Changeset 9363 for branches/2017

Timestamp:

2018-02-28T10:29:22+01:00 (6 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:

• Annex_C.tex (modified) (4 diffs)
• Annex_E.tex (modified) (2 diffs)
• Chap_CFG.tex (modified) (5 diffs)
• Chap_DIA.tex (modified) (11 diffs)
• Chap_DOM.tex (modified) (17 diffs)
• Chap_DYN.tex (modified) (30 diffs)
• Chap_LBC.tex (modified) (12 diffs)
• Chap_LDF.tex (modified) (9 diffs)
• Chap_MISC.tex (modified) (4 diffs)
• Chap_Model_Basics.tex (modified) (3 diffs)
• Chap_Model_Basics_zstar.tex (modified) (6 diffs)
• Chap_OBS.tex (modified) (6 diffs)
• Chap_SBC.tex (modified) (21 diffs)
• Chap_STP.tex (modified) (2 diffs)
• Chap_TRA.tex (modified) (31 diffs)
• Chap_ZDF.tex (modified) (25 diffs)
• Introduction.tex (modified) (1 diff)

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

@@ -363 +363 @@
 %       Vorticity Term with ENE scheme
 % -------------------------------------------------------------------------------------------------------------
-\subsubsection{Vorticity Term with ENE scheme (\np{ln\_dynvor\_ene}=.true.)}
+\subsubsection{Vorticity Term with ENE scheme (\protect\np{ln\_dynvor\_ene}=.true.)}
 \label{Apdx_C_vorENE} 
 
@@ -400 +400 @@
 %       Vorticity Term with EEN scheme
 % -------------------------------------------------------------------------------------------------------------
-\subsubsection{Vorticity Term with EEN scheme (\np{ln\_dynvor\_een}=.true.)}
+\subsubsection{Vorticity Term with EEN scheme (\protect\np{ln\_dynvor\_een}=.true.)}
 \label{Apdx_C_vorEEN} 
 
@@ -883 +883 @@
 %       Vorticity Term with ENS scheme
 % -------------------------------------------------------------------------------------------------------------
-\subsubsection{Vorticity Term with ENS scheme  (\np{ln\_dynvor\_ens}=.true.)}
+\subsubsection{Vorticity Term with ENS scheme  (\protect\np{ln\_dynvor\_ens}=.true.)}
 \label{Apdx_C_vorENS} 
 
@@ -943 +943 @@
 %       Vorticity Term with EEN scheme
 % -------------------------------------------------------------------------------------------------------------
-\subsubsection{Vorticity Term with EEN scheme (\np{ln\_dynvor\_een}=.true.)}
+\subsubsection{Vorticity Term with EEN scheme (\protect\np{ln\_dynvor\_een}=.true.)}
 \label{Apdx_C_vorEEN} 
 

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Annex_E.tex

@@ -19 +19 @@
 %        UBS scheme  
 % -------------------------------------------------------------------------------------------------------------
-\section{Upstream Biased Scheme (UBS) (\np{ln\_traadv\_ubs}=T)}
+\section{Upstream Biased Scheme (UBS) (\protect\np{ln\_traadv\_ubs}=T)}
 \label{TRA_adv_ubs}
 
@@ -302 +302 @@
 \begin{center}
 \includegraphics[width=0.70\textwidth]{Fig_ISO_triad}
-\caption{  \label{Fig_ISO_triad}   
+\caption{  \protect\label{Fig_ISO_triad}   
 Triads used in the Griffies's like iso-neutral diffision scheme for 
 $u$-component (upper panel) and $w$-component (lower panel).}

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_CFG.tex

@@ -32 +32 @@
 % 1D model configuration
 % ================================================================
-\section{Water column model: 1D model (C1D) (\key{c1d}) }
+\section{Water column model: 1D model (C1D) (\protect\key{c1d}) }
 \label{CFG_c1d}
 
@@ -95 +95 @@
 \begin{figure}[!t]   \begin{center}
 \includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh}
-\caption{  \label{Fig_MISC_ORCA_msh}     
+\caption{  \protect\label{Fig_MISC_ORCA_msh}     
 ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN.
 The two "north pole" are the foci of a series of embedded ellipses (blue curves) 
@@ -123 +123 @@
 \includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
 \includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso}
-\caption {  \label{Fig_MISC_ORCA_e1e2}
+\caption {  \protect\label{Fig_MISC_ORCA_e1e2}
 \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and 
 \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
@@ -175 +175 @@
 \hline   \hline
 \end{tabular}
-\caption{ \label{Tab_ORCA}   
+\caption{ \protect\label{Tab_ORCA}   
 Domain size of ORCA family configurations.
 The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file. }
@@ -267 +267 @@
 \begin{figure}[!t]   \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_GYRE}
-\caption{  \label{Fig_GYRE}   
+\caption{  \protect\label{Fig_GYRE}   
 Snapshot of relative vorticity at the surface of the model domain 
 in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.}

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_DIA.tex

@@ -1092 +1092 @@
 %       NetCDF4 support
 % ================================================================
-\section{NetCDF4 Support (\key{netcdf4})}
+\section{NetCDF4 Support (\protect\key{netcdf4})}
 \label{DIA_iom}
 
@@ -1198 +1198 @@
 ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\%\\
 \end{tabular}
-\caption{   \label{Tab_NC4} 
+\caption{   \protect\label{Tab_NC4} 
 Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression}
 \end{table}
@@ -1218 +1218 @@
 % -------------------------------------------------------------------------------------------------------------
 \section[Tracer/Dynamics Trends (TRD)]
-                  {Tracer/Dynamics Trends  (\ngn{namtrd})}
+                  {Tracer/Dynamics Trends  (\protect\ngn{namtrd})}
 \label{DIA_trd}
 
@@ -1258 +1258 @@
 %       On-line Floats trajectories
 % -------------------------------------------------------------------------------------------------------------
-\section{On-line Floats trajectories (FLO) (\key{floats})}
+\section{On-line Floats trajectories (FLO) (\protect\key{floats})}
 \label{FLO}
 %--------------------------------------------namflo-------------------------------------------------------
@@ -1371 +1371 @@
 %       Harmonic analysis of tidal constituents
 % -------------------------------------------------------------------------------------------------------------
-\section{Harmonic analysis of tidal constituents (\key{diaharm}) }
+\section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) }
 \label{DIA_diag_harm}
 
@@ -1413 +1413 @@
 %       Sections transports
 % -------------------------------------------------------------------------------------------------------------
-\section{Transports across sections (\key{diadct}) }
+\section{Transports across sections (\protect\key{diadct}) }
 \label{DIA_diag_dct}
 
@@ -1719 +1719 @@
 %       Other Diagnostics
 % -------------------------------------------------------------------------------------------------------------
-\section{Other Diagnostics (\key{diahth}, \key{diaar5})}
+\section{Other Diagnostics (\protect\key{diahth}, \protect\key{diaar5})}
 \label{DIA_diag_others}
 
@@ -1726 +1726 @@
 The available ready-to-add diagnostics modules can be found in directory DIA. 
 
-\subsection{Depth of various quantities (\mdl{diahth})}
+\subsection{Depth of various quantities (\protect\mdl{diahth})}
 
 Among the available diagnostics the following ones are obtained when defining 
@@ -1743 +1743 @@
 % -----------------------------------------------------------
 
-\subsection{Poleward heat and salt transports (\mdl{diaptr})}
+\subsection{Poleward heat and salt transports (\protect\mdl{diaptr})}
 
 %------------------------------------------namptr-----------------------------------------
@@ -1761 +1761 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_mask_subasins}
-\caption{   \label{Fig_mask_subasins}
+\caption{   \protect\label{Fig_mask_subasins}
 Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute
 the heat and salt transports as well as the meridional stream-function: Atlantic basin (red), 
@@ -1775 +1775 @@
 %       CMIP specific diagnostics 
 % -----------------------------------------------------------
-\subsection{CMIP specific diagnostics (\mdl{diaar5})}
+\subsection{CMIP specific diagnostics (\protect\mdl{diaar5})}
 
 A series of diagnostics has been added in the \mdl{diaar5}. 

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_DOM.tex

@@ -43 +43 @@
 \begin{figure}[!tb]    \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_cell}
-\caption{ \label{Fig_cell}    
+\caption{ \protect\label{Fig_cell}    
 Arrangement of variables. $t$ indicates scalar points where temperature, 
 salinity, density, pressure and horizontal divergence are defined. ($u$,$v$,$w$) 
@@ -95 +95 @@
 fw & $i+1/2$   & $j+1/2$   & $k+1/2$   \\ \hline
 \end{tabular}
-\caption{ \label{Tab_cell}
+\caption{ \protect\label{Tab_cell}
 Location of grid-points as a function of integer or integer and a half value of the column, 
 line or level. This indexing is only used for the writing of the semi-discrete equation. 
@@ -204 +204 @@
 \begin{figure}[!tb]  \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_index_hor}
-\caption{   \label{Fig_index_hor}    
+\caption{   \protect\label{Fig_index_hor}    
 Horizontal integer indexing used in the \textsc{Fortran} code. The dashed area indicates 
 the cell in which variables contained in arrays have the same $i$- and $j$-indices}
@@ -254 +254 @@
 \begin{figure}[!pt]    \begin{center}
 \includegraphics[width=.90\textwidth]{Fig_index_vert}
-\caption{ \label{Fig_index_vert}     
+\caption{ \protect\label{Fig_index_vert}     
 Vertical integer indexing used in the \textsc{Fortran } code. Note that 
 the $k$-axis is orientated downward. The dashed area indicates the cell in 
@@ -324 +324 @@
 % ================================================================
 \section  [Domain: Horizontal Grid (mesh) (\textit{domhgr})]               
-      {Domain: Horizontal Grid (mesh) \small{(\mdl{domhgr} module)} }
+      {Domain: Horizontal Grid (mesh) \small{(\protect\mdl{domhgr} module)} }
 \label{DOM_hgr}
 
@@ -388 +388 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_zgr_e3}
-\caption{ \label{Fig_zgr_e3}    
+\caption{ \protect\label{Fig_zgr_e3}    
 Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical, 
 and (b) analytically derived grid-point position and scale factors. 
@@ -428 +428 @@
 % ================================================================
 \section  [Domain: Vertical Grid (\textit{domzgr})]
-      {Domain: Vertical Grid \small{(\mdl{domzgr} module)} }
+      {Domain: Vertical Grid \small{(\protect\mdl{domzgr} module)} }
 \label{DOM_zgr}
 %-----------------------------------------nam_zgr & namdom-------------------------------------------
@@ -447 +447 @@
 \begin{figure}[!tb]    \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_z_zps_s_sps}
-\caption{  \label{Fig_z_zps_s_sps}   
+\caption{  \protect\label{Fig_z_zps_s_sps}   
 The ocean bottom as seen by the model: 
 (a) $z$-coordinate with full step, 
@@ -454 +454 @@
 (d) hybrid $s-z$ coordinate, 
 (e) hybrid $s-z$ coordinate with partial step, and 
-(f) same as (e) but in the non-linear free surface (\np{ln\_linssh}=false). 
+(f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}=false). 
 Note that the non-linear free surface can be used with any of the 
 5 coordinates (a) to (e).}
@@ -550 +550 @@
 %        z-coordinate  and reference coordinate transformation
 % -------------------------------------------------------------------------------------------------------------
-\subsection[$z$-coordinate (\np{ln\_zco}]
-        {$z$-coordinate (\np{ln\_zco}=true) and reference coordinate}
+\subsection[$z$-coordinate (\protect\np{ln\_zco}]
+        {$z$-coordinate (\protect\np{ln\_zco}=true) and reference coordinate}
 \label{DOM_zco}
 
@@ -557 +557 @@
 \begin{figure}[!tb]    \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_zgr}
-\caption{ \label{Fig_zgr}    
+\caption{ \protect\label{Fig_zgr}    
 Default vertical mesh for ORCA2: 30 ocean levels (L30). Vertical level functions for 
 (a) T-point depth and (b) the associated scale factor as computed 
@@ -679 +679 @@
 31 &  \textbf{5250.23}& 5000.00 &   \textbf{500.56} & 500.33 \\ \hline
 \end{tabular} \end{center} 
-\caption{ \label{Tab_orca_zgr}   
+\caption{ \protect\label{Tab_orca_zgr}   
 Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration as computed 
 from \eqref{DOM_zgr_ana} using the coefficients given in \eqref{DOM_zgr_coef}}
@@ -688 +688 @@
 %        z-coordinate with partial step
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [$z$-coordinate with partial step (\np{ln\_zps})]
-         {$z$-coordinate with partial step (\np{ln\_zps}=.true.)}
+\subsection   [$z$-coordinate with partial step (\protect\np{ln\_zps})]
+         {$z$-coordinate with partial step (\protect\np{ln\_zps}=.true.)}
 \label{DOM_zps}
 %--------------------------------------------namdom-------------------------------------------------------
@@ -721 +721 @@
 %        s-coordinate
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [$s$-coordinate (\np{ln\_sco})]
-           {$s$-coordinate (\np{ln\_sco}=true)}
+\subsection   [$s$-coordinate (\protect\np{ln\_sco})]
+           {$s$-coordinate (\protect\np{ln\_sco}=true)}
 \label{DOM_sco}
 %------------------------------------------nam_zgr_sco---------------------------------------------------
@@ -790 +790 @@
 \begin{figure}[!ht]    \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_sco_function}
-\caption{  \label{Fig_sco_function}   
+\caption{  \protect\label{Fig_sco_function}   
 Examples of the stretching function applied to a seamount; from left to right: 
 surface, surface and bottom, and bottom intensified resolutions}
@@ -850 +850 @@
 %        z*- or s*-coordinate
 % -------------------------------------------------------------------------------------------------------------
-\subsection{$z^*$- or $s^*$-coordinate (\np{ln\_linssh}=false) }
+\subsection{$z^*$- or $s^*$-coordinate (\protect\np{ln\_linssh}=false) }
 \label{DOM_zgr_star}
 
@@ -913 +913 @@
 % ================================================================
 \section  [Domain: Initial State (\textit{istate and dtatsd})]
-      {Domain: Initial State \small{(\mdl{istate} and \mdl{dtatsd} modules)} }
+      {Domain: Initial State \small{(\protect\mdl{istate} and \protect\mdl{dtatsd} modules)} }
 \label{DTA_tsd}
 %-----------------------------------------namtsd-------------------------------------------

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_DYN.tex

@@ -70 +70 @@
 %--------------------------------------------------------------------------------------------------------------
 \subsection   [Horizontal divergence and relative vorticity (\textit{divcur})]
-         {Horizontal divergence and relative vorticity (\mdl{divcur})}
+         {Horizontal divergence and relative vorticity (\protect\mdl{divcur})}
 \label{DYN_divcur}
 
@@ -103 +103 @@
 %--------------------------------------------------------------------------------------------------------------
 \subsection   [Sea surface height evolution and vertical velocity (\textit{sshwzv})]
-         {Horizontal divergence and relative vorticity (\mdl{sshwzv})}
+         {Horizontal divergence and relative vorticity (\protect\mdl{sshwzv})}
 \label{DYN_sshwzv}
 
@@ -179 +179 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Vorticity term (\textit{dynvor}) ]
-         {Vorticity term (\mdl{dynvor})}
+         {Vorticity term (\protect\mdl{dynvor})}
 \label{DYN_vor}
 %------------------------------------------nam_dynvor----------------------------------------------------
@@ -200 +200 @@
 %                 enstrophy conserving scheme
 %-------------------------------------------------------------
-\subsubsection{Enstrophy conserving scheme (\np{ln\_dynvor\_ens}=true)}
+\subsubsection{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}=true)}
 \label{DYN_vor_ens}
 
@@ -221 +221 @@
 %                 energy conserving scheme
 %-------------------------------------------------------------
-\subsubsection{Energy conserving scheme (\np{ln\_dynvor\_ene}=true)}
+\subsubsection{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}=true)}
 \label{DYN_vor_ene}
 
@@ -238 +238 @@
 %                 mix energy/enstrophy conserving scheme
 %-------------------------------------------------------------
-\subsubsection{Mixed energy/enstrophy conserving scheme (\np{ln\_dynvor\_mix}=true) }
+\subsubsection{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}=true) }
 \label{DYN_vor_mix}
 
@@ -261 +261 @@
 %                 energy and enstrophy conserving scheme
 %-------------------------------------------------------------
-\subsubsection{Energy and enstrophy conserving scheme (\np{ln\_dynvor\_een}=true) }
+\subsubsection{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}=true) }
 \label{DYN_vor_een}
 
@@ -297 +297 @@
 \begin{figure}[!ht]    \begin{center}
 \includegraphics[width=0.70\textwidth]{Fig_DYN_een_triad}
-\caption{ \label{Fig_DYN_een_triad}  
+\caption{ \protect\label{Fig_DYN_een_triad}  
 Triads used in the energy and enstrophy conserving scheme (een) for 
 $u$-component (upper panel) and $v$-component (lower panel).}
@@ -347 +347 @@
 %--------------------------------------------------------------------------------------------------------------
 \subsection   [Kinetic Energy Gradient term (\textit{dynkeg})]
-         {Kinetic Energy Gradient term (\mdl{dynkeg})}
+         {Kinetic Energy Gradient term (\protect\mdl{dynkeg})}
 \label{DYN_keg}
 
@@ -364 +364 @@
 %--------------------------------------------------------------------------------------------------------------
 \subsection   [Vertical advection term (\textit{dynzad}) ]
-         {Vertical advection term (\mdl{dynzad}) }
+         {Vertical advection term (\protect\mdl{dynzad}) }
 \label{DYN_zad}
 
@@ -406 +406 @@
 %--------------------------------------------------------------------------------------------------------------
 \subsection   [Coriolis plus curvature metric terms (\textit{dynvor}) ]
-         {Coriolis plus curvature metric terms (\mdl{dynvor}) }
+         {Coriolis plus curvature metric terms (\protect\mdl{dynvor}) }
 \label{DYN_cor_flux}
 
@@ -428 +428 @@
 %--------------------------------------------------------------------------------------------------------------
 \subsection   [Flux form Advection term (\textit{dynadv}) ]
-         {Flux form Advection term (\mdl{dynadv}) }
+         {Flux form Advection term (\protect\mdl{dynadv}) }
 \label{DYN_adv_flux}
 
@@ -460 +460 @@
 %                 2nd order centred scheme
 %-------------------------------------------------------------
-\subsubsection{$2^{nd}$ order centred scheme (cen2) (\np{ln\_dynadv\_cen2}=true)}
+\subsubsection{$2^{nd}$ order centred scheme (cen2) (\protect\np{ln\_dynadv\_cen2}=true)}
 \label{DYN_adv_cen2}
 
@@ -481 +481 @@
 %                 UBS scheme
 %-------------------------------------------------------------
-\subsubsection{Upstream Biased Scheme (UBS) (\np{ln\_dynadv\_ubs}=true)}
+\subsubsection{Upstream Biased Scheme (UBS) (\protect\np{ln\_dynadv\_ubs}=true)}
 \label{DYN_adv_ubs}
 
@@ -533 +533 @@
 % ================================================================
 \section  [Hydrostatic pressure gradient (\textit{dynhpg})]
-      {Hydrostatic pressure gradient (\mdl{dynhpg})}
+      {Hydrostatic pressure gradient (\protect\mdl{dynhpg})}
 \label{DYN_hpg}
 %------------------------------------------nam_dynhpg---------------------------------------------------
@@ -554 +554 @@
 %           z-coordinate with full step
 %--------------------------------------------------------------------------------------------------------------
-\subsection   [$z$-coordinate with full step (\np{ln\_dynhpg\_zco}) ]
-         {$z$-coordinate with full step (\np{ln\_dynhpg\_zco}=true)}
+\subsection   [$z$-coordinate with full step (\protect\np{ln\_dynhpg\_zco}) ]
+         {$z$-coordinate with full step (\protect\np{ln\_dynhpg\_zco}=true)}
 \label{DYN_hpg_zco}
 
@@ -595 +595 @@
 %           z-coordinate with partial step
 %--------------------------------------------------------------------------------------------------------------
-\subsection   [$z$-coordinate with partial step (\np{ln\_dynhpg\_zps})]
-         {$z$-coordinate with partial step (\np{ln\_dynhpg\_zps}=true)}
+\subsection   [$z$-coordinate with partial step (\protect\np{ln\_dynhpg\_zps})]
+         {$z$-coordinate with partial step (\protect\np{ln\_dynhpg\_zps}=true)}
 \label{DYN_hpg_zps}
 
@@ -673 +673 @@
 %           Time-scheme
 %--------------------------------------------------------------------------------------------------------------
-\subsection   [Time-scheme (\np{ln\_dynhpg\_imp}) ]
-         {Time-scheme (\np{ln\_dynhpg\_imp}= true/false)}
+\subsection   [Time-scheme (\protect\np{ln\_dynhpg\_imp}) ]
+         {Time-scheme (\protect\np{ln\_dynhpg\_imp}= true/false)}
 \label{DYN_hpg_imp}
 
@@ -733 +733 @@
 % ================================================================
 \section  [Surface pressure gradient (\textit{dynspg}) ]
-      {Surface pressure gradient (\mdl{dynspg})}
+      {Surface pressure gradient (\protect\mdl{dynspg})}
 \label{DYN_spg}
 %-----------------------------------------nam_dynspg----------------------------------------------------
@@ -772 +772 @@
 % Explicit free surface formulation
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Explicit free surface (\key{dynspg\_exp})}
+\subsection{Explicit free surface (\protect\key{dynspg\_exp})}
 \label{DYN_spg_exp}
 
@@ -793 +793 @@
 % Split-explict free surface formulation
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Split-Explicit free surface (\key{dynspg\_ts})}
+\subsection{Split-Explicit free surface (\protect\key{dynspg\_ts})}
 \label{DYN_spg_ts}
 %------------------------------------------namsplit-----------------------------------------------------------
@@ -830 +830 @@
 \begin{figure}[!t]    \begin{center}
 \includegraphics[width=0.7\textwidth]{Fig_DYN_dynspg_ts}
-\caption{  \label{Fig_DYN_dynspg_ts}
+\caption{  \protect\label{Fig_DYN_dynspg_ts}
 Schematic of the split-explicit time stepping scheme for the external 
 and internal modes. Time increases to the right. In this particular exemple, 
@@ -839 +839 @@
 The former are used to obtain time filtered quantities at $t+\rdt$ while the latter are used to obtain time averaged 
 transports to advect tracers.
-a) Forward time integration: \np{ln\_bt\_fw}=true,  \np{ln\_bt\_av}=true. 
-b) Centred time integration: \np{ln\_bt\_fw}=false, \np{ln\_bt\_av}=true. 
-c) Forward time integration with no time filtering (POM-like scheme): \np{ln\_bt\_fw}=true, \np{ln\_bt\_av}=false. }
+a) Forward time integration: \protect\np{ln\_bt\_fw}=true,  \protect\np{ln\_bt\_av}=true. 
+b) Centred time integration: \protect\np{ln\_bt\_fw}=false, \protect\np{ln\_bt\_av}=true. 
+c) Forward time integration with no time filtering (POM-like scheme): \protect\np{ln\_bt\_fw}=true, \protect\np{ln\_bt\_av}=false. }
 \end{center}    \end{figure}
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >
@@ -975 +975 @@
 % Filtered free surface formulation
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Filtered free surface (\key{dynspg\_flt})}
+\subsection{Filtered free surface (\protect\key{dynspg\_flt})}
 \label{DYN_spg_fltp}
 
@@ -1002 +1002 @@
 % ================================================================
 \section  [Lateral diffusion term (\textit{dynldf})]
-      {Lateral diffusion term (\mdl{dynldf})}
+      {Lateral diffusion term (\protect\mdl{dynldf})}
 \label{DYN_ldf}
 %------------------------------------------nam_dynldf----------------------------------------------------
@@ -1036 +1036 @@
 
 % ================================================================
-\subsection   [Iso-level laplacian operator (\np{ln\_dynldf\_lap}) ]
-         {Iso-level laplacian operator (\np{ln\_dynldf\_lap}=true)}
+\subsection   [Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}) ]
+         {Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}=true)}
 \label{DYN_ldf_lap}
 
@@ -1060 +1060 @@
 %           Rotated laplacian operator
 %--------------------------------------------------------------------------------------------------------------
-\subsection   [Rotated laplacian operator (\np{ln\_dynldf\_iso}) ]
-         {Rotated laplacian operator (\np{ln\_dynldf\_iso}=true)}
+\subsection   [Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}) ]
+         {Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}=true)}
 \label{DYN_ldf_iso}
 
@@ -1129 +1129 @@
 %           Iso-level bilaplacian operator
 %--------------------------------------------------------------------------------------------------------------
-\subsection   [Iso-level bilaplacian operator (\np{ln\_dynldf\_bilap})]
-         {Iso-level bilaplacian operator (\np{ln\_dynldf\_bilap}=true)}
+\subsection   [Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap})]
+         {Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}=true)}
 \label{DYN_ldf_bilap}
 
@@ -1145 +1145 @@
 %           Vertical diffusion term
 % ================================================================
-\section  [Vertical diffusion term (\mdl{dynzdf})]
-      {Vertical diffusion term (\mdl{dynzdf})}
+\section  [Vertical diffusion term (\protect\mdl{dynzdf})]
+      {Vertical diffusion term (\protect\mdl{dynzdf})}
 \label{DYN_zdf}
 %----------------------------------------------namzdf------------------------------------------------------
@@ -1223 +1223 @@
 % ================================================================
 \section  [Time evolution term (\textit{dynnxt})]
-      {Time evolution term (\mdl{dynnxt})}
+      {Time evolution term (\protect\mdl{dynnxt})}
 \label{DYN_nxt}
 

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_LBC.tex

@@ -17 +17 @@
 % Boundary Condition at the Coast
 % ================================================================
-\section{Boundary Condition at the Coast (\np{rn\_shlat})}
+\section{Boundary Condition at the Coast (\protect\np{rn\_shlat})}
 \label{LBC_coast}
 %--------------------------------------------nam_lbc-------------------------------------------------------
@@ -56 +56 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_LBC_uv}
-\caption{  \label{Fig_LBC_uv}
+\caption{  \protect\label{Fig_LBC_uv}
 Lateral boundary (thick line) at T-level. The velocity normal to the boundary is set to zero.}
 \end{center}   \end{figure}
@@ -79 +79 @@
 \begin{figure}[!p] \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_LBC_shlat}
-\caption{     \label{Fig_LBC_shlat} 
+\caption{     \protect\label{Fig_LBC_shlat} 
 lateral boundary condition (a) free-slip ($rn\_shlat=0$) ; (b) no-slip ($rn\_shlat=2$) 
 ; (c) "partial" free-slip ($0<rn\_shlat<2$) and (d) "strong" no-slip ($2<rn\_shlat$). 
@@ -133 +133 @@
 % Boundary Condition around the Model Domain
 % ================================================================
-\section{Model Domain Boundary Condition (\np{jperio})}
+\section{Model Domain Boundary Condition (\protect\np{jperio})}
 \label{LBC_jperio}
 
@@ -143 +143 @@
 %        Closed, cyclic, south symmetric (\np{jperio} = 0, 1 or 2) 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Closed, cyclic, south symmetric (\np{jperio} = 0, 1 or 2)}
+\subsection{Closed, cyclic, south symmetric (\protect\np{jperio} = 0, 1 or 2)}
 \label{LBC_jperio012}
 
@@ -180 +180 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_LBC_jperio}
-\caption{    \label{Fig_LBC_jperio}
+\caption{    \protect\label{Fig_LBC_jperio}
 setting of (a) east-west cyclic  (b) symmetric across the equator boundary conditions.}
 \end{center}   \end{figure}
@@ -199 +199 @@
 \begin{figure}[!t]    \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_North_Fold_T}
-\caption{    \label{Fig_North_Fold_T} 
+\caption{    \protect\label{Fig_North_Fold_T} 
 North fold boundary with a $T$-point pivot and cyclic east-west boundary condition 
 ($jperio=4$), as used in ORCA 2, 1/4, and 1/12. Pink shaded area corresponds 
@@ -210 +210 @@
 % ====================================================================
 \section  [Exchange with neighbouring processors (\textit{lbclnk}, \textit{lib\_mpp})]
-      {Exchange with neighbouring processors (\mdl{lbclnk}, \mdl{lib\_mpp})}
+      {Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})}
 \label{LBC_mpp}
 
@@ -262 +262 @@
 \begin{figure}[!t]    \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_mpp}
-\caption{   \label{Fig_mpp} 
+\caption{   \protect\label{Fig_mpp} 
 Positioning of a sub-domain when massively parallel processing is used. }
 \end{center}   \end{figure}
@@ -336 +336 @@
 \begin{figure}[!ht]     \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_mppini2}
-\caption {    \label{Fig_mppini2}
+\caption {    \protect\label{Fig_mppini2}
 Example of Atlantic domain defined for the CLIPPER projet. Initial grid is 
 composed of 773 x 1236 horizontal points. 
@@ -567 +567 @@
 \begin{figure}[!t]      \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_LBC_bdy_geom}
-\caption {      \label{Fig_LBC_bdy_geom}
+\caption {      \protect\label{Fig_LBC_bdy_geom}
 Example of geometry of unstructured open boundary}
 \end{center}   \end{figure}
@@ -608 +608 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_LBC_nc_header}
-\caption {     \label{Fig_LBC_nc_header} 
+\caption {     \protect\label{Fig_LBC_nc_header} 
 Example of the header for a coordinates.bdy.nc file}
 \end{center}   \end{figure}

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_LDF.tex

@@ -37 +37 @@
 % ================================================================
 \section  [Direction of Lateral Mixing (\textit{ldfslp})]
-      {Direction of Lateral Mixing (\mdl{ldfslp})}
+      {Direction of Lateral Mixing (\protect\mdl{ldfslp})}
 \label{LDF_slp}
 
@@ -231 +231 @@
 \begin{figure}[!ht]      \begin{center}
 \includegraphics[width=0.70\textwidth]{Fig_LDF_ZDF1}
-\caption {    \label{Fig_LDF_ZDF1}
+\caption {    \protect\label{Fig_LDF_ZDF1}
 averaging procedure for isopycnal slope computation.}
 \end{center}    \end{figure}
@@ -259 +259 @@
 \begin{figure}[!ht]     \begin{center}
 \includegraphics[width=0.70\textwidth]{Fig_eiv_slp}
-\caption {     \label{Fig_eiv_slp}
+\caption {     \protect\label{Fig_eiv_slp}
 Vertical profile of the slope used for lateral mixing in the mixed layer : 
 \textit{(a)} in the real ocean the slope is the iso-neutral slope in the ocean interior, 
@@ -307 +307 @@
 % ================================================================
 \section [Lateral Mixing Operators (\textit{ldftra}, \textit{ldfdyn})] 
-        {Lateral Mixing Operators (\mdl{traldf}, \mdl{traldf}) }
+        {Lateral Mixing Operators (\protect\mdl{traldf}, \protect\mdl{traldf}) }
 \label{LDF_op}
 
@@ -316 +316 @@
 % ================================================================
 \section [Lateral Mixing Coefficient (\textit{ldftra}, \textit{ldfdyn})] 
-        {Lateral Mixing Coefficient (\mdl{ldftra}, \mdl{ldfdyn}) }
+        {Lateral Mixing Coefficient (\protect\mdl{ldftra}, \protect\mdl{ldfdyn}) }
 \label{LDF_coef}
 
@@ -350 +350 @@
 parameters.
 
-\subsubsection{Vertically varying Mixing Coefficients (\key{traldf\_c1d} and \key{dynldf\_c1d})} 
+\subsubsection{Vertically varying Mixing Coefficients (\protect\key{traldf\_c1d} and \key{dynldf\_c1d})} 
 The 1D option is only available when using the $z$-coordinate with full step. 
 Indeed in all the other types of vertical coordinate, the depth is a 3D function 
@@ -361 +361 @@
 This profile is hard coded in file \hf{traldf\_c1d}, but can be easily modified by users.
 
-\subsubsection{Horizontally Varying Mixing Coefficients (\key{traldf\_c2d} and \key{dynldf\_c2d})}
+\subsubsection{Horizontally Varying Mixing Coefficients (\protect\key{traldf\_c2d} and \protect\key{dynldf\_c2d})}
 By default the horizontal variation of the eddy coefficient depends on the local mesh 
 size and the type of operator used:
@@ -391 +391 @@
 sub-domain options of ORCA2 and ORCA05 (see \&namcfg namelist).
 
-\subsubsection{Space Varying Mixing Coefficients (\key{traldf\_c3d} and \key{dynldf\_c3d})}
+\subsubsection{Space Varying Mixing Coefficients (\protect\key{traldf\_c3d} and \key{dynldf\_c3d})}
 
 The 3D space variation of the mixing coefficient is simply the combination of the 
@@ -447 +447 @@
 % ================================================================
 \section  [Eddy Induced Velocity (\textit{traadv\_eiv}, \textit{ldfeiv})]
-      {Eddy Induced Velocity (\mdl{traadv\_eiv}, \mdl{ldfeiv})}
+      {Eddy Induced Velocity (\protect\mdl{traadv\_eiv}, \protect\mdl{ldfeiv})}
 \label{LDF_eiv}
 

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_MISC.tex

@@ -64 +64 @@
 \includegraphics[width=0.80\textwidth]{Fig_Gibraltar}
 \includegraphics[width=0.80\textwidth]{Fig_Gibraltar2}
-\caption{   \label{Fig_MISC_strait_hand} 
+\caption{   \protect\label{Fig_MISC_strait_hand} 
 Example of the Gibraltar strait defined in a $1^{\circ} \times 1^{\circ}$ mesh. 
 \textit{Top}: using partially open cells. The meridional scale factor at $v$-point 
@@ -80 +80 @@
 % Closed seas
 % ================================================================
-\section{Closed seas (\mdl{closea})}
+\section{Closed seas (\protect\mdl{closea})}
 \label{MISC_closea}
 
@@ -151 +151 @@
 \begin{figure}[!ht]    \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_LBC_zoom}
-\caption{   \label{Fig_LBC_zoom}
+\caption{   \protect\label{Fig_LBC_zoom}
 Position of a model domain compared to the data input domain when the zoom functionality is used.}
 \end{center}   \end{figure}
@@ -160 +160 @@
 % Accuracy and Reproducibility
 % ================================================================
-\section{Accuracy and Reproducibility (\mdl{lib\_fortran})}
+\section{Accuracy and Reproducibility (\protect\mdl{lib\_fortran})}
 \label{MISC_fortran}
 
-\subsection{Issues with intrinsinc SIGN function (\key{nosignedzero})}
+\subsection{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})}
 \label{MISC_sign}
 

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

@@ -117 +117 @@
 \begin{figure}[!ht]   \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_I_ocean_bc}
-\caption{    \label{Fig_ocean_bc} 
+\caption{    \protect\label{Fig_ocean_bc} 
 The ocean is bounded by two surfaces, $z=-H(i,j)$ and $z=\eta(i,j,t)$, where $H$ 
 is the depth of the sea floor and $\eta$ the height of the sea surface. 
@@ -315 +315 @@
 \begin{figure}[!tb]   \begin{center}
 \includegraphics[width=0.60\textwidth]{Fig_I_earth_referential}
-\caption{   \label{Fig_referential} 
+\caption{   \protect\label{Fig_referential} 
 the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear 
 coordinate system (\textbf{i},\textbf{j},\textbf{k}). }
@@ -810 +810 @@
 \begin{figure}[!b]    \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_z_zstar}
-\caption{   \label{Fig_z_zstar} 
+\caption{   \protect\label{Fig_z_zstar} 
 (a) $z$-coordinate in linear free-surface case ; 
 (b) $z-$coordinate in non-linear free surface case ; 

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex

@@ -75 +75 @@
 % Surface Pressure Gradient and Sea Surface Height
 % ================================================================
-\section{Surface pressure gradient and Sea Surface Heigth (\mdl{dynspg})}
+\section{Surface pressure gradient and Sea Surface Heigth (\protect\mdl{dynspg})}
 \label{DYN_hpg_spg}
 %-----------------------------------------nam_dynspg----------------------------------------------------
@@ -86 +86 @@
 % Explicit
 %-------------------------------------------------------------
-\subsubsection{Explicit (\key{dynspg\_exp})}
+\subsubsection{Explicit (\protect\key{dynspg\_exp})}
 \label{DYN_spg_exp}
 
@@ -112 +112 @@
 % Split-explicit time-stepping
 %-------------------------------------------------------------
-\subsubsection{Split-explicit time-stepping (\key{dynspg\_ts})}
+\subsubsection{Split-explicit time-stepping (\protect\key{dynspg\_ts})}
 \label{DYN_spg_ts}
 %--------------------------------------------namdom----------------------------------------------------
@@ -124 +124 @@
 \begin{figure}[!t]   \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_DYN_dynspg_ts}
-\caption{    \label{Fig_DYN_dynspg_ts}
+\caption{    \protect\label{Fig_DYN_dynspg_ts}
 Schematic of the split-explicit time stepping scheme for the barotropic and baroclinic modes, 
 after \citet{Griffies2004}. Time increases to the right. Baroclinic time steps are denoted by 
@@ -241 +241 @@
 % Filtered formulation 
 %-------------------------------------------------------------
-\subsubsection{Filtered formulation (\key{dynspg\_flt})}
+\subsubsection{Filtered formulation (\protect\key{dynspg\_flt})}
 \label{DYN_spg_flt}
 
@@ -252 +252 @@
 % Non-linear free surface formulation 
 %-------------------------------------------------------------
-\subsection{Non-linear free surface formulation (\key{vvl})}
+\subsection{Non-linear free surface formulation (\protect\key{vvl})}
 \label{DYN_spg_vvl}
 

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_OBS.tex

@@ -700 +700 @@
 \begin{figure}      \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_OBS_avg_rec}
-\caption{      \label{fig:obsavgrec}
+\caption{      \protect\label{fig:obsavgrec}
 Weights 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.}
 \end{center}      \end{figure}
@@ -708 +708 @@
 \begin{figure}      \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_OBS_avg_rad}
-\caption{      \label{fig:obsavgrad}
+\caption{      \protect\label{fig:obsavgrad}
 Weights 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.} 
 \end{center}      \end{figure}
@@ -800 +800 @@
 \begin{figure}      \begin{center}
 \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_local}
-\caption{      \label{fig:obslocal}
+\caption{      \protect\label{fig:obslocal}
 Example of the distribution of observations with the geographical distribution of observational data.} 
 \end{center}      \end{figure}
@@ -827 +827 @@
 \begin{figure}     \begin{center}
 \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_global}
-\caption{      \label{fig:obsglobal}
+\caption{      \protect\label{fig:obsglobal}
 Example of the distribution of observations with the round-robin distribution of observational data.}
 \end{center}     \end{figure}
@@ -1445 +1445 @@
 %\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_main}
 \includegraphics[width=9cm,angle=-90.]{Fig_OBS_dataplot_main}
-\caption{      \label{fig:obsdataplotmain}
+\caption{      \protect\label{fig:obsdataplotmain}
 Main window of dataplot.}
 \end{center}     \end{figure}
@@ -1457 +1457 @@
 %\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_prof}
 \includegraphics[width=7cm,angle=-90.]{Fig_OBS_dataplot_prof}
-\caption{      \label{fig:obsdataplotprofile}
+\caption{      \protect\label{fig:obsdataplotprofile}
 Profile plot from dataplot produced by right clicking on a point in the main window.}
 \end{center}     \end{figure}

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_SBC.tex

@@ -144 +144 @@
 Sea surface salinty              & sss\_m & $psu$        & T \\   \hline
 \end{tabular}
-\caption{  \label{Tab_ssm}   
+\caption{  \protect\label{Tab_ssm}   
 Ocean variables provided by the ocean to the surface module (SBC). 
 The variable are averaged over nn{\_}fsbc time step, 
@@ -192 +192 @@
 % Input Data specification (\mdl{fldread})
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Input Data specification (\mdl{fldread})}
+\subsection{Input Data specification (\protect\mdl{fldread})}
 \label{SBC_fldread}
 
@@ -220 +220 @@
 \end{tabular}
 \end{center}
-\caption{ \label{Tab_fldread}   naming nomenclature for climatological or interannual input file, 
+\caption{ \protect\label{Tab_fldread}   naming nomenclature for climatological or interannual input file, 
 as a function of the Open/close frequency. The stem name is assumed to be 'fn'. 
 For 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 
@@ -484 +484 @@
 % ================================================================
 \section  [Analytical formulation (\textit{sbcana}) ]
-      {Analytical formulation (\mdl{sbcana} module) }
+      {Analytical formulation (\protect\mdl{sbcana} module) }
 \label{SBC_ana}
 
@@ -509 +509 @@
 % ================================================================
 \section  [Flux formulation (\textit{sbcflx}) ]
-      {Flux formulation (\mdl{sbcflx} module) }
+      {Flux formulation (\protect\mdl{sbcflx} module) }
 \label{SBC_flx}
 %------------------------------------------namsbc_flx----------------------------------------------------
@@ -531 +531 @@
 % ================================================================
 \section  [Bulk formulation (\textit{sbcblk\_core}, \textit{sbcblk\_clio} or \textit{sbcblk\_mfs}) ]
-      {Bulk formulation \small{(\mdl{sbcblk\_core} \mdl{sbcblk\_clio} \mdl{sbcblk\_mfs} modules)} }
+      {Bulk formulation \small{(\protect\mdl{sbcblk\_core} \protect\mdl{sbcblk\_clio} \protect\mdl{sbcblk\_mfs} modules)} }
 \label{SBC_blk}
 
@@ -548 +548 @@
 %        CORE Bulk formulea
 % -------------------------------------------------------------------------------------------------------------
-\subsection    [CORE Bulk formulea (\np{ln\_core}=true)]
-            {CORE Bulk formulea (\np{ln\_core}=true, \mdl{sbcblk\_core})}
+\subsection    [CORE Bulk formulea (\protect\np{ln\_core}=true)]
+            {CORE Bulk formulea (\protect\np{ln\_core}=true, \protect\mdl{sbcblk\_core})}
 \label{SBC_blk_core}
 %------------------------------------------namsbc_core----------------------------------------------------
@@ -613 +613 @@
 %        CLIO Bulk formulea
 % -------------------------------------------------------------------------------------------------------------
-\subsection    [CLIO Bulk formulea (\np{ln\_clio}=true)]
-            {CLIO Bulk formulea (\np{ln\_clio}=true, \mdl{sbcblk\_clio})}
+\subsection    [CLIO Bulk formulea (\protect\np{ln\_clio}=true)]
+            {CLIO Bulk formulea (\protect\np{ln\_clio}=true, \protect\mdl{sbcblk\_clio})}
 \label{SBC_blk_clio}
 %------------------------------------------namsbc_clio----------------------------------------------------
@@ -654 +654 @@
 %        MFS Bulk formulae
 % -------------------------------------------------------------------------------------------------------------
-\subsection    [MFS Bulk formulea (\np{ln\_mfs}=true)]
-            {MFS Bulk formulea (\np{ln\_mfs}=true, \mdl{sbcblk\_mfs})}
+\subsection    [MFS Bulk formulea (\protect\np{ln\_mfs}=true)]
+            {MFS Bulk formulea (\protect\np{ln\_mfs}=true, \protect\mdl{sbcblk\_mfs})}
 \label{SBC_blk_mfs}
 %------------------------------------------namsbc_mfs----------------------------------------------------
@@ -694 +694 @@
 % ================================================================
 \section  [Coupled formulation (\textit{sbccpl}) ]
-      {Coupled formulation (\mdl{sbccpl} module)}
+      {Coupled formulation (\protect\mdl{sbccpl} module)}
 \label{SBC_cpl}
 %------------------------------------------namsbc_cpl----------------------------------------------------
@@ -733 +733 @@
 % ================================================================
 \section   [Atmospheric pressure (\textit{sbcapr})]
-         {Atmospheric pressure (\mdl{sbcapr})}
+         {Atmospheric pressure (\protect\mdl{sbcapr})}
 \label{SBC_apr}
 %------------------------------------------namsbc_apr----------------------------------------------------
@@ -768 +768 @@
 % ================================================================
 \section   [Tidal Potential (\textit{sbctide})]
-                        {Tidal Potential (\mdl{sbctide})}
+                        {Tidal Potential (\protect\mdl{sbctide})}
 \label{SBC_tide}
 
@@ -824 +824 @@
 % ================================================================
 \section   [River runoffs (\textit{sbcrnf})]
-         {River runoffs (\mdl{sbcrnf})}
+         {River runoffs (\protect\mdl{sbcrnf})}
 \label{SBC_rnf}
 %------------------------------------------namsbc_rnf----------------------------------------------------
@@ -940 +940 @@
 % ================================================================
 \section   [Ice shelf melting (\textit{sbcisf})]
-                        {Ice shelf melting (\mdl{sbcisf})}
+                        {Ice shelf melting (\protect\mdl{sbcisf})}
 \label{SBC_isf}
 %------------------------------------------namsbc_isf----------------------------------------------------
@@ -1131 +1131 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Diurnal  cycle (\textit{sbcdcy})]
-         {Diurnal cycle (\mdl{sbcdcy})}
+         {Diurnal cycle (\protect\mdl{sbcdcy})}
 \label{SBC_dcy}
 %------------------------------------------namsbc_rnf----------------------------------------------------
@@ -1140 +1140 @@
 \begin{figure}[!t]    \begin{center}
 \includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal}
-\caption{ \label{Fig_SBC_diurnal}    
+\caption{ \protect\label{Fig_SBC_diurnal}    
 Example of recontruction of the diurnal cycle variation of short wave flux  
 from daily mean values. The reconstructed diurnal cycle (black line) is chosen 
@@ -1173 +1173 @@
 \begin{figure}[!t]  \begin{center}
 \includegraphics[width=0.7\textwidth]{Fig_SBC_dcy}
-\caption{ \label{Fig_SBC_dcy}   
+\caption{ \protect\label{Fig_SBC_dcy}   
 Example of recontruction of the diurnal cycle variation of short wave flux  
 from daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm). 
@@ -1208 +1208 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection    [Surface restoring to observed SST and/or SSS (\textit{sbcssr})]
-         {Surface restoring to observed SST and/or SSS (\mdl{sbcssr})}
+         {Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
 \label{SBC_ssr}
 %------------------------------------------namsbc_ssr----------------------------------------------------
@@ -1278 +1278 @@
 
 \subsection   [Interface to CICE (\textit{sbcice\_cice})]
-         {Interface to CICE (\mdl{sbcice\_cice})}
+         {Interface to CICE (\protect\mdl{sbcice\_cice})}
 \label{SBC_cice}
 
@@ -1306 +1306 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Freshwater budget control (\textit{sbcfwb})]
-         {Freshwater budget control (\mdl{sbcfwb})}
+         {Freshwater budget control (\protect\mdl{sbcfwb})}
 \label{SBC_fwb}
 
@@ -1328 +1328 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Neutral drag coefficient from external wave model (\textit{sbcwave})]
-              {Neutral drag coefficient from external wave model (\mdl{sbcwave})}
+              {Neutral drag coefficient from external wave model (\protect\mdl{sbcwave})}
 \label{SBC_wave}
 %------------------------------------------namwave----------------------------------------------------

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_STP.tex

@@ -207 +207 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=0.7\textwidth]{Fig_TimeStepping_flowchart}
-\caption{   \label{Fig_TimeStep_flowchart}
+\caption{   \protect\label{Fig_TimeStep_flowchart}
 Sketch of the leapfrog time stepping sequence in \NEMO from \citet{Leclair_Madec_OM09}. 
 The use of a semi-implicit computation of the hydrostatic pressure gradient requires
@@ -269 +269 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_MLF_forcing}
-\caption{   \label{Fig_MLF_forcing}
+\caption{   \protect\label{Fig_MLF_forcing}
 Illustration of forcing integration methods. 
 (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

@@ -64 +64 @@
 % ================================================================
 \section  [Tracer Advection (\textit{traadv})]
-      {Tracer Advection (\mdl{traadv})}
+      {Tracer Advection (\protect\mdl{traadv})}
 \label{TRA_adv}
 %------------------------------------------namtra_adv-----------------------------------------------------
@@ -93 +93 @@
 \begin{figure}[!t]    \begin{center}
 \includegraphics[width=0.9\textwidth]{Fig_adv_scheme}
-\caption{   \label{Fig_adv_scheme} 
+\caption{   \protect\label{Fig_adv_scheme} 
 Schematic representation of some ways used to evaluate the tracer value 
 at $u$-point and the amount of tracer exchanged between two neighbouring grid 
@@ -174 +174 @@
 %        2nd and 4th order centred schemes
 % -------------------------------------------------------------------------------------------------------------
-\subsection [Centred schemes (CEN) (\np{ln\_traadv\_cen})]
-            {Centred schemes (CEN) (\np{ln\_traadv\_cen}=true)}
+\subsection [Centred schemes (CEN) (\protect\np{ln\_traadv\_cen})]
+            {Centred schemes (CEN) (\protect\np{ln\_traadv\_cen}=true)}
 \label{TRA_adv_cen}
 
@@ -246 +246 @@
 %        FCT scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [Flux Corrected Transport schemes (FCT) (\np{ln\_traadv\_fct})]
-         {Flux Corrected Transport schemes (FCT) (\np{ln\_traadv\_fct}=true)}
+\subsection   [Flux Corrected Transport schemes (FCT) (\protect\np{ln\_traadv\_fct})]
+         {Flux Corrected Transport schemes (FCT) (\protect\np{ln\_traadv\_fct}=true)}
 \label{TRA_adv_tvd}
 
@@ -293 +293 @@
 %        MUSCL scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection[MUSCL scheme  (\np{ln\_traadv\_mus})]
-   {Monotone Upstream Scheme for Conservative Laws (MUSCL) (\np{ln\_traadv\_mus}=T)}
+\subsection[MUSCL scheme  (\protect\np{ln\_traadv\_mus})]
+   {Monotone Upstream Scheme for Conservative Laws (MUSCL) (\protect\np{ln\_traadv\_mus}=T)}
 \label{TRA_adv_mus}
 
@@ -326 +326 @@
 %        UBS scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [Upstream-Biased Scheme (UBS) (\np{ln\_traadv\_ubs})]
-         {Upstream-Biased Scheme (UBS) (\np{ln\_traadv\_ubs}=true)}
+\subsection   [Upstream-Biased Scheme (UBS) (\protect\np{ln\_traadv\_ubs})]
+         {Upstream-Biased Scheme (UBS) (\protect\np{ln\_traadv\_ubs}=true)}
 \label{TRA_adv_ubs}
 
@@ -401 +401 @@
 %        QCK scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [QUICKEST scheme (QCK) (\np{ln\_traadv\_qck})]
-         {QUICKEST scheme (QCK) (\np{ln\_traadv\_qck}=true)}
+\subsection   [QUICKEST scheme (QCK) (\protect\np{ln\_traadv\_qck})]
+         {QUICKEST scheme (QCK) (\protect\np{ln\_traadv\_qck}=true)}
 \label{TRA_adv_qck}
 
@@ -429 +429 @@
 % ================================================================
 \section  [Tracer Lateral Diffusion (\textit{traldf})]
-      {Tracer Lateral Diffusion (\mdl{traldf})}
+      {Tracer Lateral Diffusion (\protect\mdl{traldf})}
 \label{TRA_ldf}
 %-----------------------------------------nam_traldf------------------------------------------------------
@@ -455 +455 @@
 %        Type of operator
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [Type of operator (\np{ln\_traldf\{\_NONE, \_lap, \_blp\}})]
-              {Type of operator (\np{ln\_traldf\_NONE}, \np{ln\_traldf\_lap}, or \np{ln\_traldf\_blp} = true) } 
+\subsection   [Type of operator (\protect\np{ln\_traldf\{\_NONE, \_lap, \_blp\}})]
+              {Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp} = true) } 
 \label{TRA_ldf_op}
 
@@ -488 +488 @@
 %        Direction of action
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [Direction of action (\np{ln\_traldf\{\_lev, \_hor, \_iso, \_triad\}})]
-              {Direction of action (\np{ln\_traldf\_lev}, \textit{...\_hor}, \textit{...\_iso}, or \textit{...\_triad} = true) } 
+\subsection   [Direction of action (\protect\np{ln\_traldf\{\_lev, \_hor, \_iso, \_triad\}})]
+              {Direction of action (\protect\np{ln\_traldf\_lev}, \textit{...\_hor}, \textit{...\_iso}, or \textit{...\_triad} = true) } 
 \label{TRA_ldf_dir}
 
@@ -515 +515 @@
 %       iso-level operator
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [Iso-level (bi-)laplacian operator ( \np{ln\_traldf\_iso})]
-         {Iso-level (bi-)laplacian operator ( \np{ln\_traldf\_iso}) }
+\subsection   [Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})]
+         {Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso}) }
 \label{TRA_ldf_lev}
 
@@ -555 +555 @@
 %&&    Standard rotated (bi-)laplacian operator
 %&& ----------------------------------------------
-\subsubsection   [Standard rotated (bi-)laplacian operator (\mdl{traldf\_iso})]
-                 {Standard rotated (bi-)laplacian operator (\mdl{traldf\_iso})}
+\subsubsection   [Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})]
+                 {Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})}
 \label{TRA_ldf_iso}
 The general form of the second order lateral tracer subgrid scale physics 
@@ -609 +609 @@
 %&&     Triad rotated (bi-)laplacian operator
 %&&  -------------------------------------------
-\subsubsection   [Triad rotated (bi-)laplacian operator (\np{ln\_traldf\_triad})]
-                 {Triad rotated (bi-)laplacian operator (\np{ln\_traldf\_triad})}
+\subsubsection   [Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})]
+                 {Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})}
 \label{TRA_ldf_triad}
 
@@ -649 +649 @@
 % ================================================================
 \section  [Tracer Vertical Diffusion (\textit{trazdf})]
-      {Tracer Vertical Diffusion (\mdl{trazdf})}
+      {Tracer Vertical Diffusion (\protect\mdl{trazdf})}
 \label{TRA_zdf}
 %--------------------------------------------namzdf---------------------------------------------------------
@@ -703 +703 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Surface boundary condition (\textit{trasbc})]
-         {Surface boundary condition (\mdl{trasbc})}
+         {Surface boundary condition (\protect\mdl{trasbc})}
 \label{TRA_sbc}
 
@@ -774 +774 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Solar Radiation Penetration (\textit{traqsr})]
-         {Solar Radiation Penetration (\mdl{traqsr})}
+         {Solar Radiation Penetration (\protect\mdl{traqsr})}
 \label{TRA_qsr}
 %--------------------------------------------namqsr--------------------------------------------------------
@@ -872 +872 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_TRA_Irradiance}
-\caption{    \label{Fig_traqsr_irradiance}
+\caption{    \protect\label{Fig_traqsr_irradiance}
 Penetration profile of the downward solar irradiance calculated by four models. 
 Two waveband chlorophyll-independent formulation (blue), a chlorophyll-dependent 
@@ -885 +885 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Bottom Boundary Condition (\textit{trabbc})]
-         {Bottom Boundary Condition (\mdl{trabbc})}
+         {Bottom Boundary Condition (\protect\mdl{trabbc})}
 \label{TRA_bbc}
 %--------------------------------------------nambbc--------------------------------------------------------
@@ -893 +893 @@
 \begin{figure}[!t]     \begin{center}
 \includegraphics[width=1.0\textwidth]{Fig_TRA_geoth}
-\caption{   \label{Fig_geothermal}
+\caption{   \protect\label{Fig_geothermal}
 Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{Emile-Geay_Madec_OS09}.
 It is inferred from the age of the sea floor and the formulae of \citet{Stein_Stein_Nat92}.}
@@ -923 +923 @@
 % Bottom Boundary Layer
 % ================================================================
-\section  [Bottom Boundary Layer (\mdl{trabbl} - \key{trabbl})]
-      {Bottom Boundary Layer (\mdl{trabbl} - \key{trabbl})}
+\section  [Bottom Boundary Layer (\protect\mdl{trabbl} - \protect\key{trabbl})]
+      {Bottom Boundary Layer (\protect\mdl{trabbl} - \protect\key{trabbl})}
 \label{TRA_bbl}
 %--------------------------------------------nambbl---------------------------------------------------------
@@ -959 +959 @@
 %        Diffusive BBL
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Diffusive Bottom Boundary layer (\np{nn\_bbl\_ldf}=1)}
+\subsection{Diffusive Bottom Boundary layer (\protect\np{nn\_bbl\_ldf}=1)}
 \label{TRA_bbl_diff}
 
@@ -994 +994 @@
 %        Advective BBL
 % -------------------------------------------------------------------------------------------------------------
-\subsection   {Advective Bottom Boundary Layer  (\np{nn\_bbl\_adv}= 1 or 2)}
+\subsection   {Advective Bottom Boundary Layer  (\protect\np{nn\_bbl\_adv}= 1 or 2)}
 \label{TRA_bbl_adv}
 
@@ -1003 +1003 @@
 \begin{figure}[!t]   \begin{center}
 \includegraphics[width=0.7\textwidth]{Fig_BBL_adv}
-\caption{   \label{Fig_bbl}  
+\caption{   \protect\label{Fig_bbl}  
 Advective/diffusive Bottom Boundary Layer. The BBL parameterisation is 
 activated when $\rho^i_{kup}$ is larger than $\rho^{i+1}_{kdnw}$. 
@@ -1084 +1084 @@
 % ================================================================
 \section  [Tracer damping (\textit{tradmp})]
-      {Tracer damping (\mdl{tradmp})}
+      {Tracer damping (\protect\mdl{tradmp})}
 \label{TRA_dmp}
 %--------------------------------------------namtra_dmp-------------------------------------------------
@@ -1169 +1169 @@
 % ================================================================
 \section  [Tracer time evolution (\textit{tranxt})]
-      {Tracer time evolution (\mdl{tranxt})}
+      {Tracer time evolution (\protect\mdl{tranxt})}
 \label{TRA_nxt}
 %--------------------------------------------namdom-----------------------------------------------------
@@ -1208 +1208 @@
 % ================================================================
 \section  [Equation of State (\textit{eosbn2}) ]
-      {Equation of State (\mdl{eosbn2}) }
+      {Equation of State (\protect\mdl{eosbn2}) }
 \label{TRA_eosbn2}
 %--------------------------------------------nameos-----------------------------------------------------
@@ -1217 +1217 @@
 %        Equation of State
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Equation Of Seawater (\np{nn\_eos} = -1, 0, or 1)}
+\subsection{Equation Of Seawater (\protect\np{nn\_eos} = -1, 0, or 1)}
 \label{TRA_eos}
 
@@ -1323 +1323 @@
 $\mu_2$     & \np{rn\_mu2}    & 1.1090 $10^{-5}$ &  thermobaric coeff. in S            \\ \hline
 \end{tabular}
-\caption{ \label{Tab_SEOS}
+\caption{ \protect\label{Tab_SEOS}
 Standard value of S-EOS coefficients. }
 \end{center}
@@ -1333 +1333 @@
 %        Brunt-V\"{a}is\"{a}l\"{a} Frequency
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Brunt-V\"{a}is\"{a}l\"{a} Frequency (\np{nn\_eos} = 0, 1 or 2)}
+\subsection{Brunt-V\"{a}is\"{a}l\"{a} Frequency (\protect\np{nn\_eos} = 0, 1 or 2)}
 \label{TRA_bn2}
 
@@ -1389 +1389 @@
 % ================================================================
 \section  [Horizontal Derivative in \textit{zps}-coordinate (\textit{zpshde})]
-      {Horizontal Derivative in \textit{zps}-coordinate (\mdl{zpshde})}
+      {Horizontal Derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})}
 \label{TRA_zpshde}
 
@@ -1411 +1411 @@
 \begin{figure}[!p]    \begin{center}
 \includegraphics[width=0.9\textwidth]{Partial_step_scheme}
-\caption{   \label{Fig_Partial_step_scheme} 
+\caption{   \protect\label{Fig_Partial_step_scheme} 
 Discretisation of the horizontal difference and average of tracers in the $z$-partial 
-step coordinate (\np{ln\_zps}=true) in the case $( e3w_k^{i+1} - e3w_k^i  )>0$. 
+step coordinate (\protect\np{ln\_zps}=true) in the case $( e3w_k^{i+1} - e3w_k^i  )>0$. 
 A linear interpolation is used to estimate $\widetilde{T}_k^{i+1}$, the tracer value 
 at 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

@@ -49 +49 @@
 %        Constant 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Constant (\key{zdfcst})}
+\subsection{Constant (\protect\key{zdfcst})}
 \label{ZDF_cst}
 %--------------------------------------------namzdf---------------------------------------------------------
@@ -74 +74 @@
 %        Richardson Number Dependent
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Richardson Number Dependent (\key{zdfric})}
+\subsection{Richardson Number Dependent (\protect\key{zdfric})}
 \label{ZDF_ric}
 
@@ -132 +132 @@
 %        TKE Turbulent Closure Scheme 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{TKE Turbulent Closure Scheme (\key{zdftke})}
+\subsection{TKE Turbulent Closure Scheme (\protect\key{zdftke})}
 \label{ZDF_tke}
 
@@ -237 +237 @@
 \begin{figure}[!t] \begin{center}
 \includegraphics[width=1.00\textwidth]{Fig_mixing_length}
-\caption{ \label{Fig_mixing_length} 
+\caption{ \protect\label{Fig_mixing_length} 
 Illustration of the mixing length computation. }
 \end{center}  
@@ -405 +405 @@
 %        TKE discretization considerations
 % -------------------------------------------------------------------------------------------------------------
-\subsection{TKE discretization considerations (\key{zdftke})}
+\subsection{TKE discretization considerations (\protect\key{zdftke})}
 \label{ZDF_tke_ene}
 
@@ -411 +411 @@
 \begin{figure}[!t]   \begin{center}
 \includegraphics[width=1.00\textwidth]{Fig_ZDF_TKE_time_scheme}
-\caption{ \label{Fig_TKE_time_scheme} 
+\caption{ \protect\label{Fig_TKE_time_scheme} 
 Illustration of the TKE time integration and its links to the momentum and tracer time integration. }
 \end{center}  
@@ -508 +508 @@
 %        GLS Generic Length Scale Scheme 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{GLS Generic Length Scale (\key{zdfgls})}
+\subsection{GLS Generic Length Scale (\protect\key{zdfgls})}
 \label{ZDF_gls}
 
@@ -579 +579 @@
 \hline
 \end{tabular}
-\caption{   \label{Tab_GLS} 
+\caption{   \protect\label{Tab_GLS} 
 Set of predefined GLS parameters, or equivalently predefined turbulence models available 
-with \key{zdfgls} and controlled by the \np{nn\_clos} namelist variable in \ngn{namzdf\_gls} .}
+with \protect\key{zdfgls} and controlled by the \protect\np{nn\_clos} namelist variable in \protect\ngn{namzdf\_gls} .}
 \end{center}   \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -615 +615 @@
 %        OSM OSMOSIS BL Scheme 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{OSM OSMOSIS Boundary Layer scheme (\key{zdfosm})}
+\subsection{OSM OSMOSIS Boundary Layer scheme (\protect\key{zdfosm})}
 \label{ZDF_osm}
 
@@ -646 +646 @@
 %       Non-Penetrative Convective Adjustment 
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [Non-Penetrative Convective Adjustment (\np{ln\_tranpc}) ]
-         {Non-Penetrative Convective Adjustment (\np{ln\_tranpc}=.true.) }
+\subsection   [Non-Penetrative Convective Adjustment (\protect\np{ln\_tranpc}) ]
+         {Non-Penetrative Convective Adjustment (\protect\np{ln\_tranpc}=.true.) }
 \label{ZDF_npc}
 
@@ -657 +657 @@
 \begin{figure}[!htb]    \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_npc}
-\caption{  \label{Fig_npc} 
+\caption{  \protect\label{Fig_npc} 
 Example of an unstable density profile treated by the non penetrative 
 convective adjustment algorithm. $1^{st}$ step: the initial profile is checked from 
@@ -713 +713 @@
 %       Enhanced Vertical Diffusion 
 % -------------------------------------------------------------------------------------------------------------
-\subsection   [Enhanced Vertical Diffusion (\np{ln\_zdfevd})]
-              {Enhanced Vertical Diffusion (\np{ln\_zdfevd}=true)}
+\subsection   [Enhanced Vertical Diffusion (\protect\np{ln\_zdfevd})]
+              {Enhanced Vertical Diffusion (\protect\np{ln\_zdfevd}=true)}
 \label{ZDF_evd}
 
@@ -745 +745 @@
 %       Turbulent Closure Scheme 
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Turbulent Closure Scheme (\key{zdf\{tke, gls, osm\}})]{Turbulent Closure Scheme (\key{zdftke}, \key{zdfgls} or \key{zdfosm})}
+\subsection[Turbulent Closure Scheme (\protect\key{zdf\{tke, gls, osm\}})]{Turbulent Closure Scheme (\protect\key{zdftke}, \protect\key{zdfgls} or \protect\key{zdfosm})}
 \label{ZDF_tcs}
 
@@ -772 +772 @@
 % Double Diffusion Mixing
 % ================================================================
-\section  [Double Diffusion Mixing (\key{zdfddm})]
-      {Double Diffusion Mixing (\key{zdfddm})}
+\section  [Double Diffusion Mixing (\protect\key{zdfddm})]
+      {Double Diffusion Mixing (\protect\key{zdfddm})}
 \label{ZDF_ddm}
 
@@ -813 +813 @@
 \begin{figure}[!t]   \begin{center}
 \includegraphics[width=0.99\textwidth]{Fig_zdfddm}
-\caption{  \label{Fig_zdfddm}
+\caption{  \protect\label{Fig_zdfddm}
 From \citet{Merryfield1999} : (a) Diapycnal diffusivities $A_f^{vT}$ 
 and $A_f^{vS}$ for temperature and salt in regions of salt fingering. Heavy 
@@ -855 +855 @@
 % Bottom Friction
 % ================================================================
-\section  [Bottom and Top Friction (\textit{zdfbfr})]   {Bottom and Top Friction (\mdl{zdfbfr} module)}
+\section  [Bottom and Top Friction (\textit{zdfbfr})]   {Bottom and Top Friction (\protect\mdl{zdfbfr} module)}
 \label{ZDF_bfr}
 
@@ -918 +918 @@
 %       Linear Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Linear Bottom Friction (\np{nn\_botfr} = 0 or 1) }
+\subsection{Linear Bottom Friction (\protect\np{nn\_botfr} = 0 or 1) }
 \label{ZDF_bfr_linear}
 
@@ -962 +962 @@
 %       Non-Linear Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Non-Linear Bottom Friction (\np{nn\_botfr} = 2)}
+\subsection{Non-Linear Bottom Friction (\protect\np{nn\_botfr} = 2)}
 \label{ZDF_bfr_nonlinear}
 
@@ -1003 +1003 @@
 %       Bottom Friction Log-layer
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Log-layer Bottom Friction enhancement (\np{ln\_loglayer} = .true.)]{Log-layer Bottom Friction enhancement (\np{nn\_botfr} = 2, \np{ln\_loglayer} = .true.)}
+\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.)}
 \label{ZDF_bfr_loglayer}
 
@@ -1082 +1082 @@
 %       Implicit Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Implicit Bottom Friction (\np{ln\_bfrimp})]{Implicit Bottom Friction (\np{ln\_bfrimp}$=$\textit{T})}
+\subsection[Implicit Bottom Friction (\protect\np{ln\_bfrimp})]{Implicit Bottom Friction (\protect\np{ln\_bfrimp}$=$\textit{T})}
 \label{ZDF_bfr_imp}
 
@@ -1135 +1135 @@
 %       Bottom Friction with split-explicit time splitting
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Bottom Friction with split-explicit time splitting]{Bottom Friction with split-explicit time splitting (\np{ln\_bfrimp})}
+\subsection[Bottom Friction with split-explicit time splitting]{Bottom Friction with split-explicit time splitting (\protect\np{ln\_bfrimp})}
 \label{ZDF_bfr_ts}
 
@@ -1192 +1192 @@
 % Tidal Mixing
 % ================================================================
-\section{Tidal Mixing (\key{zdftmx})}
+\section{Tidal Mixing (\protect\key{zdftmx})}
 \label{ZDF_tmx}
 
@@ -1258 +1258 @@
 \begin{figure}[!t]   \begin{center}
 \includegraphics[width=0.90\textwidth]{Fig_ZDF_M2_K1_tmx}
-\caption{  \label{Fig_ZDF_M2_K1_tmx} 
+\caption{  \protect\label{Fig_ZDF_M2_K1_tmx} 
 (a) M2 and (b) K1 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). }
 \end{center}   \end{figure}
@@ -1266 +1266 @@
 %        Indonesian area specific treatment 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Indonesian area specific treatment (\np{ln\_zdftmx\_itf})}
+\subsection{Indonesian area specific treatment (\protect\np{ln\_zdftmx\_itf})}
 \label{ZDF_tmx_itf}
 
@@ -1314 +1314 @@
 % Internal wave-driven mixing
 % ================================================================
-\section{Internal wave-driven mixing (\key{zdftmx\_new})}
+\section{Internal wave-driven mixing (\protect\key{zdftmx\_new})}
 \label{ZDF_tmx_new}
 

branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Introduction.tex

@@ -155 +155 @@
 \begin{table}[!t] 
 %\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline
-\caption{ \label{Tab_chap}   Organization of Chapters mimicking the one of the model directories. }
+\caption{ \protect\label{Tab_chap}   Organization of Chapters mimicking the one of the model directories. }
 \begin{center}    \begin{tabular}{|l|l|l|}   \hline
 Chapter \ref{STP} & -                 & model time STePping environment \\    \hline