Changeset 9363


Ignore:
Timestamp:
2018-02-28T10:29:22+01:00 (2 years ago)
Author:
nicolasmartin
Message:

Working with htlatex (LaTeX to HTML): disable floatrow package globally, fix several issues by adding \protect to all "fragile" commands (\mdl, \np, \key and \ngn) inside floats (caption or table). Still few specific issues inside Annnex_ISO

Location:
branches/2017/dev_merge_2017/DOC/TexFiles/Chapters
Files:
17 edited

Legend:

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  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Annex_C.tex

    r6997 r9363  
    363363%       Vorticity Term with ENE scheme 
    364364% ------------------------------------------------------------------------------------------------------------- 
    365 \subsubsection{Vorticity Term with ENE scheme (\np{ln\_dynvor\_ene}=.true.)} 
     365\subsubsection{Vorticity Term with ENE scheme (\protect\np{ln\_dynvor\_ene}=.true.)} 
    366366\label{Apdx_C_vorENE}  
    367367 
     
    400400%       Vorticity Term with EEN scheme 
    401401% ------------------------------------------------------------------------------------------------------------- 
    402 \subsubsection{Vorticity Term with EEN scheme (\np{ln\_dynvor\_een}=.true.)} 
     402\subsubsection{Vorticity Term with EEN scheme (\protect\np{ln\_dynvor\_een}=.true.)} 
    403403\label{Apdx_C_vorEEN}  
    404404 
     
    883883%       Vorticity Term with ENS scheme 
    884884% ------------------------------------------------------------------------------------------------------------- 
    885 \subsubsection{Vorticity Term with ENS scheme  (\np{ln\_dynvor\_ens}=.true.)} 
     885\subsubsection{Vorticity Term with ENS scheme  (\protect\np{ln\_dynvor\_ens}=.true.)} 
    886886\label{Apdx_C_vorENS}  
    887887 
     
    943943%       Vorticity Term with EEN scheme 
    944944% ------------------------------------------------------------------------------------------------------------- 
    945 \subsubsection{Vorticity Term with EEN scheme (\np{ln\_dynvor\_een}=.true.)} 
     945\subsubsection{Vorticity Term with EEN scheme (\protect\np{ln\_dynvor\_een}=.true.)} 
    946946\label{Apdx_C_vorEEN}  
    947947 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Annex_E.tex

    r6997 r9363  
    1919%        UBS scheme   
    2020% ------------------------------------------------------------------------------------------------------------- 
    21 \section{Upstream Biased Scheme (UBS) (\np{ln\_traadv\_ubs}=T)} 
     21\section{Upstream Biased Scheme (UBS) (\protect\np{ln\_traadv\_ubs}=T)} 
    2222\label{TRA_adv_ubs} 
    2323 
     
    302302\begin{center} 
    303303\includegraphics[width=0.70\textwidth]{Fig_ISO_triad} 
    304 \caption{  \label{Fig_ISO_triad}    
     304\caption{  \protect\label{Fig_ISO_triad}    
    305305Triads used in the Griffies's like iso-neutral diffision scheme for  
    306306$u$-component (upper panel) and $w$-component (lower panel).} 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_CFG.tex

    r9038 r9363  
    3232% 1D model configuration 
    3333% ================================================================ 
    34 \section{Water column model: 1D model (C1D) (\key{c1d}) } 
     34\section{Water column model: 1D model (C1D) (\protect\key{c1d}) } 
    3535\label{CFG_c1d} 
    3636 
     
    9595\begin{figure}[!t]   \begin{center} 
    9696\includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh} 
    97 \caption{  \label{Fig_MISC_ORCA_msh}      
     97\caption{  \protect\label{Fig_MISC_ORCA_msh}      
    9898ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN. 
    9999The two "north pole" are the foci of a series of embedded ellipses (blue curves)  
     
    123123\includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
    124124\includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso} 
    125 \caption {  \label{Fig_MISC_ORCA_e1e2} 
     125\caption {  \protect\label{Fig_MISC_ORCA_e1e2} 
    126126\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and  
    127127\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) 
     
    175175\hline   \hline 
    176176\end{tabular} 
    177 \caption{ \label{Tab_ORCA}    
     177\caption{ \protect\label{Tab_ORCA}    
    178178Domain size of ORCA family configurations. 
    179179The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file. } 
     
    267267\begin{figure}[!t]   \begin{center} 
    268268\includegraphics[width=1.0\textwidth]{Fig_GYRE} 
    269 \caption{  \label{Fig_GYRE}    
     269\caption{  \protect\label{Fig_GYRE}    
    270270Snapshot of relative vorticity at the surface of the model domain  
    271271in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.} 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_DIA.tex

    r6997 r9363  
    10921092%       NetCDF4 support 
    10931093% ================================================================ 
    1094 \section{NetCDF4 Support (\key{netcdf4})} 
     1094\section{NetCDF4 Support (\protect\key{netcdf4})} 
    10951095\label{DIA_iom} 
    10961096 
     
    11981198ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\%\\ 
    11991199\end{tabular} 
    1200 \caption{   \label{Tab_NC4}  
     1200\caption{   \protect\label{Tab_NC4}  
    12011201Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression} 
    12021202\end{table} 
     
    12181218% ------------------------------------------------------------------------------------------------------------- 
    12191219\section[Tracer/Dynamics Trends (TRD)] 
    1220                   {Tracer/Dynamics Trends  (\ngn{namtrd})} 
     1220                  {Tracer/Dynamics Trends  (\protect\ngn{namtrd})} 
    12211221\label{DIA_trd} 
    12221222 
     
    12581258%       On-line Floats trajectories 
    12591259% ------------------------------------------------------------------------------------------------------------- 
    1260 \section{On-line Floats trajectories (FLO) (\key{floats})} 
     1260\section{On-line Floats trajectories (FLO) (\protect\key{floats})} 
    12611261\label{FLO} 
    12621262%--------------------------------------------namflo------------------------------------------------------- 
     
    13711371%       Harmonic analysis of tidal constituents 
    13721372% ------------------------------------------------------------------------------------------------------------- 
    1373 \section{Harmonic analysis of tidal constituents (\key{diaharm}) } 
     1373\section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) } 
    13741374\label{DIA_diag_harm} 
    13751375 
     
    14131413%       Sections transports 
    14141414% ------------------------------------------------------------------------------------------------------------- 
    1415 \section{Transports across sections (\key{diadct}) } 
     1415\section{Transports across sections (\protect\key{diadct}) } 
    14161416\label{DIA_diag_dct} 
    14171417 
     
    17191719%       Other Diagnostics 
    17201720% ------------------------------------------------------------------------------------------------------------- 
    1721 \section{Other Diagnostics (\key{diahth}, \key{diaar5})} 
     1721\section{Other Diagnostics (\protect\key{diahth}, \protect\key{diaar5})} 
    17221722\label{DIA_diag_others} 
    17231723 
     
    17261726The available ready-to-add diagnostics modules can be found in directory DIA.  
    17271727 
    1728 \subsection{Depth of various quantities (\mdl{diahth})} 
     1728\subsection{Depth of various quantities (\protect\mdl{diahth})} 
    17291729 
    17301730Among the available diagnostics the following ones are obtained when defining  
     
    17431743% ----------------------------------------------------------- 
    17441744 
    1745 \subsection{Poleward heat and salt transports (\mdl{diaptr})} 
     1745\subsection{Poleward heat and salt transports (\protect\mdl{diaptr})} 
    17461746 
    17471747%------------------------------------------namptr----------------------------------------- 
     
    17611761\begin{figure}[!t]     \begin{center} 
    17621762\includegraphics[width=1.0\textwidth]{Fig_mask_subasins} 
    1763 \caption{   \label{Fig_mask_subasins} 
     1763\caption{   \protect\label{Fig_mask_subasins} 
    17641764Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute 
    17651765the heat and salt transports as well as the meridional stream-function: Atlantic basin (red),  
     
    17751775%       CMIP specific diagnostics  
    17761776% ----------------------------------------------------------- 
    1777 \subsection{CMIP specific diagnostics (\mdl{diaar5})} 
     1777\subsection{CMIP specific diagnostics (\protect\mdl{diaar5})} 
    17781778 
    17791779A series of diagnostics has been added in the \mdl{diaar5}.  
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_DOM.tex

    r9019 r9363  
    4343\begin{figure}[!tb]    \begin{center} 
    4444\includegraphics[width=0.90\textwidth]{Fig_cell} 
    45 \caption{ \label{Fig_cell}     
     45\caption{ \protect\label{Fig_cell}     
    4646Arrangement of variables. $t$ indicates scalar points where temperature,  
    4747salinity, density, pressure and horizontal divergence are defined. ($u$,$v$,$w$)  
     
    9595fw & $i+1/2$   & $j+1/2$   & $k+1/2$   \\ \hline 
    9696\end{tabular} 
    97 \caption{ \label{Tab_cell} 
     97\caption{ \protect\label{Tab_cell} 
    9898Location of grid-points as a function of integer or integer and a half value of the column,  
    9999line or level. This indexing is only used for the writing of the semi-discrete equation.  
     
    204204\begin{figure}[!tb]  \begin{center} 
    205205\includegraphics[width=0.90\textwidth]{Fig_index_hor} 
    206 \caption{   \label{Fig_index_hor}     
     206\caption{   \protect\label{Fig_index_hor}     
    207207Horizontal integer indexing used in the \textsc{Fortran} code. The dashed area indicates  
    208208the cell in which variables contained in arrays have the same $i$- and $j$-indices} 
     
    254254\begin{figure}[!pt]    \begin{center} 
    255255\includegraphics[width=.90\textwidth]{Fig_index_vert} 
    256 \caption{ \label{Fig_index_vert}      
     256\caption{ \protect\label{Fig_index_vert}      
    257257Vertical integer indexing used in the \textsc{Fortran } code. Note that  
    258258the $k$-axis is orientated downward. The dashed area indicates the cell in  
     
    324324% ================================================================ 
    325325\section  [Domain: Horizontal Grid (mesh) (\textit{domhgr})]                
    326       {Domain: Horizontal Grid (mesh) \small{(\mdl{domhgr} module)} } 
     326      {Domain: Horizontal Grid (mesh) \small{(\protect\mdl{domhgr} module)} } 
    327327\label{DOM_hgr} 
    328328 
     
    388388\begin{figure}[!t]     \begin{center} 
    389389\includegraphics[width=0.90\textwidth]{Fig_zgr_e3} 
    390 \caption{ \label{Fig_zgr_e3}     
     390\caption{ \protect\label{Fig_zgr_e3}     
    391391Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical,  
    392392and (b) analytically derived grid-point position and scale factors.  
     
    428428% ================================================================ 
    429429\section  [Domain: Vertical Grid (\textit{domzgr})] 
    430       {Domain: Vertical Grid \small{(\mdl{domzgr} module)} } 
     430      {Domain: Vertical Grid \small{(\protect\mdl{domzgr} module)} } 
    431431\label{DOM_zgr} 
    432432%-----------------------------------------nam_zgr & namdom------------------------------------------- 
     
    447447\begin{figure}[!tb]    \begin{center} 
    448448\includegraphics[width=1.0\textwidth]{Fig_z_zps_s_sps} 
    449 \caption{  \label{Fig_z_zps_s_sps}    
     449\caption{  \protect\label{Fig_z_zps_s_sps}    
    450450The ocean bottom as seen by the model:  
    451451(a) $z$-coordinate with full step,  
     
    454454(d) hybrid $s-z$ coordinate,  
    455455(e) hybrid $s-z$ coordinate with partial step, and  
    456 (f) same as (e) but in the non-linear free surface (\np{ln\_linssh}=false).  
     456(f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}=false).  
    457457Note that the non-linear free surface can be used with any of the  
    4584585 coordinates (a) to (e).} 
     
    550550%        z-coordinate  and reference coordinate transformation 
    551551% ------------------------------------------------------------------------------------------------------------- 
    552 \subsection[$z$-coordinate (\np{ln\_zco}] 
    553         {$z$-coordinate (\np{ln\_zco}=true) and reference coordinate} 
     552\subsection[$z$-coordinate (\protect\np{ln\_zco}] 
     553        {$z$-coordinate (\protect\np{ln\_zco}=true) and reference coordinate} 
    554554\label{DOM_zco} 
    555555 
     
    557557\begin{figure}[!tb]    \begin{center} 
    558558\includegraphics[width=0.90\textwidth]{Fig_zgr} 
    559 \caption{ \label{Fig_zgr}     
     559\caption{ \protect\label{Fig_zgr}     
    560560Default vertical mesh for ORCA2: 30 ocean levels (L30). Vertical level functions for  
    561561(a) T-point depth and (b) the associated scale factor as computed  
     
    67967931 &  \textbf{5250.23}& 5000.00 &   \textbf{500.56} & 500.33 \\ \hline 
    680680\end{tabular} \end{center}  
    681 \caption{ \label{Tab_orca_zgr}    
     681\caption{ \protect\label{Tab_orca_zgr}    
    682682Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration as computed  
    683683from \eqref{DOM_zgr_ana} using the coefficients given in \eqref{DOM_zgr_coef}} 
     
    688688%        z-coordinate with partial step 
    689689% ------------------------------------------------------------------------------------------------------------- 
    690 \subsection   [$z$-coordinate with partial step (\np{ln\_zps})] 
    691          {$z$-coordinate with partial step (\np{ln\_zps}=.true.)} 
     690\subsection   [$z$-coordinate with partial step (\protect\np{ln\_zps})] 
     691         {$z$-coordinate with partial step (\protect\np{ln\_zps}=.true.)} 
    692692\label{DOM_zps} 
    693693%--------------------------------------------namdom------------------------------------------------------- 
     
    721721%        s-coordinate 
    722722% ------------------------------------------------------------------------------------------------------------- 
    723 \subsection   [$s$-coordinate (\np{ln\_sco})] 
    724            {$s$-coordinate (\np{ln\_sco}=true)} 
     723\subsection   [$s$-coordinate (\protect\np{ln\_sco})] 
     724           {$s$-coordinate (\protect\np{ln\_sco}=true)} 
    725725\label{DOM_sco} 
    726726%------------------------------------------nam_zgr_sco--------------------------------------------------- 
     
    790790\begin{figure}[!ht]    \begin{center} 
    791791\includegraphics[width=1.0\textwidth]{Fig_sco_function} 
    792 \caption{  \label{Fig_sco_function}    
     792\caption{  \protect\label{Fig_sco_function}    
    793793Examples of the stretching function applied to a seamount; from left to right:  
    794794surface, surface and bottom, and bottom intensified resolutions} 
     
    850850%        z*- or s*-coordinate 
    851851% ------------------------------------------------------------------------------------------------------------- 
    852 \subsection{$z^*$- or $s^*$-coordinate (\np{ln\_linssh}=false) } 
     852\subsection{$z^*$- or $s^*$-coordinate (\protect\np{ln\_linssh}=false) } 
    853853\label{DOM_zgr_star} 
    854854 
     
    913913% ================================================================ 
    914914\section  [Domain: Initial State (\textit{istate and dtatsd})] 
    915       {Domain: Initial State \small{(\mdl{istate} and \mdl{dtatsd} modules)} } 
     915      {Domain: Initial State \small{(\protect\mdl{istate} and \protect\mdl{dtatsd} modules)} } 
    916916\label{DTA_tsd} 
    917917%-----------------------------------------namtsd------------------------------------------- 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_DYN.tex

    r7646 r9363  
    7070%-------------------------------------------------------------------------------------------------------------- 
    7171\subsection   [Horizontal divergence and relative vorticity (\textit{divcur})] 
    72          {Horizontal divergence and relative vorticity (\mdl{divcur})} 
     72         {Horizontal divergence and relative vorticity (\protect\mdl{divcur})} 
    7373\label{DYN_divcur} 
    7474 
     
    103103%-------------------------------------------------------------------------------------------------------------- 
    104104\subsection   [Sea surface height evolution and vertical velocity (\textit{sshwzv})] 
    105          {Horizontal divergence and relative vorticity (\mdl{sshwzv})} 
     105         {Horizontal divergence and relative vorticity (\protect\mdl{sshwzv})} 
    106106\label{DYN_sshwzv} 
    107107 
     
    179179% ------------------------------------------------------------------------------------------------------------- 
    180180\subsection   [Vorticity term (\textit{dynvor}) ] 
    181          {Vorticity term (\mdl{dynvor})} 
     181         {Vorticity term (\protect\mdl{dynvor})} 
    182182\label{DYN_vor} 
    183183%------------------------------------------nam_dynvor---------------------------------------------------- 
     
    200200%                 enstrophy conserving scheme 
    201201%------------------------------------------------------------- 
    202 \subsubsection{Enstrophy conserving scheme (\np{ln\_dynvor\_ens}=true)} 
     202\subsubsection{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}=true)} 
    203203\label{DYN_vor_ens} 
    204204 
     
    221221%                 energy conserving scheme 
    222222%------------------------------------------------------------- 
    223 \subsubsection{Energy conserving scheme (\np{ln\_dynvor\_ene}=true)} 
     223\subsubsection{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}=true)} 
    224224\label{DYN_vor_ene} 
    225225 
     
    238238%                 mix energy/enstrophy conserving scheme 
    239239%------------------------------------------------------------- 
    240 \subsubsection{Mixed energy/enstrophy conserving scheme (\np{ln\_dynvor\_mix}=true) } 
     240\subsubsection{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}=true) } 
    241241\label{DYN_vor_mix} 
    242242 
     
    261261%                 energy and enstrophy conserving scheme 
    262262%------------------------------------------------------------- 
    263 \subsubsection{Energy and enstrophy conserving scheme (\np{ln\_dynvor\_een}=true) } 
     263\subsubsection{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}=true) } 
    264264\label{DYN_vor_een} 
    265265 
     
    297297\begin{figure}[!ht]    \begin{center} 
    298298\includegraphics[width=0.70\textwidth]{Fig_DYN_een_triad} 
    299 \caption{ \label{Fig_DYN_een_triad}   
     299\caption{ \protect\label{Fig_DYN_een_triad}   
    300300Triads used in the energy and enstrophy conserving scheme (een) for  
    301301$u$-component (upper panel) and $v$-component (lower panel).} 
     
    347347%-------------------------------------------------------------------------------------------------------------- 
    348348\subsection   [Kinetic Energy Gradient term (\textit{dynkeg})] 
    349          {Kinetic Energy Gradient term (\mdl{dynkeg})} 
     349         {Kinetic Energy Gradient term (\protect\mdl{dynkeg})} 
    350350\label{DYN_keg} 
    351351 
     
    364364%-------------------------------------------------------------------------------------------------------------- 
    365365\subsection   [Vertical advection term (\textit{dynzad}) ] 
    366          {Vertical advection term (\mdl{dynzad}) } 
     366         {Vertical advection term (\protect\mdl{dynzad}) } 
    367367\label{DYN_zad} 
    368368 
     
    406406%-------------------------------------------------------------------------------------------------------------- 
    407407\subsection   [Coriolis plus curvature metric terms (\textit{dynvor}) ] 
    408          {Coriolis plus curvature metric terms (\mdl{dynvor}) } 
     408         {Coriolis plus curvature metric terms (\protect\mdl{dynvor}) } 
    409409\label{DYN_cor_flux} 
    410410 
     
    428428%-------------------------------------------------------------------------------------------------------------- 
    429429\subsection   [Flux form Advection term (\textit{dynadv}) ] 
    430          {Flux form Advection term (\mdl{dynadv}) } 
     430         {Flux form Advection term (\protect\mdl{dynadv}) } 
    431431\label{DYN_adv_flux} 
    432432 
     
    460460%                 2nd order centred scheme 
    461461%------------------------------------------------------------- 
    462 \subsubsection{$2^{nd}$ order centred scheme (cen2) (\np{ln\_dynadv\_cen2}=true)} 
     462\subsubsection{$2^{nd}$ order centred scheme (cen2) (\protect\np{ln\_dynadv\_cen2}=true)} 
    463463\label{DYN_adv_cen2} 
    464464 
     
    481481%                 UBS scheme 
    482482%------------------------------------------------------------- 
    483 \subsubsection{Upstream Biased Scheme (UBS) (\np{ln\_dynadv\_ubs}=true)} 
     483\subsubsection{Upstream Biased Scheme (UBS) (\protect\np{ln\_dynadv\_ubs}=true)} 
    484484\label{DYN_adv_ubs} 
    485485 
     
    533533% ================================================================ 
    534534\section  [Hydrostatic pressure gradient (\textit{dynhpg})] 
    535       {Hydrostatic pressure gradient (\mdl{dynhpg})} 
     535      {Hydrostatic pressure gradient (\protect\mdl{dynhpg})} 
    536536\label{DYN_hpg} 
    537537%------------------------------------------nam_dynhpg--------------------------------------------------- 
     
    554554%           z-coordinate with full step 
    555555%-------------------------------------------------------------------------------------------------------------- 
    556 \subsection   [$z$-coordinate with full step (\np{ln\_dynhpg\_zco}) ] 
    557          {$z$-coordinate with full step (\np{ln\_dynhpg\_zco}=true)} 
     556\subsection   [$z$-coordinate with full step (\protect\np{ln\_dynhpg\_zco}) ] 
     557         {$z$-coordinate with full step (\protect\np{ln\_dynhpg\_zco}=true)} 
    558558\label{DYN_hpg_zco} 
    559559 
     
    595595%           z-coordinate with partial step 
    596596%-------------------------------------------------------------------------------------------------------------- 
    597 \subsection   [$z$-coordinate with partial step (\np{ln\_dynhpg\_zps})] 
    598          {$z$-coordinate with partial step (\np{ln\_dynhpg\_zps}=true)} 
     597\subsection   [$z$-coordinate with partial step (\protect\np{ln\_dynhpg\_zps})] 
     598         {$z$-coordinate with partial step (\protect\np{ln\_dynhpg\_zps}=true)} 
    599599\label{DYN_hpg_zps} 
    600600 
     
    673673%           Time-scheme 
    674674%-------------------------------------------------------------------------------------------------------------- 
    675 \subsection   [Time-scheme (\np{ln\_dynhpg\_imp}) ] 
    676          {Time-scheme (\np{ln\_dynhpg\_imp}= true/false)} 
     675\subsection   [Time-scheme (\protect\np{ln\_dynhpg\_imp}) ] 
     676         {Time-scheme (\protect\np{ln\_dynhpg\_imp}= true/false)} 
    677677\label{DYN_hpg_imp} 
    678678 
     
    733733% ================================================================ 
    734734\section  [Surface pressure gradient (\textit{dynspg}) ] 
    735       {Surface pressure gradient (\mdl{dynspg})} 
     735      {Surface pressure gradient (\protect\mdl{dynspg})} 
    736736\label{DYN_spg} 
    737737%-----------------------------------------nam_dynspg---------------------------------------------------- 
     
    772772% Explicit free surface formulation 
    773773%-------------------------------------------------------------------------------------------------------------- 
    774 \subsection{Explicit free surface (\key{dynspg\_exp})} 
     774\subsection{Explicit free surface (\protect\key{dynspg\_exp})} 
    775775\label{DYN_spg_exp} 
    776776 
     
    793793% Split-explict free surface formulation 
    794794%-------------------------------------------------------------------------------------------------------------- 
    795 \subsection{Split-Explicit free surface (\key{dynspg\_ts})} 
     795\subsection{Split-Explicit free surface (\protect\key{dynspg\_ts})} 
    796796\label{DYN_spg_ts} 
    797797%------------------------------------------namsplit----------------------------------------------------------- 
     
    830830\begin{figure}[!t]    \begin{center} 
    831831\includegraphics[width=0.7\textwidth]{Fig_DYN_dynspg_ts} 
    832 \caption{  \label{Fig_DYN_dynspg_ts} 
     832\caption{  \protect\label{Fig_DYN_dynspg_ts} 
    833833Schematic of the split-explicit time stepping scheme for the external  
    834834and internal modes. Time increases to the right. In this particular exemple,  
     
    839839The former are used to obtain time filtered quantities at $t+\rdt$ while the latter are used to obtain time averaged  
    840840transports to advect tracers. 
    841 a) Forward time integration: \np{ln\_bt\_fw}=true,  \np{ln\_bt\_av}=true.  
    842 b) Centred time integration: \np{ln\_bt\_fw}=false, \np{ln\_bt\_av}=true.  
    843 c) Forward time integration with no time filtering (POM-like scheme): \np{ln\_bt\_fw}=true, \np{ln\_bt\_av}=false. } 
     841a) Forward time integration: \protect\np{ln\_bt\_fw}=true,  \protect\np{ln\_bt\_av}=true.  
     842b) Centred time integration: \protect\np{ln\_bt\_fw}=false, \protect\np{ln\_bt\_av}=true.  
     843c) Forward time integration with no time filtering (POM-like scheme): \protect\np{ln\_bt\_fw}=true, \protect\np{ln\_bt\_av}=false. } 
    844844\end{center}    \end{figure} 
    845845%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
     
    975975% Filtered free surface formulation 
    976976%-------------------------------------------------------------------------------------------------------------- 
    977 \subsection{Filtered free surface (\key{dynspg\_flt})} 
     977\subsection{Filtered free surface (\protect\key{dynspg\_flt})} 
    978978\label{DYN_spg_fltp} 
    979979 
     
    10021002% ================================================================ 
    10031003\section  [Lateral diffusion term (\textit{dynldf})] 
    1004       {Lateral diffusion term (\mdl{dynldf})} 
     1004      {Lateral diffusion term (\protect\mdl{dynldf})} 
    10051005\label{DYN_ldf} 
    10061006%------------------------------------------nam_dynldf---------------------------------------------------- 
     
    10361036 
    10371037% ================================================================ 
    1038 \subsection   [Iso-level laplacian operator (\np{ln\_dynldf\_lap}) ] 
    1039          {Iso-level laplacian operator (\np{ln\_dynldf\_lap}=true)} 
     1038\subsection   [Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}) ] 
     1039         {Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}=true)} 
    10401040\label{DYN_ldf_lap} 
    10411041 
     
    10601060%           Rotated laplacian operator 
    10611061%-------------------------------------------------------------------------------------------------------------- 
    1062 \subsection   [Rotated laplacian operator (\np{ln\_dynldf\_iso}) ] 
    1063          {Rotated laplacian operator (\np{ln\_dynldf\_iso}=true)} 
     1062\subsection   [Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}) ] 
     1063         {Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}=true)} 
    10641064\label{DYN_ldf_iso} 
    10651065 
     
    11291129%           Iso-level bilaplacian operator 
    11301130%-------------------------------------------------------------------------------------------------------------- 
    1131 \subsection   [Iso-level bilaplacian operator (\np{ln\_dynldf\_bilap})] 
    1132          {Iso-level bilaplacian operator (\np{ln\_dynldf\_bilap}=true)} 
     1131\subsection   [Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap})] 
     1132         {Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}=true)} 
    11331133\label{DYN_ldf_bilap} 
    11341134 
     
    11451145%           Vertical diffusion term 
    11461146% ================================================================ 
    1147 \section  [Vertical diffusion term (\mdl{dynzdf})] 
    1148       {Vertical diffusion term (\mdl{dynzdf})} 
     1147\section  [Vertical diffusion term (\protect\mdl{dynzdf})] 
     1148      {Vertical diffusion term (\protect\mdl{dynzdf})} 
    11491149\label{DYN_zdf} 
    11501150%----------------------------------------------namzdf------------------------------------------------------ 
     
    12231223% ================================================================ 
    12241224\section  [Time evolution term (\textit{dynnxt})] 
    1225       {Time evolution term (\mdl{dynnxt})} 
     1225      {Time evolution term (\protect\mdl{dynnxt})} 
    12261226\label{DYN_nxt} 
    12271227 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_LBC.tex

    r7646 r9363  
    1717% Boundary Condition at the Coast 
    1818% ================================================================ 
    19 \section{Boundary Condition at the Coast (\np{rn\_shlat})} 
     19\section{Boundary Condition at the Coast (\protect\np{rn\_shlat})} 
    2020\label{LBC_coast} 
    2121%--------------------------------------------nam_lbc------------------------------------------------------- 
     
    5656\begin{figure}[!t]     \begin{center} 
    5757\includegraphics[width=0.90\textwidth]{Fig_LBC_uv} 
    58 \caption{  \label{Fig_LBC_uv} 
     58\caption{  \protect\label{Fig_LBC_uv} 
    5959Lateral boundary (thick line) at T-level. The velocity normal to the boundary is set to zero.} 
    6060\end{center}   \end{figure} 
     
    7979\begin{figure}[!p] \begin{center} 
    8080\includegraphics[width=0.90\textwidth]{Fig_LBC_shlat} 
    81 \caption{     \label{Fig_LBC_shlat}  
     81\caption{     \protect\label{Fig_LBC_shlat}  
    8282lateral boundary condition (a) free-slip ($rn\_shlat=0$) ; (b) no-slip ($rn\_shlat=2$)  
    8383; (c) "partial" free-slip ($0<rn\_shlat<2$) and (d) "strong" no-slip ($2<rn\_shlat$).  
     
    133133% Boundary Condition around the Model Domain 
    134134% ================================================================ 
    135 \section{Model Domain Boundary Condition (\np{jperio})} 
     135\section{Model Domain Boundary Condition (\protect\np{jperio})} 
    136136\label{LBC_jperio} 
    137137 
     
    143143%        Closed, cyclic, south symmetric (\np{jperio} = 0, 1 or 2)  
    144144% ------------------------------------------------------------------------------------------------------------- 
    145 \subsection{Closed, cyclic, south symmetric (\np{jperio} = 0, 1 or 2)} 
     145\subsection{Closed, cyclic, south symmetric (\protect\np{jperio} = 0, 1 or 2)} 
    146146\label{LBC_jperio012} 
    147147 
     
    180180\begin{figure}[!t]     \begin{center} 
    181181\includegraphics[width=1.0\textwidth]{Fig_LBC_jperio} 
    182 \caption{    \label{Fig_LBC_jperio} 
     182\caption{    \protect\label{Fig_LBC_jperio} 
    183183setting of (a) east-west cyclic  (b) symmetric across the equator boundary conditions.} 
    184184\end{center}   \end{figure} 
     
    199199\begin{figure}[!t]    \begin{center} 
    200200\includegraphics[width=0.90\textwidth]{Fig_North_Fold_T} 
    201 \caption{    \label{Fig_North_Fold_T}  
     201\caption{    \protect\label{Fig_North_Fold_T}  
    202202North fold boundary with a $T$-point pivot and cyclic east-west boundary condition  
    203203($jperio=4$), as used in ORCA 2, 1/4, and 1/12. Pink shaded area corresponds  
     
    210210% ==================================================================== 
    211211\section  [Exchange with neighbouring processors (\textit{lbclnk}, \textit{lib\_mpp})] 
    212       {Exchange with neighbouring processors (\mdl{lbclnk}, \mdl{lib\_mpp})} 
     212      {Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})} 
    213213\label{LBC_mpp} 
    214214 
     
    262262\begin{figure}[!t]    \begin{center} 
    263263\includegraphics[width=0.90\textwidth]{Fig_mpp} 
    264 \caption{   \label{Fig_mpp}  
     264\caption{   \protect\label{Fig_mpp}  
    265265Positioning of a sub-domain when massively parallel processing is used. } 
    266266\end{center}   \end{figure} 
     
    336336\begin{figure}[!ht]     \begin{center} 
    337337\includegraphics[width=0.90\textwidth]{Fig_mppini2} 
    338 \caption {    \label{Fig_mppini2} 
     338\caption {    \protect\label{Fig_mppini2} 
    339339Example of Atlantic domain defined for the CLIPPER projet. Initial grid is  
    340340composed of 773 x 1236 horizontal points.  
     
    567567\begin{figure}[!t]      \begin{center} 
    568568\includegraphics[width=1.0\textwidth]{Fig_LBC_bdy_geom} 
    569 \caption {      \label{Fig_LBC_bdy_geom} 
     569\caption {      \protect\label{Fig_LBC_bdy_geom} 
    570570Example of geometry of unstructured open boundary} 
    571571\end{center}   \end{figure} 
     
    608608\begin{figure}[!t]     \begin{center} 
    609609\includegraphics[width=1.0\textwidth]{Fig_LBC_nc_header} 
    610 \caption {     \label{Fig_LBC_nc_header}  
     610\caption {     \protect\label{Fig_LBC_nc_header}  
    611611Example of the header for a coordinates.bdy.nc file} 
    612612\end{center}   \end{figure} 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_LDF.tex

    r6997 r9363  
    3737% ================================================================ 
    3838\section  [Direction of Lateral Mixing (\textit{ldfslp})] 
    39       {Direction of Lateral Mixing (\mdl{ldfslp})} 
     39      {Direction of Lateral Mixing (\protect\mdl{ldfslp})} 
    4040\label{LDF_slp} 
    4141 
     
    231231\begin{figure}[!ht]      \begin{center} 
    232232\includegraphics[width=0.70\textwidth]{Fig_LDF_ZDF1} 
    233 \caption {    \label{Fig_LDF_ZDF1} 
     233\caption {    \protect\label{Fig_LDF_ZDF1} 
    234234averaging procedure for isopycnal slope computation.} 
    235235\end{center}    \end{figure} 
     
    259259\begin{figure}[!ht]     \begin{center} 
    260260\includegraphics[width=0.70\textwidth]{Fig_eiv_slp} 
    261 \caption {     \label{Fig_eiv_slp} 
     261\caption {     \protect\label{Fig_eiv_slp} 
    262262Vertical profile of the slope used for lateral mixing in the mixed layer :  
    263263\textit{(a)} in the real ocean the slope is the iso-neutral slope in the ocean interior,  
     
    307307% ================================================================ 
    308308\section [Lateral Mixing Operators (\textit{ldftra}, \textit{ldfdyn})]  
    309         {Lateral Mixing Operators (\mdl{traldf}, \mdl{traldf}) } 
     309        {Lateral Mixing Operators (\protect\mdl{traldf}, \protect\mdl{traldf}) } 
    310310\label{LDF_op} 
    311311 
     
    316316% ================================================================ 
    317317\section [Lateral Mixing Coefficient (\textit{ldftra}, \textit{ldfdyn})]  
    318         {Lateral Mixing Coefficient (\mdl{ldftra}, \mdl{ldfdyn}) } 
     318        {Lateral Mixing Coefficient (\protect\mdl{ldftra}, \protect\mdl{ldfdyn}) } 
    319319\label{LDF_coef} 
    320320 
     
    350350parameters. 
    351351 
    352 \subsubsection{Vertically varying Mixing Coefficients (\key{traldf\_c1d} and \key{dynldf\_c1d})}  
     352\subsubsection{Vertically varying Mixing Coefficients (\protect\key{traldf\_c1d} and \key{dynldf\_c1d})}  
    353353The 1D option is only available when using the $z$-coordinate with full step.  
    354354Indeed in all the other types of vertical coordinate, the depth is a 3D function  
     
    361361This profile is hard coded in file \hf{traldf\_c1d}, but can be easily modified by users. 
    362362 
    363 \subsubsection{Horizontally Varying Mixing Coefficients (\key{traldf\_c2d} and \key{dynldf\_c2d})} 
     363\subsubsection{Horizontally Varying Mixing Coefficients (\protect\key{traldf\_c2d} and \protect\key{dynldf\_c2d})} 
    364364By default the horizontal variation of the eddy coefficient depends on the local mesh  
    365365size and the type of operator used: 
     
    391391sub-domain options of ORCA2 and ORCA05 (see \&namcfg namelist). 
    392392 
    393 \subsubsection{Space Varying Mixing Coefficients (\key{traldf\_c3d} and \key{dynldf\_c3d})} 
     393\subsubsection{Space Varying Mixing Coefficients (\protect\key{traldf\_c3d} and \key{dynldf\_c3d})} 
    394394 
    395395The 3D space variation of the mixing coefficient is simply the combination of the  
     
    447447% ================================================================ 
    448448\section  [Eddy Induced Velocity (\textit{traadv\_eiv}, \textit{ldfeiv})] 
    449       {Eddy Induced Velocity (\mdl{traadv\_eiv}, \mdl{ldfeiv})} 
     449      {Eddy Induced Velocity (\protect\mdl{traadv\_eiv}, \protect\mdl{ldfeiv})} 
    450450\label{LDF_eiv} 
    451451 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_MISC.tex

    r9019 r9363  
    6464\includegraphics[width=0.80\textwidth]{Fig_Gibraltar} 
    6565\includegraphics[width=0.80\textwidth]{Fig_Gibraltar2} 
    66 \caption{   \label{Fig_MISC_strait_hand}  
     66\caption{   \protect\label{Fig_MISC_strait_hand}  
    6767Example of the Gibraltar strait defined in a $1^{\circ} \times 1^{\circ}$ mesh.  
    6868\textit{Top}: using partially open cells. The meridional scale factor at $v$-point  
     
    8080% Closed seas 
    8181% ================================================================ 
    82 \section{Closed seas (\mdl{closea})} 
     82\section{Closed seas (\protect\mdl{closea})} 
    8383\label{MISC_closea} 
    8484 
     
    151151\begin{figure}[!ht]    \begin{center} 
    152152\includegraphics[width=0.90\textwidth]{Fig_LBC_zoom} 
    153 \caption{   \label{Fig_LBC_zoom} 
     153\caption{   \protect\label{Fig_LBC_zoom} 
    154154Position of a model domain compared to the data input domain when the zoom functionality is used.} 
    155155\end{center}   \end{figure} 
     
    160160% Accuracy and Reproducibility 
    161161% ================================================================ 
    162 \section{Accuracy and Reproducibility (\mdl{lib\_fortran})} 
     162\section{Accuracy and Reproducibility (\protect\mdl{lib\_fortran})} 
    163163\label{MISC_fortran} 
    164164 
    165 \subsection{Issues with intrinsinc SIGN function (\key{nosignedzero})} 
     165\subsection{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})} 
    166166\label{MISC_sign} 
    167167 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

    r9347 r9363  
    117117\begin{figure}[!ht]   \begin{center} 
    118118\includegraphics[width=0.90\textwidth]{Fig_I_ocean_bc} 
    119 \caption{    \label{Fig_ocean_bc}  
     119\caption{    \protect\label{Fig_ocean_bc}  
    120120The ocean is bounded by two surfaces, $z=-H(i,j)$ and $z=\eta(i,j,t)$, where $H$  
    121121is the depth of the sea floor and $\eta$ the height of the sea surface.  
     
    315315\begin{figure}[!tb]   \begin{center} 
    316316\includegraphics[width=0.60\textwidth]{Fig_I_earth_referential} 
    317 \caption{   \label{Fig_referential}  
     317\caption{   \protect\label{Fig_referential}  
    318318the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear  
    319319coordinate system (\textbf{i},\textbf{j},\textbf{k}). } 
     
    810810\begin{figure}[!b]    \begin{center} 
    811811\includegraphics[width=1.0\textwidth]{Fig_z_zstar} 
    812 \caption{   \label{Fig_z_zstar}  
     812\caption{   \protect\label{Fig_z_zstar}  
    813813(a) $z$-coordinate in linear free-surface case ;  
    814814(b) $z-$coordinate in non-linear free surface case ;  
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex

    r6997 r9363  
    7575% Surface Pressure Gradient and Sea Surface Height 
    7676% ================================================================ 
    77 \section{Surface pressure gradient and Sea Surface Heigth (\mdl{dynspg})} 
     77\section{Surface pressure gradient and Sea Surface Heigth (\protect\mdl{dynspg})} 
    7878\label{DYN_hpg_spg} 
    7979%-----------------------------------------nam_dynspg---------------------------------------------------- 
     
    8686% Explicit 
    8787%------------------------------------------------------------- 
    88 \subsubsection{Explicit (\key{dynspg\_exp})} 
     88\subsubsection{Explicit (\protect\key{dynspg\_exp})} 
    8989\label{DYN_spg_exp} 
    9090 
     
    112112% Split-explicit time-stepping 
    113113%------------------------------------------------------------- 
    114 \subsubsection{Split-explicit time-stepping (\key{dynspg\_ts})} 
     114\subsubsection{Split-explicit time-stepping (\protect\key{dynspg\_ts})} 
    115115\label{DYN_spg_ts} 
    116116%--------------------------------------------namdom---------------------------------------------------- 
     
    124124\begin{figure}[!t]   \begin{center} 
    125125\includegraphics[width=0.90\textwidth]{Fig_DYN_dynspg_ts} 
    126 \caption{    \label{Fig_DYN_dynspg_ts} 
     126\caption{    \protect\label{Fig_DYN_dynspg_ts} 
    127127Schematic of the split-explicit time stepping scheme for the barotropic and baroclinic modes,  
    128128after \citet{Griffies2004}. Time increases to the right. Baroclinic time steps are denoted by  
     
    241241% Filtered formulation  
    242242%------------------------------------------------------------- 
    243 \subsubsection{Filtered formulation (\key{dynspg\_flt})} 
     243\subsubsection{Filtered formulation (\protect\key{dynspg\_flt})} 
    244244\label{DYN_spg_flt} 
    245245 
     
    252252% Non-linear free surface formulation  
    253253%------------------------------------------------------------- 
    254 \subsection{Non-linear free surface formulation (\key{vvl})} 
     254\subsection{Non-linear free surface formulation (\protect\key{vvl})} 
    255255\label{DYN_spg_vvl} 
    256256 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_OBS.tex

    r9350 r9363  
    700700\begin{figure}      \begin{center} 
    701701\includegraphics[width=0.90\textwidth]{Fig_OBS_avg_rec} 
    702 \caption{      \label{fig:obsavgrec} 
     702\caption{      \protect\label{fig:obsavgrec} 
    703703Weights associated with each model grid box (blue lines and numbers) for an observation at -170.5E, 56.0N with a rectangular footprint of 1\deg x 1\deg.} 
    704704\end{center}      \end{figure} 
     
    708708\begin{figure}      \begin{center} 
    709709\includegraphics[width=0.90\textwidth]{Fig_OBS_avg_rad} 
    710 \caption{      \label{fig:obsavgrad} 
     710\caption{      \protect\label{fig:obsavgrad} 
    711711Weights associated with each model grid box (blue lines and numbers) for an observation at -170.5E, 56.0N with a radial footprint with diameter 1\deg.}  
    712712\end{center}      \end{figure} 
     
    800800\begin{figure}      \begin{center} 
    801801\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_local} 
    802 \caption{      \label{fig:obslocal} 
     802\caption{      \protect\label{fig:obslocal} 
    803803Example of the distribution of observations with the geographical distribution of observational data.}  
    804804\end{center}      \end{figure} 
     
    827827\begin{figure}     \begin{center} 
    828828\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_global} 
    829 \caption{      \label{fig:obsglobal} 
     829\caption{      \protect\label{fig:obsglobal} 
    830830Example of the distribution of observations with the round-robin distribution of observational data.} 
    831831\end{center}     \end{figure} 
     
    14451445%\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_main} 
    14461446\includegraphics[width=9cm,angle=-90.]{Fig_OBS_dataplot_main} 
    1447 \caption{      \label{fig:obsdataplotmain} 
     1447\caption{      \protect\label{fig:obsdataplotmain} 
    14481448Main window of dataplot.} 
    14491449\end{center}     \end{figure} 
     
    14571457%\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_prof} 
    14581458\includegraphics[width=7cm,angle=-90.]{Fig_OBS_dataplot_prof} 
    1459 \caption{      \label{fig:obsdataplotprofile} 
     1459\caption{      \protect\label{fig:obsdataplotprofile} 
    14601460Profile plot from dataplot produced by right clicking on a point in the main window.} 
    14611461\end{center}     \end{figure} 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_SBC.tex

    r9345 r9363  
    144144Sea surface salinty              & sss\_m & $psu$        & T \\   \hline 
    145145\end{tabular} 
    146 \caption{  \label{Tab_ssm}    
     146\caption{  \protect\label{Tab_ssm}    
    147147Ocean variables provided by the ocean to the surface module (SBC).  
    148148The variable are averaged over nn{\_}fsbc time step,  
     
    192192% Input Data specification (\mdl{fldread}) 
    193193% ------------------------------------------------------------------------------------------------------------- 
    194 \subsection{Input Data specification (\mdl{fldread})} 
     194\subsection{Input Data specification (\protect\mdl{fldread})} 
    195195\label{SBC_fldread} 
    196196 
     
    220220\end{tabular} 
    221221\end{center} 
    222 \caption{ \label{Tab_fldread}   naming nomenclature for climatological or interannual input file,  
     222\caption{ \protect\label{Tab_fldread}   naming nomenclature for climatological or interannual input file,  
    223223as a function of the Open/close frequency. The stem name is assumed to be 'fn'.  
    224224For weekly files, the 'LLL' corresponds to the first three letters of the first day of the week ($i.e.$ 'sun','sat','fri','thu','wed','tue','mon'). The 'YYYY', 'MM' and 'DD' should be replaced by the  
     
    484484% ================================================================ 
    485485\section  [Analytical formulation (\textit{sbcana}) ] 
    486       {Analytical formulation (\mdl{sbcana} module) } 
     486      {Analytical formulation (\protect\mdl{sbcana} module) } 
    487487\label{SBC_ana} 
    488488 
     
    509509% ================================================================ 
    510510\section  [Flux formulation (\textit{sbcflx}) ] 
    511       {Flux formulation (\mdl{sbcflx} module) } 
     511      {Flux formulation (\protect\mdl{sbcflx} module) } 
    512512\label{SBC_flx} 
    513513%------------------------------------------namsbc_flx---------------------------------------------------- 
     
    531531% ================================================================ 
    532532\section  [Bulk formulation (\textit{sbcblk\_core}, \textit{sbcblk\_clio} or \textit{sbcblk\_mfs}) ] 
    533       {Bulk formulation \small{(\mdl{sbcblk\_core} \mdl{sbcblk\_clio} \mdl{sbcblk\_mfs} modules)} } 
     533      {Bulk formulation \small{(\protect\mdl{sbcblk\_core} \protect\mdl{sbcblk\_clio} \protect\mdl{sbcblk\_mfs} modules)} } 
    534534\label{SBC_blk} 
    535535 
     
    548548%        CORE Bulk formulea 
    549549% ------------------------------------------------------------------------------------------------------------- 
    550 \subsection    [CORE Bulk formulea (\np{ln\_core}=true)] 
    551             {CORE Bulk formulea (\np{ln\_core}=true, \mdl{sbcblk\_core})} 
     550\subsection    [CORE Bulk formulea (\protect\np{ln\_core}=true)] 
     551            {CORE Bulk formulea (\protect\np{ln\_core}=true, \protect\mdl{sbcblk\_core})} 
    552552\label{SBC_blk_core} 
    553553%------------------------------------------namsbc_core---------------------------------------------------- 
     
    613613%        CLIO Bulk formulea 
    614614% ------------------------------------------------------------------------------------------------------------- 
    615 \subsection    [CLIO Bulk formulea (\np{ln\_clio}=true)] 
    616             {CLIO Bulk formulea (\np{ln\_clio}=true, \mdl{sbcblk\_clio})} 
     615\subsection    [CLIO Bulk formulea (\protect\np{ln\_clio}=true)] 
     616            {CLIO Bulk formulea (\protect\np{ln\_clio}=true, \protect\mdl{sbcblk\_clio})} 
    617617\label{SBC_blk_clio} 
    618618%------------------------------------------namsbc_clio---------------------------------------------------- 
     
    654654%        MFS Bulk formulae 
    655655% ------------------------------------------------------------------------------------------------------------- 
    656 \subsection    [MFS Bulk formulea (\np{ln\_mfs}=true)] 
    657             {MFS Bulk formulea (\np{ln\_mfs}=true, \mdl{sbcblk\_mfs})} 
     656\subsection    [MFS Bulk formulea (\protect\np{ln\_mfs}=true)] 
     657            {MFS Bulk formulea (\protect\np{ln\_mfs}=true, \protect\mdl{sbcblk\_mfs})} 
    658658\label{SBC_blk_mfs} 
    659659%------------------------------------------namsbc_mfs---------------------------------------------------- 
     
    694694% ================================================================ 
    695695\section  [Coupled formulation (\textit{sbccpl}) ] 
    696       {Coupled formulation (\mdl{sbccpl} module)} 
     696      {Coupled formulation (\protect\mdl{sbccpl} module)} 
    697697\label{SBC_cpl} 
    698698%------------------------------------------namsbc_cpl---------------------------------------------------- 
     
    733733% ================================================================ 
    734734\section   [Atmospheric pressure (\textit{sbcapr})] 
    735          {Atmospheric pressure (\mdl{sbcapr})} 
     735         {Atmospheric pressure (\protect\mdl{sbcapr})} 
    736736\label{SBC_apr} 
    737737%------------------------------------------namsbc_apr---------------------------------------------------- 
     
    768768% ================================================================ 
    769769\section   [Tidal Potential (\textit{sbctide})] 
    770                         {Tidal Potential (\mdl{sbctide})} 
     770                        {Tidal Potential (\protect\mdl{sbctide})} 
    771771\label{SBC_tide} 
    772772 
     
    824824% ================================================================ 
    825825\section   [River runoffs (\textit{sbcrnf})] 
    826          {River runoffs (\mdl{sbcrnf})} 
     826         {River runoffs (\protect\mdl{sbcrnf})} 
    827827\label{SBC_rnf} 
    828828%------------------------------------------namsbc_rnf---------------------------------------------------- 
     
    940940% ================================================================ 
    941941\section   [Ice shelf melting (\textit{sbcisf})] 
    942                         {Ice shelf melting (\mdl{sbcisf})} 
     942                        {Ice shelf melting (\protect\mdl{sbcisf})} 
    943943\label{SBC_isf} 
    944944%------------------------------------------namsbc_isf---------------------------------------------------- 
     
    11311131% ------------------------------------------------------------------------------------------------------------- 
    11321132\subsection   [Diurnal  cycle (\textit{sbcdcy})] 
    1133          {Diurnal cycle (\mdl{sbcdcy})} 
     1133         {Diurnal cycle (\protect\mdl{sbcdcy})} 
    11341134\label{SBC_dcy} 
    11351135%------------------------------------------namsbc_rnf---------------------------------------------------- 
     
    11401140\begin{figure}[!t]    \begin{center} 
    11411141\includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal} 
    1142 \caption{ \label{Fig_SBC_diurnal}     
     1142\caption{ \protect\label{Fig_SBC_diurnal}     
    11431143Example of recontruction of the diurnal cycle variation of short wave flux   
    11441144from daily mean values. The reconstructed diurnal cycle (black line) is chosen  
     
    11731173\begin{figure}[!t]  \begin{center} 
    11741174\includegraphics[width=0.7\textwidth]{Fig_SBC_dcy} 
    1175 \caption{ \label{Fig_SBC_dcy}    
     1175\caption{ \protect\label{Fig_SBC_dcy}    
    11761176Example of recontruction of the diurnal cycle variation of short wave flux   
    11771177from daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm).  
     
    12081208% ------------------------------------------------------------------------------------------------------------- 
    12091209\subsection    [Surface restoring to observed SST and/or SSS (\textit{sbcssr})] 
    1210          {Surface restoring to observed SST and/or SSS (\mdl{sbcssr})} 
     1210         {Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})} 
    12111211\label{SBC_ssr} 
    12121212%------------------------------------------namsbc_ssr---------------------------------------------------- 
     
    12781278 
    12791279\subsection   [Interface to CICE (\textit{sbcice\_cice})] 
    1280          {Interface to CICE (\mdl{sbcice\_cice})} 
     1280         {Interface to CICE (\protect\mdl{sbcice\_cice})} 
    12811281\label{SBC_cice} 
    12821282 
     
    13061306% ------------------------------------------------------------------------------------------------------------- 
    13071307\subsection   [Freshwater budget control (\textit{sbcfwb})] 
    1308          {Freshwater budget control (\mdl{sbcfwb})} 
     1308         {Freshwater budget control (\protect\mdl{sbcfwb})} 
    13091309\label{SBC_fwb} 
    13101310 
     
    13281328% ------------------------------------------------------------------------------------------------------------- 
    13291329\subsection   [Neutral drag coefficient from external wave model (\textit{sbcwave})] 
    1330               {Neutral drag coefficient from external wave model (\mdl{sbcwave})} 
     1330              {Neutral drag coefficient from external wave model (\protect\mdl{sbcwave})} 
    13311331\label{SBC_wave} 
    13321332%------------------------------------------namwave---------------------------------------------------- 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_STP.tex

    r9360 r9363  
    207207\begin{figure}[!t]     \begin{center} 
    208208\includegraphics[width=0.7\textwidth]{Fig_TimeStepping_flowchart} 
    209 \caption{   \label{Fig_TimeStep_flowchart} 
     209\caption{   \protect\label{Fig_TimeStep_flowchart} 
    210210Sketch of the leapfrog time stepping sequence in \NEMO from \citet{Leclair_Madec_OM09}.  
    211211The use of a semi-implicit computation of the hydrostatic pressure gradient requires 
     
    269269\begin{figure}[!t]     \begin{center} 
    270270\includegraphics[width=0.90\textwidth]{Fig_MLF_forcing} 
    271 \caption{   \label{Fig_MLF_forcing} 
     271\caption{   \protect\label{Fig_MLF_forcing} 
    272272Illustration of forcing integration methods.  
    273273(top) ''Traditional'' formulation : the forcing is defined at the same time as the variable  
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_TRA.tex

    r9350 r9363  
    6464% ================================================================ 
    6565\section  [Tracer Advection (\textit{traadv})] 
    66       {Tracer Advection (\mdl{traadv})} 
     66      {Tracer Advection (\protect\mdl{traadv})} 
    6767\label{TRA_adv} 
    6868%------------------------------------------namtra_adv----------------------------------------------------- 
     
    9393\begin{figure}[!t]    \begin{center} 
    9494\includegraphics[width=0.9\textwidth]{Fig_adv_scheme} 
    95 \caption{   \label{Fig_adv_scheme}  
     95\caption{   \protect\label{Fig_adv_scheme}  
    9696Schematic representation of some ways used to evaluate the tracer value  
    9797at $u$-point and the amount of tracer exchanged between two neighbouring grid  
     
    174174%        2nd and 4th order centred schemes 
    175175% ------------------------------------------------------------------------------------------------------------- 
    176 \subsection [Centred schemes (CEN) (\np{ln\_traadv\_cen})] 
    177             {Centred schemes (CEN) (\np{ln\_traadv\_cen}=true)} 
     176\subsection [Centred schemes (CEN) (\protect\np{ln\_traadv\_cen})] 
     177            {Centred schemes (CEN) (\protect\np{ln\_traadv\_cen}=true)} 
    178178\label{TRA_adv_cen} 
    179179 
     
    246246%        FCT scheme   
    247247% ------------------------------------------------------------------------------------------------------------- 
    248 \subsection   [Flux Corrected Transport schemes (FCT) (\np{ln\_traadv\_fct})] 
    249          {Flux Corrected Transport schemes (FCT) (\np{ln\_traadv\_fct}=true)} 
     248\subsection   [Flux Corrected Transport schemes (FCT) (\protect\np{ln\_traadv\_fct})] 
     249         {Flux Corrected Transport schemes (FCT) (\protect\np{ln\_traadv\_fct}=true)} 
    250250\label{TRA_adv_tvd} 
    251251 
     
    293293%        MUSCL scheme   
    294294% ------------------------------------------------------------------------------------------------------------- 
    295 \subsection[MUSCL scheme  (\np{ln\_traadv\_mus})] 
    296    {Monotone Upstream Scheme for Conservative Laws (MUSCL) (\np{ln\_traadv\_mus}=T)} 
     295\subsection[MUSCL scheme  (\protect\np{ln\_traadv\_mus})] 
     296   {Monotone Upstream Scheme for Conservative Laws (MUSCL) (\protect\np{ln\_traadv\_mus}=T)} 
    297297\label{TRA_adv_mus} 
    298298 
     
    326326%        UBS scheme   
    327327% ------------------------------------------------------------------------------------------------------------- 
    328 \subsection   [Upstream-Biased Scheme (UBS) (\np{ln\_traadv\_ubs})] 
    329          {Upstream-Biased Scheme (UBS) (\np{ln\_traadv\_ubs}=true)} 
     328\subsection   [Upstream-Biased Scheme (UBS) (\protect\np{ln\_traadv\_ubs})] 
     329         {Upstream-Biased Scheme (UBS) (\protect\np{ln\_traadv\_ubs}=true)} 
    330330\label{TRA_adv_ubs} 
    331331 
     
    401401%        QCK scheme   
    402402% ------------------------------------------------------------------------------------------------------------- 
    403 \subsection   [QUICKEST scheme (QCK) (\np{ln\_traadv\_qck})] 
    404          {QUICKEST scheme (QCK) (\np{ln\_traadv\_qck}=true)} 
     403\subsection   [QUICKEST scheme (QCK) (\protect\np{ln\_traadv\_qck})] 
     404         {QUICKEST scheme (QCK) (\protect\np{ln\_traadv\_qck}=true)} 
    405405\label{TRA_adv_qck} 
    406406 
     
    429429% ================================================================ 
    430430\section  [Tracer Lateral Diffusion (\textit{traldf})] 
    431       {Tracer Lateral Diffusion (\mdl{traldf})} 
     431      {Tracer Lateral Diffusion (\protect\mdl{traldf})} 
    432432\label{TRA_ldf} 
    433433%-----------------------------------------nam_traldf------------------------------------------------------ 
     
    455455%        Type of operator 
    456456% ------------------------------------------------------------------------------------------------------------- 
    457 \subsection   [Type of operator (\np{ln\_traldf\{\_NONE, \_lap, \_blp\}})] 
    458               {Type of operator (\np{ln\_traldf\_NONE}, \np{ln\_traldf\_lap}, or \np{ln\_traldf\_blp} = true) }  
     457\subsection   [Type of operator (\protect\np{ln\_traldf\{\_NONE, \_lap, \_blp\}})] 
     458              {Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp} = true) }  
    459459\label{TRA_ldf_op} 
    460460 
     
    488488%        Direction of action 
    489489% ------------------------------------------------------------------------------------------------------------- 
    490 \subsection   [Direction of action (\np{ln\_traldf\{\_lev, \_hor, \_iso, \_triad\}})] 
    491               {Direction of action (\np{ln\_traldf\_lev}, \textit{...\_hor}, \textit{...\_iso}, or \textit{...\_triad} = true) }  
     490\subsection   [Direction of action (\protect\np{ln\_traldf\{\_lev, \_hor, \_iso, \_triad\}})] 
     491              {Direction of action (\protect\np{ln\_traldf\_lev}, \textit{...\_hor}, \textit{...\_iso}, or \textit{...\_triad} = true) }  
    492492\label{TRA_ldf_dir} 
    493493 
     
    515515%       iso-level operator 
    516516% ------------------------------------------------------------------------------------------------------------- 
    517 \subsection   [Iso-level (bi-)laplacian operator ( \np{ln\_traldf\_iso})] 
    518          {Iso-level (bi-)laplacian operator ( \np{ln\_traldf\_iso}) } 
     517\subsection   [Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})] 
     518         {Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso}) } 
    519519\label{TRA_ldf_lev} 
    520520 
     
    555555%&&    Standard rotated (bi-)laplacian operator 
    556556%&& ---------------------------------------------- 
    557 \subsubsection   [Standard rotated (bi-)laplacian operator (\mdl{traldf\_iso})] 
    558                  {Standard rotated (bi-)laplacian operator (\mdl{traldf\_iso})} 
     557\subsubsection   [Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})] 
     558                 {Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})} 
    559559\label{TRA_ldf_iso} 
    560560The general form of the second order lateral tracer subgrid scale physics  
     
    609609%&&     Triad rotated (bi-)laplacian operator 
    610610%&&  ------------------------------------------- 
    611 \subsubsection   [Triad rotated (bi-)laplacian operator (\np{ln\_traldf\_triad})] 
    612                  {Triad rotated (bi-)laplacian operator (\np{ln\_traldf\_triad})} 
     611\subsubsection   [Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})] 
     612                 {Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})} 
    613613\label{TRA_ldf_triad} 
    614614 
     
    649649% ================================================================ 
    650650\section  [Tracer Vertical Diffusion (\textit{trazdf})] 
    651       {Tracer Vertical Diffusion (\mdl{trazdf})} 
     651      {Tracer Vertical Diffusion (\protect\mdl{trazdf})} 
    652652\label{TRA_zdf} 
    653653%--------------------------------------------namzdf--------------------------------------------------------- 
     
    703703% ------------------------------------------------------------------------------------------------------------- 
    704704\subsection   [Surface boundary condition (\textit{trasbc})] 
    705          {Surface boundary condition (\mdl{trasbc})} 
     705         {Surface boundary condition (\protect\mdl{trasbc})} 
    706706\label{TRA_sbc} 
    707707 
     
    774774% ------------------------------------------------------------------------------------------------------------- 
    775775\subsection   [Solar Radiation Penetration (\textit{traqsr})] 
    776          {Solar Radiation Penetration (\mdl{traqsr})} 
     776         {Solar Radiation Penetration (\protect\mdl{traqsr})} 
    777777\label{TRA_qsr} 
    778778%--------------------------------------------namqsr-------------------------------------------------------- 
     
    872872\begin{figure}[!t]     \begin{center} 
    873873\includegraphics[width=1.0\textwidth]{Fig_TRA_Irradiance} 
    874 \caption{    \label{Fig_traqsr_irradiance} 
     874\caption{    \protect\label{Fig_traqsr_irradiance} 
    875875Penetration profile of the downward solar irradiance calculated by four models.  
    876876Two waveband chlorophyll-independent formulation (blue), a chlorophyll-dependent  
     
    885885% ------------------------------------------------------------------------------------------------------------- 
    886886\subsection   [Bottom Boundary Condition (\textit{trabbc})] 
    887          {Bottom Boundary Condition (\mdl{trabbc})} 
     887         {Bottom Boundary Condition (\protect\mdl{trabbc})} 
    888888\label{TRA_bbc} 
    889889%--------------------------------------------nambbc-------------------------------------------------------- 
     
    893893\begin{figure}[!t]     \begin{center} 
    894894\includegraphics[width=1.0\textwidth]{Fig_TRA_geoth} 
    895 \caption{   \label{Fig_geothermal} 
     895\caption{   \protect\label{Fig_geothermal} 
    896896Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{Emile-Geay_Madec_OS09}. 
    897897It is inferred from the age of the sea floor and the formulae of \citet{Stein_Stein_Nat92}.} 
     
    923923% Bottom Boundary Layer 
    924924% ================================================================ 
    925 \section  [Bottom Boundary Layer (\mdl{trabbl} - \key{trabbl})] 
    926       {Bottom Boundary Layer (\mdl{trabbl} - \key{trabbl})} 
     925\section  [Bottom Boundary Layer (\protect\mdl{trabbl} - \protect\key{trabbl})] 
     926      {Bottom Boundary Layer (\protect\mdl{trabbl} - \protect\key{trabbl})} 
    927927\label{TRA_bbl} 
    928928%--------------------------------------------nambbl--------------------------------------------------------- 
     
    959959%        Diffusive BBL 
    960960% ------------------------------------------------------------------------------------------------------------- 
    961 \subsection{Diffusive Bottom Boundary layer (\np{nn\_bbl\_ldf}=1)} 
     961\subsection{Diffusive Bottom Boundary layer (\protect\np{nn\_bbl\_ldf}=1)} 
    962962\label{TRA_bbl_diff} 
    963963 
     
    994994%        Advective BBL 
    995995% ------------------------------------------------------------------------------------------------------------- 
    996 \subsection   {Advective Bottom Boundary Layer  (\np{nn\_bbl\_adv}= 1 or 2)} 
     996\subsection   {Advective Bottom Boundary Layer  (\protect\np{nn\_bbl\_adv}= 1 or 2)} 
    997997\label{TRA_bbl_adv} 
    998998 
     
    10031003\begin{figure}[!t]   \begin{center} 
    10041004\includegraphics[width=0.7\textwidth]{Fig_BBL_adv} 
    1005 \caption{   \label{Fig_bbl}   
     1005\caption{   \protect\label{Fig_bbl}   
    10061006Advective/diffusive Bottom Boundary Layer. The BBL parameterisation is  
    10071007activated when $\rho^i_{kup}$ is larger than $\rho^{i+1}_{kdnw}$.  
     
    10841084% ================================================================ 
    10851085\section  [Tracer damping (\textit{tradmp})] 
    1086       {Tracer damping (\mdl{tradmp})} 
     1086      {Tracer damping (\protect\mdl{tradmp})} 
    10871087\label{TRA_dmp} 
    10881088%--------------------------------------------namtra_dmp------------------------------------------------- 
     
    11691169% ================================================================ 
    11701170\section  [Tracer time evolution (\textit{tranxt})] 
    1171       {Tracer time evolution (\mdl{tranxt})} 
     1171      {Tracer time evolution (\protect\mdl{tranxt})} 
    11721172\label{TRA_nxt} 
    11731173%--------------------------------------------namdom----------------------------------------------------- 
     
    12081208% ================================================================ 
    12091209\section  [Equation of State (\textit{eosbn2}) ] 
    1210       {Equation of State (\mdl{eosbn2}) } 
     1210      {Equation of State (\protect\mdl{eosbn2}) } 
    12111211\label{TRA_eosbn2} 
    12121212%--------------------------------------------nameos----------------------------------------------------- 
     
    12171217%        Equation of State 
    12181218% ------------------------------------------------------------------------------------------------------------- 
    1219 \subsection{Equation Of Seawater (\np{nn\_eos} = -1, 0, or 1)} 
     1219\subsection{Equation Of Seawater (\protect\np{nn\_eos} = -1, 0, or 1)} 
    12201220\label{TRA_eos} 
    12211221 
     
    13231323$\mu_2$     & \np{rn\_mu2}    & 1.1090 $10^{-5}$ &  thermobaric coeff. in S            \\ \hline 
    13241324\end{tabular} 
    1325 \caption{ \label{Tab_SEOS} 
     1325\caption{ \protect\label{Tab_SEOS} 
    13261326Standard value of S-EOS coefficients. } 
    13271327\end{center} 
     
    13331333%        Brunt-V\"{a}is\"{a}l\"{a} Frequency 
    13341334% ------------------------------------------------------------------------------------------------------------- 
    1335 \subsection{Brunt-V\"{a}is\"{a}l\"{a} Frequency (\np{nn\_eos} = 0, 1 or 2)} 
     1335\subsection{Brunt-V\"{a}is\"{a}l\"{a} Frequency (\protect\np{nn\_eos} = 0, 1 or 2)} 
    13361336\label{TRA_bn2} 
    13371337 
     
    13891389% ================================================================ 
    13901390\section  [Horizontal Derivative in \textit{zps}-coordinate (\textit{zpshde})] 
    1391       {Horizontal Derivative in \textit{zps}-coordinate (\mdl{zpshde})} 
     1391      {Horizontal Derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})} 
    13921392\label{TRA_zpshde} 
    13931393 
     
    14111411\begin{figure}[!p]    \begin{center} 
    14121412\includegraphics[width=0.9\textwidth]{Partial_step_scheme} 
    1413 \caption{   \label{Fig_Partial_step_scheme}  
     1413\caption{   \protect\label{Fig_Partial_step_scheme}  
    14141414Discretisation of the horizontal difference and average of tracers in the $z$-partial  
    1415 step coordinate (\np{ln\_zps}=true) in the case $( e3w_k^{i+1} - e3w_k^i  )>0$.  
     1415step coordinate (\protect\np{ln\_zps}=true) in the case $( e3w_k^{i+1} - e3w_k^i  )>0$.  
    14161416A linear interpolation is used to estimate $\widetilde{T}_k^{i+1}$, the tracer value  
    14171417at the depth of the shallower tracer point of the two adjacent bottom $T$-points.  
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_ZDF.tex

    r9350 r9363  
    4949%        Constant  
    5050% ------------------------------------------------------------------------------------------------------------- 
    51 \subsection{Constant (\key{zdfcst})} 
     51\subsection{Constant (\protect\key{zdfcst})} 
    5252\label{ZDF_cst} 
    5353%--------------------------------------------namzdf--------------------------------------------------------- 
     
    7474%        Richardson Number Dependent 
    7575% ------------------------------------------------------------------------------------------------------------- 
    76 \subsection{Richardson Number Dependent (\key{zdfric})} 
     76\subsection{Richardson Number Dependent (\protect\key{zdfric})} 
    7777\label{ZDF_ric} 
    7878 
     
    132132%        TKE Turbulent Closure Scheme  
    133133% ------------------------------------------------------------------------------------------------------------- 
    134 \subsection{TKE Turbulent Closure Scheme (\key{zdftke})} 
     134\subsection{TKE Turbulent Closure Scheme (\protect\key{zdftke})} 
    135135\label{ZDF_tke} 
    136136 
     
    237237\begin{figure}[!t] \begin{center} 
    238238\includegraphics[width=1.00\textwidth]{Fig_mixing_length} 
    239 \caption{ \label{Fig_mixing_length}  
     239\caption{ \protect\label{Fig_mixing_length}  
    240240Illustration of the mixing length computation. } 
    241241\end{center}   
     
    405405%        TKE discretization considerations 
    406406% ------------------------------------------------------------------------------------------------------------- 
    407 \subsection{TKE discretization considerations (\key{zdftke})} 
     407\subsection{TKE discretization considerations (\protect\key{zdftke})} 
    408408\label{ZDF_tke_ene} 
    409409 
     
    411411\begin{figure}[!t]   \begin{center} 
    412412\includegraphics[width=1.00\textwidth]{Fig_ZDF_TKE_time_scheme} 
    413 \caption{ \label{Fig_TKE_time_scheme}  
     413\caption{ \protect\label{Fig_TKE_time_scheme}  
    414414Illustration of the TKE time integration and its links to the momentum and tracer time integration. } 
    415415\end{center}   
     
    508508%        GLS Generic Length Scale Scheme  
    509509% ------------------------------------------------------------------------------------------------------------- 
    510 \subsection{GLS Generic Length Scale (\key{zdfgls})} 
     510\subsection{GLS Generic Length Scale (\protect\key{zdfgls})} 
    511511\label{ZDF_gls} 
    512512 
     
    579579\hline 
    580580\end{tabular} 
    581 \caption{   \label{Tab_GLS}  
     581\caption{   \protect\label{Tab_GLS}  
    582582Set of predefined GLS parameters, or equivalently predefined turbulence models available  
    583 with \key{zdfgls} and controlled by the \np{nn\_clos} namelist variable in \ngn{namzdf\_gls} .} 
     583with \protect\key{zdfgls} and controlled by the \protect\np{nn\_clos} namelist variable in \protect\ngn{namzdf\_gls} .} 
    584584\end{center}   \end{table} 
    585585%-------------------------------------------------------------------------------------------------------------- 
     
    615615%        OSM OSMOSIS BL Scheme  
    616616% ------------------------------------------------------------------------------------------------------------- 
    617 \subsection{OSM OSMOSIS Boundary Layer scheme (\key{zdfosm})} 
     617\subsection{OSM OSMOSIS Boundary Layer scheme (\protect\key{zdfosm})} 
    618618\label{ZDF_osm} 
    619619 
     
    646646%       Non-Penetrative Convective Adjustment  
    647647% ------------------------------------------------------------------------------------------------------------- 
    648 \subsection   [Non-Penetrative Convective Adjustment (\np{ln\_tranpc}) ] 
    649          {Non-Penetrative Convective Adjustment (\np{ln\_tranpc}=.true.) } 
     648\subsection   [Non-Penetrative Convective Adjustment (\protect\np{ln\_tranpc}) ] 
     649         {Non-Penetrative Convective Adjustment (\protect\np{ln\_tranpc}=.true.) } 
    650650\label{ZDF_npc} 
    651651 
     
    657657\begin{figure}[!htb]    \begin{center} 
    658658\includegraphics[width=0.90\textwidth]{Fig_npc} 
    659 \caption{  \label{Fig_npc}  
     659\caption{  \protect\label{Fig_npc}  
    660660Example of an unstable density profile treated by the non penetrative  
    661661convective adjustment algorithm. $1^{st}$ step: the initial profile is checked from  
     
    713713%       Enhanced Vertical Diffusion  
    714714% ------------------------------------------------------------------------------------------------------------- 
    715 \subsection   [Enhanced Vertical Diffusion (\np{ln\_zdfevd})] 
    716               {Enhanced Vertical Diffusion (\np{ln\_zdfevd}=true)} 
     715\subsection   [Enhanced Vertical Diffusion (\protect\np{ln\_zdfevd})] 
     716              {Enhanced Vertical Diffusion (\protect\np{ln\_zdfevd}=true)} 
    717717\label{ZDF_evd} 
    718718 
     
    745745%       Turbulent Closure Scheme  
    746746% ------------------------------------------------------------------------------------------------------------- 
    747 \subsection[Turbulent Closure Scheme (\key{zdf\{tke, gls, osm\}})]{Turbulent Closure Scheme (\key{zdftke}, \key{zdfgls} or \key{zdfosm})} 
     747\subsection[Turbulent Closure Scheme (\protect\key{zdf\{tke, gls, osm\}})]{Turbulent Closure Scheme (\protect\key{zdftke}, \protect\key{zdfgls} or \protect\key{zdfosm})} 
    748748\label{ZDF_tcs} 
    749749 
     
    772772% Double Diffusion Mixing 
    773773% ================================================================ 
    774 \section  [Double Diffusion Mixing (\key{zdfddm})] 
    775       {Double Diffusion Mixing (\key{zdfddm})} 
     774\section  [Double Diffusion Mixing (\protect\key{zdfddm})] 
     775      {Double Diffusion Mixing (\protect\key{zdfddm})} 
    776776\label{ZDF_ddm} 
    777777 
     
    813813\begin{figure}[!t]   \begin{center} 
    814814\includegraphics[width=0.99\textwidth]{Fig_zdfddm} 
    815 \caption{  \label{Fig_zdfddm} 
     815\caption{  \protect\label{Fig_zdfddm} 
    816816From \citet{Merryfield1999} : (a) Diapycnal diffusivities $A_f^{vT}$  
    817817and $A_f^{vS}$ for temperature and salt in regions of salt fingering. Heavy  
     
    855855% Bottom Friction 
    856856% ================================================================ 
    857 \section  [Bottom and Top Friction (\textit{zdfbfr})]   {Bottom and Top Friction (\mdl{zdfbfr} module)} 
     857\section  [Bottom and Top Friction (\textit{zdfbfr})]   {Bottom and Top Friction (\protect\mdl{zdfbfr} module)} 
    858858\label{ZDF_bfr} 
    859859 
     
    918918%       Linear Bottom Friction 
    919919% ------------------------------------------------------------------------------------------------------------- 
    920 \subsection{Linear Bottom Friction (\np{nn\_botfr} = 0 or 1) } 
     920\subsection{Linear Bottom Friction (\protect\np{nn\_botfr} = 0 or 1) } 
    921921\label{ZDF_bfr_linear} 
    922922 
     
    962962%       Non-Linear Bottom Friction 
    963963% ------------------------------------------------------------------------------------------------------------- 
    964 \subsection{Non-Linear Bottom Friction (\np{nn\_botfr} = 2)} 
     964\subsection{Non-Linear Bottom Friction (\protect\np{nn\_botfr} = 2)} 
    965965\label{ZDF_bfr_nonlinear} 
    966966 
     
    10031003%       Bottom Friction Log-layer 
    10041004% ------------------------------------------------------------------------------------------------------------- 
    1005 \subsection[Log-layer Bottom Friction enhancement (\np{ln\_loglayer} = .true.)]{Log-layer Bottom Friction enhancement (\np{nn\_botfr} = 2, \np{ln\_loglayer} = .true.)} 
     1005\subsection[Log-layer Bottom Friction enhancement (\protect\np{ln\_loglayer} = .true.)]{Log-layer Bottom Friction enhancement (\protect\np{nn\_botfr} = 2, \protect\np{ln\_loglayer} = .true.)} 
    10061006\label{ZDF_bfr_loglayer} 
    10071007 
     
    10821082%       Implicit Bottom Friction 
    10831083% ------------------------------------------------------------------------------------------------------------- 
    1084 \subsection[Implicit Bottom Friction (\np{ln\_bfrimp})]{Implicit Bottom Friction (\np{ln\_bfrimp}$=$\textit{T})} 
     1084\subsection[Implicit Bottom Friction (\protect\np{ln\_bfrimp})]{Implicit Bottom Friction (\protect\np{ln\_bfrimp}$=$\textit{T})} 
    10851085\label{ZDF_bfr_imp} 
    10861086 
     
    11351135%       Bottom Friction with split-explicit time splitting 
    11361136% ------------------------------------------------------------------------------------------------------------- 
    1137 \subsection[Bottom Friction with split-explicit time splitting]{Bottom Friction with split-explicit time splitting (\np{ln\_bfrimp})} 
     1137\subsection[Bottom Friction with split-explicit time splitting]{Bottom Friction with split-explicit time splitting (\protect\np{ln\_bfrimp})} 
    11381138\label{ZDF_bfr_ts} 
    11391139 
     
    11921192% Tidal Mixing 
    11931193% ================================================================ 
    1194 \section{Tidal Mixing (\key{zdftmx})} 
     1194\section{Tidal Mixing (\protect\key{zdftmx})} 
    11951195\label{ZDF_tmx} 
    11961196 
     
    12581258\begin{figure}[!t]   \begin{center} 
    12591259\includegraphics[width=0.90\textwidth]{Fig_ZDF_M2_K1_tmx} 
    1260 \caption{  \label{Fig_ZDF_M2_K1_tmx}  
     1260\caption{  \protect\label{Fig_ZDF_M2_K1_tmx}  
    12611261(a) M2 and (b) K1 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). } 
    12621262\end{center}   \end{figure} 
     
    12661266%        Indonesian area specific treatment  
    12671267% ------------------------------------------------------------------------------------------------------------- 
    1268 \subsection{Indonesian area specific treatment (\np{ln\_zdftmx\_itf})} 
     1268\subsection{Indonesian area specific treatment (\protect\np{ln\_zdftmx\_itf})} 
    12691269\label{ZDF_tmx_itf} 
    12701270 
     
    13141314% Internal wave-driven mixing 
    13151315% ================================================================ 
    1316 \section{Internal wave-driven mixing (\key{zdftmx\_new})} 
     1316\section{Internal wave-driven mixing (\protect\key{zdftmx\_new})} 
    13171317\label{ZDF_tmx_new} 
    13181318 
  • branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Introduction.tex

    r9360 r9363  
    155155\begin{table}[!t]  
    156156%\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline 
    157 \caption{ \label{Tab_chap}   Organization of Chapters mimicking the one of the model directories. } 
     157\caption{ \protect\label{Tab_chap}   Organization of Chapters mimicking the one of the model directories. } 
    158158\begin{center}    \begin{tabular}{|l|l|l|}   \hline 
    159159Chapter \ref{STP} & -                 & model time STePping environment \\    \hline 
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