwise updated every timestep. 
    416416 
    417 \onlyinsubfile{\input{../../global/epilogue}} 
     417\subinc{\input{../../global/epilogue}} 
    418418 
    419419\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r11690 r11693  
    579579an explicit computation of vertical advection relative to the moving s-surfaces. 
    580580 
    581 %\gmcomment{ 
    582 %A key point here is that the $s$-coordinate depends on $(i,j)$ ==> horizontal pressure gradient... 
     581\cmtgm{A key point here is that the $s$-coordinate depends on $(i,j)$ 
     582  ==> horizontal pressure gradient...} 
    583583The generalized vertical coordinates used in ocean modelling are not orthogonal, 
    584584which contrasts with many other applications in mathematical physics. 
     
    680680and similar expressions are used for mixing and forcing terms. 
    681681 
    682 \gmcomment{ 
     682\cmtgm{ 
    683683  \colorbox{yellow}{ to be updated $= = >$} 
    684684  Add a few works on z and zps and s and underlies the differences between all of them 
     
    11501150Nevertheless it is currently not available in the iso-neutral case. 
    11511151 
    1152 \onlyinsubfile{\input{../../global/epilogue}} 
     1152\subinc{\input{../../global/epilogue}} 
    11531153 
    11541154\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11690 r11693  
    147147\begin{figure}[!t] 
    148148  \centering 
    149   \includegraphics[width=0.66\textwidth]{MBZ_DYN_dynspg_ts} 
     149  %\includegraphics[width=0.66\textwidth]{MBZ_DYN_dynspg_ts} 
    150150  \caption[Schematic of the split-explicit time stepping scheme for 
    151151  the barotropic and baroclinic modes, after \citet{Griffies2004?}]{ 
     
    311311In particular, this means that in filtered case, the matrix to be inverted has to be recomputed at each time-step. 
    312312 
    313 \onlyinsubfile{\input{../../global/epilogue}} 
     313\subinc{\input{../../global/epilogue}} 
    314314 
    315315\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11690 r11693  
    3131% - daymod: definition of the time domain (nit000, nitend and the calendar) 
    3232 
    33 \gmcomment{STEVEN :maybe a picture of the directory structure in the introduction which 
     33\cmtgm{STEVEN :maybe a picture of the directory structure in the introduction which 
    3434could be referred to here, would help  ==> to be added} 
    3535 
     
    158158\end{equation} 
    159159 
    160 %%gm 
    161 %%gm   UPDATE the next paragraphs with time varying thickness ... 
    162 %%gm 
     160\cmtgm{UPDATE the next paragraphs with time varying thickness ...} 
    163161 
    164162This scheme is rather time consuming since it requires a matrix inversion. 
     
    213211Fast barotropic motions (such as tides) are also simulated with a better accuracy. 
    214212 
    215 %\gmcomment{ 
     213%\cmtgm{ 
    216214\begin{figure} 
    217215  \centering 
     
    328326the \nam{run}{run} namelist variables. 
    329327 
    330 \gmcomment{ 
     328\cmtgm{ 
    331329add here how to force the restart to contain only one time step for operational purposes 
    332330 
     
    338336} 
    339337 
    340 \gmcomment{       % add a subsection here 
     338\cmtgm{       % add a subsection here 
    341339 
    342340%% ================================================================================================= 
     
    353351}     %% end add 
    354352 
    355 \gmcomment{       % add implicit in vvl case  and Crant-Nicholson scheme 
     353\cmtgm{       % add implicit in vvl case  and Crant-Nicholson scheme 
    356354 
    357355Implicit time stepping in case of variable volume thickness. 
     
    404402} 
    405403 
    406 \onlyinsubfile{\input{../../global/epilogue}} 
     404\subinc{\input{../../global/epilogue}} 
    407405 
    408406\end{document} 
  • NEMO/trunk/doc/latex/global/document.tex

    r11591 r11693  
    1818%% End of common preamble between main and sub-files 
    1919%% Override custom cmds for full manual compilation 
    20 \newcommand{\onlyinsubfile}[1]{#1} 
    21 \newcommand{\notinsubfile}[1]{} 
     20\newcommand{\subinc}[1]{#1} 
     21\newcommand{\subexc}[1]{} 
    2222 
    2323\begin{document} 
    2424 
    25 \renewcommand{\onlyinsubfile}[1]{} 
    26 \renewcommand{\notinsubfile}[1]{#1} 
     25\renewcommand{\subinc}[1]{} 
     26\renewcommand{\subexc}[1]{#1} 
    2727 
    2828 
  • NEMO/trunk/doc/latex/global/new_cmds.tex

    r11584 r11693  
    3434 
    3535%% Gurvan's comments 
    36 \newcommand{\gmcomment}[1]{} 
     36\newcommand{\cmtgm}[1]{} 
    3737 
    3838%% Maths 
  • NEMO/trunk/doc/latex/global/packages.tex

    r11688 r11693  
    1818%% Issue with fontawesome pkg: path to FontAwesome.otf has to be hard-coded 
    1919\defaultfontfeatures{ 
    20     Path = /usr/local/texlive/2019/texmf-dist/fonts/opentype/public/fontawesome/ 
     20    Path = /home/ntmlod/.local/texlive2019/texmf-dist/fonts/opentype/public/fontawesome/ 
    2121} 
    2222\usepackage{academicons, fontawesome, newtxtext} 
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