Changeset 11558

Timestamp:

2019-09-17T17:04:06+02:00 (5 years ago)

Author:

nicolasmartin

Message:

Review all figure envs + activation of listoflistings

1. Figure env:
   • Replace center sub-env with only \centering cmd
   • Add alternate caption for \listoffigures (shorter one between square brackets, i.e. \caption[]{})
   • Place \label outside of \caption and remove useless \protect

2. Namelist listings
   • Put \nlst with the namelist inlcusion in a listing float env with caption and label
   • Remove namelist duplicates

-- This line, and those below, will be ignored--
M subfiles/apdx_triads.tex
M subfiles/chap_model_basics_zstar.tex
M subfiles/chap_SBC.tex
M subfiles/apdx_DOMAINcfg.tex
M subfiles/apdx_s_coord.tex
M subfiles/chap_DOM.tex
M subfiles/chap_ASM.tex
M subfiles/chap_DIU.tex
M subfiles/chap_cfgs.tex
M subfiles/chap_ZDF.tex
M subfiles/chap_OBS.tex
M subfiles/chap_model_basics.tex
M subfiles/chap_time_domain.tex
M subfiles/apdx_algos.tex
M subfiles/chap_TRA.tex
M subfiles/chap_DYN.tex
M subfiles/chap_misc.tex
M subfiles/chap_DIA.tex
M subfiles/apdx_invariants.tex
M subfiles/chap_LBC.tex
M subfiles/apdx_diff_opers.tex
M subfiles/chap_STO.tex
M subfiles/chap_LDF.tex

Location:

NEMO/trunk/doc/latex/NEMO/subfiles

Files:

• apdx_DOMAINcfg.tex (modified) (7 diffs)
• apdx_algos.tex (modified) (1 diff)
• apdx_diff_opers.tex (modified) (1 diff)
• apdx_invariants.tex (modified) (2 diffs)
• apdx_s_coord.tex (modified) (5 diffs)
• apdx_triads.tex (modified) (6 diffs)
• chap_ASM.tex (modified) (1 diff)
• chap_DIA.tex (modified) (42 diffs)
• chap_DIU.tex (modified) (1 diff)
• chap_DOM.tex (modified) (12 diffs)
• chap_DYN.tex (modified) (12 diffs)
• chap_LBC.tex (modified) (14 diffs)
• chap_LDF.tex (modified) (27 diffs)
• chap_OBS.tex (modified) (6 diffs)
• chap_SBC.tex (modified) (19 diffs)
• chap_STO.tex (modified) (1 diff)
• chap_TRA.tex (modified) (14 diffs)
• chap_ZDF.tex (modified) (21 diffs)
• chap_cfgs.tex (modified) (5 diffs)
• chap_misc.tex (modified) (5 diffs)
• chap_model_basics.tex (modified) (3 diffs)
• chap_model_basics_zstar.tex (modified) (2 diffs)
• chap_time_domain.tex (modified) (4 diffs)

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

@@ -43 +43 @@
 %--------------------------------------------namdom-------------------------------------------------------
 
-\nlst{namdom_domcfg}
+\begin{listing}
+  \nlst{namdom_domcfg}
+  \caption{\texttt{namdom\_domcfg}}
+  \label{lst:namdom_domcfg}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -103 +107 @@
 \section{Vertical grid}
 \label{sec:DOMCFG_vert}
+
 \subsection{Vertical reference coordinate}
 \label{sec:DOMCFG_zref}
@@ -108 +113 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!tb]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_zgr}
-    \caption{
-      \protect\label{fig:DOMCFG_zgr}
-      Default vertical mesh for ORCA2: 30 ocean levels (L30).
-      Vertical level functions for (a) T-point depth and (b) the associated scale factor for the $z$-coordinate case.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_zgr}
+  \caption[DOMAINcfg: default vertical mesh for ORCA2]{
+    Default vertical mesh for ORCA2: 30 ocean levels (L30).
+    Vertical level functions for (a) T-point depth and (b) the associated scale factor for
+    the $z$-coordinate case.}
+  \label{fig:DOMCFG_zgr}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -225 +229 @@
 %% %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{table}
-  \begin{center}
-    \begin{tabular}{c||r|r|r|r}
-      \hline
-      \textbf{LEVEL} & \textbf{gdept\_1d} & \textbf{gdepw\_1d} & \textbf{e3t\_1d } & \textbf{e3w\_1d} \\
-   \hline
-      1              & \textbf{     5.00} &               0.00 & \textbf{   10.00} &            10.00 \\
-      \hline
-      2              & \textbf{    15.00} &              10.00 & \textbf{   10.00} &            10.00 \\
-      \hline
-      3              & \textbf{    25.00} &              20.00 & \textbf{   10.00} &            10.00 \\
-      \hline
-      4              & \textbf{    35.01} &              30.00 & \textbf{   10.01} &            10.00 \\
-      \hline
-      5              & \textbf{    45.01} &              40.01 & \textbf{   10.01} &            10.01 \\
-      \hline
-      6              & \textbf{    55.03} &              50.02 & \textbf{   10.02} &            10.02 \\
-      \hline
-      7              & \textbf{    65.06} &              60.04 & \textbf{   10.04} &            10.03 \\
-      \hline
-      8              & \textbf{    75.13} &              70.09 & \textbf{   10.09} &            10.06 \\
-      \hline
-      9              & \textbf{    85.25} &              80.18 & \textbf{   10.17} &            10.12 \\
-      \hline
-      10             & \textbf{    95.49} &              90.35 & \textbf{   10.33} &            10.24 \\
-      \hline
-      11             & \textbf{   105.97} &             100.69 & \textbf{   10.65} &            10.47 \\
-      \hline
-      12             & \textbf{   116.90} &             111.36 & \textbf{   11.27} &            10.91 \\
-      \hline
-      13             & \textbf{   128.70} &             122.65 & \textbf{   12.47} &            11.77 \\
-      \hline
-      14             & \textbf{   142.20} &             135.16 & \textbf{   14.78} &            13.43 \\
-      \hline
-      15             & \textbf{   158.96} &             150.03 & \textbf{   19.23} &            16.65 \\
-      \hline
-      16             & \textbf{   181.96} &             169.42 & \textbf{   27.66} &            22.78 \\
-      \hline
-      17             & \textbf{   216.65} &             197.37 & \textbf{   43.26} &            34.30 \\
-      \hline
-      18             & \textbf{   272.48} &             241.13 & \textbf{   70.88} &            55.21 \\
-      \hline
-      19             & \textbf{   364.30} &             312.74 & \textbf{  116.11} &            90.99 \\
-      \hline
-      20             & \textbf{   511.53} &             429.72 & \textbf{  181.55} &           146.43 \\
-      \hline
-      21             & \textbf{   732.20} &             611.89 & \textbf{  261.03} &           220.35 \\
-      \hline
-      22             & \textbf{  1033.22} &             872.87 & \textbf{  339.39} &           301.42 \\
-      \hline
-      23             & \textbf{  1405.70} &            1211.59 & \textbf{  402.26} &           373.31 \\
-      \hline
-      24             & \textbf{  1830.89} &            1612.98 & \textbf{  444.87} &           426.00 \\
-      \hline
-      25             & \textbf{  2289.77} &            2057.13 & \textbf{  470.55} &           459.47 \\
-      \hline
-      26             & \textbf{  2768.24} &            2527.22 & \textbf{  484.95} &           478.83 \\
-      \hline
-      27             & \textbf{  3257.48} &            3011.90 & \textbf{  492.70} &           489.44 \\
-      \hline
-      28             & \textbf{  3752.44} &            3504.46 & \textbf{  496.78} &           495.07 \\
-      \hline
-      29             & \textbf{  4250.40} &            4001.16 & \textbf{  498.90} &           498.02 \\
-      \hline
-      30             & \textbf{  4749.91} &            4500.02 & \textbf{  500.00} &           499.54 \\
-      \hline
-      31             & \textbf{  5250.23} &            5000.00 & \textbf{  500.56} &           500.33 \\
-      \hline
-    \end{tabular}
-  \end{center}
-  \caption{
-    \protect\label{tab:DOMCFG_orca_zgr}
-    Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration as computed from
-    \autoref{eq:DOMCFG_zgr_ana_2} using the coefficients given in \autoref{eq:DOMCFG_zgr_coef}
-  }
+  \centering
+  \begin{tabular}{c||r|r|r|r}
+    \hline
+    \textbf{LEVEL} & \textbf{gdept\_1d} & \textbf{gdepw\_1d} & \textbf{e3t\_1d } & \textbf{e3w\_1d} \\
+    \hline
+    1              & \textbf{     5.00} &               0.00 & \textbf{   10.00} &            10.00 \\
+    \hline
+    2              & \textbf{    15.00} &              10.00 & \textbf{   10.00} &            10.00 \\
+    \hline
+    3              & \textbf{    25.00} &              20.00 & \textbf{   10.00} &            10.00 \\
+    \hline
+    4              & \textbf{    35.01} &              30.00 & \textbf{   10.01} &            10.00 \\
+    \hline
+    5              & \textbf{    45.01} &              40.01 & \textbf{   10.01} &            10.01 \\
+    \hline
+    6              & \textbf{    55.03} &              50.02 & \textbf{   10.02} &            10.02 \\
+    \hline
+    7              & \textbf{    65.06} &              60.04 & \textbf{   10.04} &            10.03 \\
+    \hline
+    8              & \textbf{    75.13} &              70.09 & \textbf{   10.09} &            10.06 \\
+    \hline
+    9              & \textbf{    85.25} &              80.18 & \textbf{   10.17} &            10.12 \\
+    \hline
+    10             & \textbf{    95.49} &              90.35 & \textbf{   10.33} &            10.24 \\
+    \hline
+    11             & \textbf{   105.97} &             100.69 & \textbf{   10.65} &            10.47 \\
+    \hline
+    12             & \textbf{   116.90} &             111.36 & \textbf{   11.27} &            10.91 \\
+    \hline
+    13             & \textbf{   128.70} &             122.65 & \textbf{   12.47} &            11.77 \\
+    \hline
+    14             & \textbf{   142.20} &             135.16 & \textbf{   14.78} &            13.43 \\
+    \hline
+    15             & \textbf{   158.96} &             150.03 & \textbf{   19.23} &            16.65 \\
+    \hline
+    16             & \textbf{   181.96} &             169.42 & \textbf{   27.66} &            22.78 \\
+    \hline
+    17             & \textbf{   216.65} &             197.37 & \textbf{   43.26} &            34.30 \\
+    \hline
+    18             & \textbf{   272.48} &             241.13 & \textbf{   70.88} &            55.21 \\
+    \hline
+    19             & \textbf{   364.30} &             312.74 & \textbf{  116.11} &            90.99 \\
+    \hline
+    20             & \textbf{   511.53} &             429.72 & \textbf{  181.55} &           146.43 \\
+    \hline
+    21             & \textbf{   732.20} &             611.89 & \textbf{  261.03} &           220.35 \\
+    \hline
+    22             & \textbf{  1033.22} &             872.87 & \textbf{  339.39} &           301.42 \\
+    \hline
+    23             & \textbf{  1405.70} &            1211.59 & \textbf{  402.26} &           373.31 \\
+    \hline
+    24             & \textbf{  1830.89} &            1612.98 & \textbf{  444.87} &           426.00 \\
+    \hline
+    25             & \textbf{  2289.77} &            2057.13 & \textbf{  470.55} &           459.47 \\
+    \hline
+    26             & \textbf{  2768.24} &            2527.22 & \textbf{  484.95} &           478.83 \\
+    \hline
+    27             & \textbf{  3257.48} &            3011.90 & \textbf{  492.70} &           489.44 \\
+    \hline
+    28             & \textbf{  3752.44} &            3504.46 & \textbf{  496.78} &           495.07 \\
+    \hline
+    29             & \textbf{  4250.40} &            4001.16 & \textbf{  498.90} &           498.02 \\
+    \hline
+    30             & \textbf{  4749.91} &            4500.02 & \textbf{  500.00} &           499.54 \\
+    \hline
+    31             & \textbf{  5250.23} &            5000.00 & \textbf{  500.56} &           500.33 \\
+    \hline
+  \end{tabular}
+  \caption[Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration]{
+    Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration as
+    computed from \autoref{eq:DOMCFG_zgr_ana_2} using
+    the coefficients given in \autoref{eq:DOMCFG_zgr_coef}}
+  \label{tab:DOMCFG_orca_zgr}
 \end{table}
 %%%YY
@@ -405 +408 @@
 %------------------------------------------nam_zgr_sco---------------------------------------------------
 %
-\nlst{namzgr_sco_domcfg}
+\begin{listing}
+  \nlst{namzgr_sco_domcfg}
+  \caption{\texttt{namzgr\_sco\_domcfg}}
+  \label{lst:namzgr_sco_domcfg}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 Options are defined in \nam{zgr\_sco} (\texttt{DOMAINcfg} only).
@@ -463 +470 @@
 %% %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_sco_function}
-    \caption{
-      \protect\label{fig:DOMCFG_sco_function}
-      Examples of the stretching function applied to a seamount;
-      from left to right: surface, surface and bottom, and bottom intensified resolutions
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_sco_function}
+  \caption[DOMAINcfg: examples of the stretching function applied to a seamount]{
+    Examples of the stretching function applied to a seamount;
+    from left to right: surface, surface and bottom, and bottom intensified resolutions}
+  \label{fig:DOMCFG_sco_function}
 \end{figure}
 %% %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -516 +521 @@
 %% %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!ht]
+  \centering
   \includegraphics[width=\textwidth]{Fig_DOM_compare_coordinates_surface}
-  \caption{
+  \caption[DOMAINcfg: comparison of $s$- and $z$-coordinate]{
     A comparison of the \citet{song.haidvogel_JCP94} $S$-coordinate (solid lines),
     a 50 level $Z$-coordinate (contoured surfaces) and
     the \citet{siddorn.furner_OM13} $S$-coordinate (dashed lines) in the surface $100~m$ for
     a idealised bathymetry that goes from $50~m$ to $5500~m$ depth.
-    For clarity every third coordinate surface is shown.
-  }
+    For clarity every third coordinate surface is shown.}
   \label{fig:DOMCFG_fig_compare_coordinates_surface}
 \end{figure}

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex

@@ -307 +307 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ISO_triad}
-    \caption{
-      \protect\label{fig:ALGOS_ISO_triad}
-      Triads used in the Griffies's like iso-neutral diffision scheme for
-      $u$-component (upper panel) and $w$-component (lower panel).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ISO_triad}
+  \caption[Triads used in the Griffies's like iso-neutral diffision scheme for
+    $u$- and $w$-components)]{
+    Triads used in the Griffies's like iso-neutral diffision scheme for
+    $u$-component (upper panel) and $w$-component (lower panel).}
+  \label{fig:ALGOS_ISO_triad}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

@@ -70 +70 @@
 Indeed, for the special case $k=z$ and thus $e_3 =1$,
 we introduce an arbitrary vertical coordinate $s = s (i,j,z)$ as in \autoref{apdx:SCOORD} and
-use \autoref{eq:SCOORD_s_slope} and \autoref{eq:SCOORD_s_chain_rule}.
+use \autoref{eq:SCOORD_s_slope} and \autoref{eq:SCOORD_s_chain_rule1}.
 Since no cross horizontal derivative $\partial _i \partial _j $ appears in \autoref{eq:DIFFOPERS_1},
 the ($i$,$z$) and ($j$,$z$) planes are independent.

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex

@@ -411 +411 @@
 With the EEN scheme, the vorticity terms are represented as:
 \begin{equation}
-  \label{eq:INVARIANTS_dynvor_een}
+  \label{eq:INVARIANTS_dynvor_een1}
   \left\{ {
       \begin{aligned}
@@ -952 +952 @@
 With the EEN scheme, the vorticity terms are represented as:
 \begin{equation}
-  \label{eq:INVARIANTS_dynvor_een}
+  \label{eq:INVARIANTS_dynvor_een2}
   \left\{ {
       \begin{aligned}

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex

@@ -63 +63 @@
 Using the first form and considering a change $\delta i$ with $j, z$ and $t$ held constant, shows that
 \begin{equation}
-  \label{eq:SCOORD_s_chain_rule}
+  \label{eq:SCOORD_s_chain_rule1}
       \left. {\frac{\partial \bullet }{\partial i}} \right|_{j,z,t}  =
       \left. {\frac{\partial \bullet }{\partial i}} \right|_{j,s,t}
@@ -102 +102 @@
 the model equations in the curvilinear $s-$coordinate system are:
 \begin{equation}
-  \label{eq:SCOORD_s_chain_rule}
+  \label{eq:SCOORD_s_chain_rule2}
   \begin{aligned}
     &\left. {\frac{\partial \bullet }{\partial t}} \right|_z  =
@@ -128 +128 @@
 \label{sec:SCOORD_continuity}
 
-Using (\autoref{eq:SCOORD_s_chain_rule}) and
+Using (\autoref{eq:SCOORD_s_chain_rule1}) and
 the fact that the horizontal scale factors $e_1$ and $e_2$ do not depend on the vertical coordinate,
 the divergence of the velocity relative to the ($i$,$j$,$z$) coordinate system is transformed as follows in order to
@@ -272 +272 @@
         +  w \;\frac{\partial u}{\partial z}      \\
         %
-      \intertext{introducing the chain rule (\autoref{eq:SCOORD_s_chain_rule}) }
+      \intertext{introducing the chain rule (\autoref{eq:SCOORD_s_chain_rule1}) }
       %
       &= \left. {\frac{\partial u }{\partial t}} \right|_z
@@ -317 +317 @@
 \end{subequations}
 %
-Applying the time derivative chain rule (first equation of (\autoref{eq:SCOORD_s_chain_rule})) to $u$ and
+Applying the time derivative chain rule (first equation of (\autoref{eq:SCOORD_s_chain_rule1})) to $u$ and
 using (\autoref{eq:SCOORD_w_in_s}) provides the expression of the last term of the right hand side,
 \[

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex

@@ -26 +26 @@
 %-----------------------------------------nam_traldf------------------------------------------------------
 
-\nlst{namtra_ldf}
 %---------------------------------------------------------------------------------------------------------
 
@@ -202 +201 @@
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[tb]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_GRIFF_triad_fluxes}
-    \caption{
-      \protect\label{fig:TRIADS_ISO_triad}
-      (a) Arrangement of triads $S_i$ and tracer gradients to
-      give lateral tracer flux from box $i,k$ to $i+1,k$
-      (b) Triads $S'_i$ and tracer gradients to give vertical tracer flux from
-      box $i,k$ to $i,k+1$.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_GRIFF_triad_fluxes}
+  \caption[Triads arrangement and tracer gradients to give lateral and vertical tracer fluxes]{
+    (a) Arrangement of triads $S_i$ and tracer gradients to
+    give lateral tracer flux from box $i,k$ to $i+1,k$
+    (b) Triads $S'_i$ and tracer gradients to give vertical tracer flux from
+    box $i,k$ to $i,k+1$.}
+  \label{fig:TRIADS_ISO_triad}
 \end{figure}
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -266 +263 @@
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[tb]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_GRIFF_qcells}
-    \caption{
-      \protect\label{fig:TRIADS_qcells}
-      Triad notation for quarter cells. $T$-cells are inside boxes,
-      while the  $i+\fractext{1}{2},k$ $u$-cell is shaded in green and
-      the $i,k+\fractext{1}{2}$ $w$-cell is shaded in pink.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_GRIFF_qcells}
+  \caption[Triad notation for quarter cells]{
+    Triad notation for quarter cells.
+    $T$-cells are inside boxes,
+    while the $i+\fractext{1}{2},k$ $u$-cell is shaded in green and
+    the $i,k+\fractext{1}{2}$ $w$-cell is shaded in pink.}
+  \label{fig:TRIADS_qcells}
 \end{figure}
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -659 +655 @@
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[h]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_GRIFF_bdry_triads}
-    \caption{
-      \protect\label{fig:TRIADS_bdry_triads}
-      (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer points (black dots),
-      and $i+1/2,1$ $u$-point (blue square).
-      Triad slopes \triad{i}{1}{R}{1/2}{-1/2} (magenta) and \triad{i+1}{1}{R}{-1/2}{-1/2} (blue) poking through
-      the ocean surface are masked (faded in figure).
-      However, the lateral $_{11}$ contributions towards \triad[u]{i}{1}{F}{1/2}{-1/2} and
-      \triad[u]{i+1}{1}{F}{-1/2}{-1/2} (yellow line) are still applied,
-      giving diapycnal diffusive fluxes.
-      \newline
-      (b) Both near bottom triad slopes \triad{i}{k}{R}{1/2}{1/2} and
-      \triad{i+1}{k}{R}{-1/2}{1/2} are masked when either of the $i,k+1$ or $i+1,k+1$ tracer points is masked,
-      \ie\ the $i,k+1$ $u$-point is masked.
-      The associated lateral fluxes (grey-black dashed line) are masked if
-      \protect\np{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked,
-      giving bottom mixing, if \protect\np{ln\_botmix\_triad}\forcode{ = .true.}
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_GRIFF_bdry_triads}
+  \caption[Boundary triads]{
+    (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer points (black dots),
+    and $i+1/2,1$ $u$-point (blue square).
+    Triad slopes \triad{i}{1}{R}{1/2}{-1/2} (magenta) and
+    \triad{i+1}{1}{R}{-1/2}{-1/2} (blue) poking through the ocean surface are masked
+    (faded in figure).
+    However,
+    the lateral $_{11}$ contributions towards \triad[u]{i}{1}{F}{1/2}{-1/2} and
+    \triad[u]{i+1}{1}{F}{-1/2}{-1/2} (yellow line) are still applied,
+    giving diapycnal diffusive fluxes.
+    \newline
+    (b) Both near bottom triad slopes \triad{i}{k}{R}{1/2}{1/2} and
+    \triad{i+1}{k}{R}{-1/2}{1/2} are masked when
+    either of the $i,k+1$ or $i+1,k+1$ tracer points is masked,
+    \ie\ the $i,k+1$ $u$-point is masked.
+    The associated lateral fluxes (grey-black dashed line) are masked if
+    \protect\np{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked,
+    giving bottom mixing, if \protect\np{ln\_botmix\_triad}\forcode{ = .true.}}
+  \label{fig:TRIADS_bdry_triads}
 \end{figure}
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -811 +808 @@
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[h]
-%  \fcapside {
-  \caption{
-    \protect\label{fig:TRIADS_MLB_triad}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_GRIFF_MLB_triads}
+  \caption[Definition of mixed-layer depth and calculation of linearly tapered triads]{
     Definition of mixed-layer depth and calculation of linearly tapered triads.
-    The figure shows a water column at a given $i,j$ (simplified to $i$), with the ocean surface at the top.
+    The figure shows a water column at a given $i,j$ (simplified to $i$),
+    with the ocean surface at the top.
     Tracer points are denoted by bullets, and black lines the edges of the tracer cells;
     $k$ increases upwards.
     \newline
-    \hspace{5 em}
-    We define the mixed-layer by setting the vertical index of the tracer point immediately below the mixed layer,
-    $k_{\mathrm{ML}}$, as the maximum $k$ (shallowest tracer point) such that
+    We define the mixed-layer by setting the vertical index of the tracer point immediately below
+    the mixed layer, $k_{\mathrm{ML}}$, as the maximum $k$ (shallowest tracer point) such that
     ${\rho_0}_{i,k}>{\rho_0}_{i,k_{10}}+\Delta\rho_c$,
     where $i,k_{10}$ is the tracer gridbox within which the depth reaches 10~m.
@@ -830 +827 @@
     Triads with different $i_p,k_p$, denoted by different colours,
     (\eg\ the green triad $i_p=1/2,k_p=-1/2$) are tapered to the appropriate basal triad.}
-  % }
-  \includegraphics[width=\textwidth]{Fig_GRIFF_MLB_triads}
+  \label{fig:TRIADS_MLB_triad}
 \end{figure}
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>

NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

@@ -149 +149 @@
 %------------------------------------------nam_asminc-----------------------------------------------------
 %
-\nlst{nam_asminc}
+\begin{listing}
+  \nlst{nam_asminc}
+  \caption{\texttt{nam\_asminc}}
+  \label{lst:nam_asminc}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

@@ -174 +174 @@
 \xmlline|<variable id="using_server" type="bool"></variable>|
 
-The {\ttfamily using\_server} setting determines whether or not the server will be used in \textit{attached mode}
-(as a library) [{\ttfamily> false <}] or in \textit{detached mode}
-(as an external executable on N additional, dedicated cpus) [{\ttfamily > true <}].
-The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications.
+The \texttt{using\_server} setting determines whether or not the server will be used in
+\textit{attached mode}
+(as a library) [\texttt{> false <}] or in \textit{detached mode}
+(as an external executable on N additional, dedicated cpus) [\texttt{ > true <}].
+The \textit{attached mode} is simpler to use but much less efficient for
+massively parallel applications.
 The type of each file can be either ''multiple\_file'' or ''one\_file''.
 
@@ -218 +220 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|lXl|}
     \hline
@@ -341 +342 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
     \hline
@@ -373 +373 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
     \hline
@@ -398 +397 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
     \hline
@@ -418 +416 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
     \hline
@@ -634 +631 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|lX|}
     \hline
@@ -695 +691 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|l|c|c|}
     \hline
@@ -894 +889 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|l|X|}
     \hline
@@ -917 +911 @@
     \hline
   \end{tabularx}
-  \caption{Context tags}
+  \caption{XIOS: context tags}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|l|}
     \hline
@@ -952 +945 @@
     \hline
   \end{tabularx}
-  \caption{Field tags ("\ttfamily{field\_*}")}
+  \caption{XIOS: field tags ("\texttt{field\_*}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|l|}
     \hline
@@ -988 +980 @@
     \hline
   \end{tabularx}
-  \caption{File tags ("\ttfamily{file\_*}")}
+  \caption{XIOS: file tags ("\texttt{file\_*}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
     \hline
@@ -1021 +1012 @@
     \hline
   \end{tabularx}
-  \caption{Axis tags ("\ttfamily{axis\_*}")}
+  \caption{XIOS: axis tags ("\texttt{axis\_*}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
     \hline
@@ -1054 +1044 @@
     \hline
   \end{tabularx}
-  \caption{Domain tags ("\ttfamily{domain\_*)}"}
+  \caption{XIOS: domain tags ("\texttt{domain\_*)}"}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
     \hline
@@ -1087 +1076 @@
     \hline
   \end{tabularx}
-  \caption{Grid tags ("\ttfamily{grid\_*}")}
+  \caption{XIOS: grid tags ("\texttt{grid\_*}")}
 \end{table}
 
@@ -1093 +1082 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|l|l|}
     \hline
@@ -1128 +1116 @@
     \hline
   \end{tabularx}
-  \caption{Reference attributes ("\ttfamily{*\_ref}")}
+  \caption{XIOS: reference attributes ("\texttt{*\_ref}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|l|l|}
     \hline
@@ -1164 +1151 @@
     \hline
   \end{tabularx}
-  \caption{Domain attributes ("\ttfamily{zoom\_*}")}
+  \caption{XIOS: domain attributes ("\texttt{zoom\_*}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|l|l|}
     \hline
@@ -1219 +1205 @@
     \hline
   \end{tabularx}
-  \caption{File attributes}
+  \caption{XIOS: file attributes}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|l|l|}
     \hline
@@ -1268 +1253 @@
     \hline
   \end{tabularx}
-  \caption{Field attributes}
+  \caption{XIOS: field attributes}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|}
     \hline
@@ -1327 +1311 @@
     \hline
   \end{tabularx}
-  \caption{Miscellaneous attributes}
+  \caption{XIOS: miscellaneous attributes}
 \end{table}
 
@@ -1366 +1350 @@
 %------------------------------------------namnc4----------------------------------------------------
 
-\nlst{namnc4}
+\begin{listing}
+  \nlst{namnc4}
+  \caption{\texttt{namnc4}}
+  \label{lst:namnc4}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1404 +1392 @@
 \end{forlines}
 
-\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\ttfamily 46x38x1} respectively in
-the mono-processor case (\ie\ global domain of {\small\ttfamily 182x149x31}).
+\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\texttt 46x38x1} respectively in
+the mono-processor case (\ie\ global domain of {\small\texttt 182x149x31}).
 An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in
 table \autoref{tab:DIA_NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with
@@ -1414 +1402 @@
 %------------------------------------------TABLE----------------------------------------------------
 \begin{table}
-  \scriptsize
   \centering
   \begin{tabular}{lrrr}
@@ -1446 +1433 @@
     ORCA2\_2d\_grid\_W\_0007.nc & 4416    & 1368     & 70\%      \\
   \end{tabular}
-  \caption{
-    \protect\label{tab:DIA_NC4}
-    Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression
-  }
+  \caption{Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression}
+  \label{tab:DIA_NC4}
 \end{table}
 %----------------------------------------------------------------------------------------------------
@@ -1471 +1456 @@
 %------------------------------------------namtrd----------------------------------------------------
 
-\nlst{namtrd}
+\begin{listing}
+  \nlst{namtrd}
+  \caption{\texttt{namtrd}}
+  \label{lst:namtrd}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1518 +1507 @@
 %--------------------------------------------namflo-------------------------------------------------------
 
-\nlst{namflo}
+\begin{listing}
+  \nlst{namflo}
+  \caption{\texttt{namflo}}
+  \label{lst:namflo}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -1536 +1529 @@
 In case of Ariane convention, input filename is \textit{init\_float\_ariane}.
 Its format is: \\
-{\scriptsize \texttt{I J K nisobfl itrash}}
+{ \texttt{I J K nisobfl itrash}}
 
 \noindent with:
@@ -1548 +1541 @@
 \noindent Example: \\
 \noindent
-{\scriptsize
+{
   \texttt{
     100.00000  90.00000  -1.50000 1.00000   0.00000   \\
@@ -1559 +1552 @@
 In the other case (longitude and latitude), input filename is init\_float.
 Its format is: \\
-{\scriptsize \texttt{Long Lat depth nisobfl ngrpfl itrash}}
+{ \texttt{Long Lat depth nisobfl ngrpfl itrash}}
 
 \noindent with:
@@ -1573 +1566 @@
 \noindent Example: \\
 \noindent
-{\scriptsize
+{
   \texttt{
     20.0 0.0 0.0 0 1 1    \\
@@ -1622 +1615 @@
 %------------------------------------------nam_diaharm----------------------------------------------------
 %
-\nlst{nam_diaharm}
+\begin{listing}
+  \nlst{nam_diaharm}
+  \caption{\texttt{nam\_diaharm}}
+  \label{lst:nam_diaharm}
+\end{listing}
 %----------------------------------------------------------------------------------------------------------
 
@@ -1670 +1667 @@
 %------------------------------------------nam_diadct----------------------------------------------------
 
-\nlst{nam_diadct}
+\begin{listing}
+  \nlst{nam_diadct}
+  \caption{\texttt{nam\_diadct}}
+  \label{lst:nam_diadct}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1704 +1705 @@
 
 Each section is defined by: \\
-\noindent {\scriptsize \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\
+\noindent { \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\
 with:
 
@@ -1721 +1722 @@
 
 \noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\
-{\scriptsize
+{
   \texttt{
     long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\
@@ -1754 +1755 @@
  and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\
  \noindent
- {\scriptsize
+ {
    \texttt{
      -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage \\
@@ -1769 +1770 @@
 
 The output format is: \\
-{\scriptsize
+{
   \texttt{
     date, time-step number, section number,                \\
@@ -1791 +1792 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|l|l|l|l|l|}
     \hline
@@ -2011 +2011 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_mask_subasins}
-    \caption{
-      \protect\label{fig:DIA_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), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).
-      Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay are removed from the sub-basins.
-      Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_mask_subasins}
+  \caption[Decomposition of the World Ocean to compute transports as well as
+  the meridional stream-function]{
+    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), Pacific basin (green),
+    Indian basin (blue), Indo-Pacific basin (blue+green).
+    Note that semi-enclosed seas (Red, Med and Baltic seas) as well as
+    Hudson Bay are removed from the sub-basins.
+    Note also that the Arctic Ocean has been split into Atlantic and
+    Pacific basins along the North fold line.
+  }
+  \label{fig:DIA_mask_subasins}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -2049 +2052 @@
 %------------------------------------------namptr-----------------------------------------
 
-\nlst{namptr}
+\begin{listing}
+  \nlst{namptr}
+  \caption{\texttt{namptr}}
+  \label{lst:namptr}
+\end{listing}
 %-----------------------------------------------------------------------------------------
 
@@ -2059 +2066 @@
 %------------------------------------------nam_dia25h-------------------------------------
 
-\nlst{nam_dia25h}
+\begin{listing}
+  \nlst{nam_dia25h}
+  \caption{\texttt{nam\_dia25h}}
+  \label{lst:nam_dia25h}
+\end{listing}
 %-----------------------------------------------------------------------------------------
 
@@ -2074 +2085 @@
 %------------------------------------------nam_diatmb-----------------------------------------------------
 
-\nlst{nam_diatmb}
+\begin{listing}
+  \nlst{nam_diatmb}
+  \caption{\texttt{nam\_diatmb}}
+  \label{lst:nam_diatmb}
+\end{listing}
 %----------------------------------------------------------------------------------------------------------
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

@@ -38 +38 @@
 Both the cool skin and warm layer models are controlled through the namelist \nam{diu}:
 
-\nlst{namdiu}
+\begin{listing}
+  \nlst{namdiu}
+  \caption{\texttt{namdiu}}
+  \label{lst:namdiu}
+\end{listing}
+
 This namelist contains only two variables:
 \begin{description}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

@@ -8 +8 @@
 \label{chap:DOM}
 
-%\chaptertoc
+\chaptertoc
 
 % Missing things:
@@ -57 +57 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!tb]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_cell}
-    \caption{
-      \protect\label{fig:DOM_cell}
-      Arrangement of variables.
-      $t$ indicates scalar points where temperature, salinity, density, pressure and
-      horizontal divergence are defined.
-      $(u,v,w)$ indicates vector points, and $f$ indicates vorticity points where both relative and
-      planetary vorticities are defined.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_cell}
+  \caption[Arrangement of variables in the unit cell of space domain]{
+    Arrangement of variables in the unit cell of space domain.
+    $t$ indicates scalar points where
+    temperature, salinity, density, pressure and horizontal divergence are defined.
+    $(u,v,w)$ indicates vector points,
+    and $f$ indicates vorticity points where
+    both relative and planetary vorticities are defined.}
+  \label{fig:DOM_cell}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -102 +101 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{table}[!tb]
-  \begin{center}
-    \begin{tabular}{|p{46pt}|p{56pt}|p{56pt}|p{56pt}|}
-      \hline
-      t  & $i      $ & $j      $ & $k      $ \\
-      \hline
-      u  & $i + 1/2$ & $j      $ & $k      $ \\
-      \hline
-      v  & $i      $ & $j + 1/2$ & $k      $ \\
-      \hline
-      w  & $i      $ & $j      $ & $k + 1/2$ \\
-      \hline
-      f  & $i + 1/2$ & $j + 1/2$ & $k      $ \\
-      \hline
-      uw & $i + 1/2$ & $j      $ & $k + 1/2$ \\
-      \hline
-      vw & $i      $ & $j + 1/2$ & $k + 1/2$ \\
-      \hline
-      fw & $i + 1/2$ & $j + 1/2$ & $k + 1/2$ \\
-      \hline
-    \end{tabular}
-    \caption{
-      \protect\label{tab:DOM_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 equations.
-      In the code, the indexing uses integer values only and is positive downwards in the vertical with $k=1$ at the surface.
-      (see \autoref{subsec:DOM_Num_Index})
-    }
-  \end{center}
+  \centering
+  \begin{tabular}{|p{46pt}|p{56pt}|p{56pt}|p{56pt}|}
+    \hline
+    t & $i      $ & $j      $ & $k      $ \\
+    \hline
+    u & $i + 1/2$ & $j      $ & $k      $ \\
+    \hline
+    v & $i      $ & $j + 1/2$ & $k      $ \\
+    \hline
+    w & $i      $ & $j      $ & $k + 1/2$ \\
+    \hline
+    f & $i + 1/2$ & $j + 1/2$ & $k      $ \\
+    \hline
+    uw   & $i + 1/2$ & $j      $ & $k + 1/2$ \\
+    \hline
+    vw   & $i      $ & $j + 1/2$ & $k + 1/2$ \\
+    \hline
+    fw   & $i + 1/2$ & $j + 1/2$ & $k + 1/2$ \\
+    \hline
+  \end{tabular}
+  \caption[Location of grid-points]{
+    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 equations.
+    In the code, the indexing uses integer values only and
+    is positive downwards in the vertical with $k=1$ at the surface.
+    (see \autoref{subsec:DOM_Num_Index})}
+  \label{tab:DOM_cell}
 \end{table}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -148 +147 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_zgr_e3}
-    \caption{
-      \protect\label{fig:DOM_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.
-      For both grids here, the same $w$-point depth has been chosen but
-      in (a) the $t$-points are set half way between $w$-points while
-      in (b) they are defined from an analytical function:
-      $z(k) = 5 \, (k - 1/2)^3 - 45 \, (k - 1/2)^2 + 140 \, (k - 1/2) - 150$.
-      Note the resulting difference between the value of the grid-size $\Delta_k$ and
-      those of the scale factor $e_k$.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_zgr_e3}
+  \caption[Comparison of grid-point position, vertical grid-size and scale factors]{
+    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.
+    For both grids here, the same $w$-point depth has been chosen but
+    in (a) the $t$-points are set half way between $w$-points while
+    in (b) they are defined from an analytical function:
+    $z(k) = 5 \, (k - 1/2)^3 - 45 \, (k - 1/2)^2 + 140 \, (k - 1/2) - 150$.
+    Note the resulting difference between the value of the grid-size $\Delta_k$ and
+    those of the scale factor $e_k$.}
+  \label{fig:DOM_zgr_e3}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -266 +263 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!tb]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_index_hor}
-    \caption{
-      \protect\label{fig:DOM_index_hor}
-      Horizontal integer indexing used in the \fortran\ code.
-      The dashed area indicates the cell in which variables contained in arrays have the same $i$- and $j$-indices
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_index_hor}
+  \caption[Horizontal integer indexing]{
+    Horizontal integer indexing used in the \fortran\ code.
+    The dashed area indicates the cell in which
+    variables contained in arrays have the same $i$- and $j$-indices}
+  \label{fig:DOM_index_hor}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -321 +317 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!pt]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_index_vert}
-    \caption{
-      \protect\label{fig:DOM_index_vert}
-      Vertical integer indexing used in the \fortran\ code.
-      Note that the $k$-axis is oriented downward.
-      The dashed area indicates the cell in which variables contained in arrays have a common $k$-index.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_index_vert}
+  \caption[Vertical integer indexing]{
+    Vertical integer indexing used in the \fortran\ code.
+    Note that the $k$-axis is oriented downward.
+    The dashed area indicates the cell in which
+    variables contained in arrays have a common $k$-index.}
+  \label{fig:DOM_index_vert}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -338 +333 @@
 \section{Spatial domain configuration}
 \label{subsec:DOM_config}
-
-\nlst{namcfg}
 
 Two typical methods are available to specify the spatial domain configuration;
@@ -468 +461 @@
 \label{subsec:DOM_zgr}
 %-----------------------------------------namdom-------------------------------------------
-\nlst{namdom}
+\begin{listing}
+  \nlst{namdom}
+  \caption{\texttt{namdom}}
+  \label{lst:namdom}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -482 +479 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!tb]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_z_zps_s_sps}
-    \caption{
-      \protect\label{fig:DOM_z_zps_s_sps}
-      The ocean bottom as seen by the model:
-      (a) $z$-coordinate with full step,
-      (b) $z$-coordinate with partial step,
-      (c) $s$-coordinate: terrain following representation,
-      (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 (\protect\np{ln\_linssh}\forcode{=.false.}).
-      Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_z_zps_s_sps}
+  \caption[Ocean bottom regarding coordinate systems ($z$, $s$ and hybrid $s-z$)]{
+    The ocean bottom as seen by the model:
+    (a) $z$-coordinate with full step,
+    (b) $z$-coordinate with partial step,
+    (c) $s$-coordinate: terrain following representation,
+    (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 (\protect\np{ln\_linssh}\forcode{=.false.}).
+    Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).}
+  \label{fig:DOM_z_zps_s_sps}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -654 +649 @@
 \label{subsec:DOM_meshmask}
 
-\nlst{namcfg}
-
 Most of the arrays relating to a particular ocean model configuration discussed in this chapter
 (grid-point position, scale factors)
@@ -665 +658 @@
 checking or confirmation is required.
 
-\nlst{namdom}
-
 Alternatively, all the arrays relating to a particular ocean model configuration
 (grid-point position, scale factors, depths and masks)
@@ -680 +671 @@
 \label{sec:DOM_DTA_tsd}
 %-----------------------------------------namtsd-------------------------------------------
-\nlst{namtsd}
+\begin{listing}
+  \nlst{namtsd}
+  \caption{\texttt{namtsd}}
+  \label{lst:namtsd}
+\end{listing}
 %------------------------------------------------------------------------------------------
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

@@ -166 +166 @@
 %-----------------------------------------nam_dynadv----------------------------------------------------
 
-\nlst{namdyn_adv}
+\begin{listing}
+  \nlst{namdyn_adv}
+  \caption{\texttt{namdyn\_adv}}
+  \label{lst:namdyn_adv}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -185 +189 @@
 %------------------------------------------nam_dynvor----------------------------------------------------
 
-\nlst{namdyn_vor}
+\begin{listing}
+  \nlst{namdyn_vor}
+  \caption{\texttt{namdyn\_vor}}
+  \label{lst:namdyn_vor}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -308 +316 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=\textwidth]{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).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_DYN_een_triad}
+  \caption[Triads used in the energy and enstrophy conserving scheme (EEN)]{
+    Triads used in the energy and enstrophy conserving scheme (EEN) for
+    $u$-component (upper panel) and $v$-component (lower panel).}
+  \label{fig:DYN_een_triad}
 \end{figure}
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -416 +422 @@
 %------------------------------------------nam_dynadv----------------------------------------------------
 
-\nlst{namdyn_adv}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -564 +569 @@
 %------------------------------------------nam_dynhpg---------------------------------------------------
 
-\nlst{namdyn_hpg}
+\begin{listing}
+  \nlst{namdyn_hpg}
+  \caption{\texttt{namdyn\_hpg}}
+  \label{lst:namdyn_hpg}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -778 +787 @@
 %-----------------------------------------nam_dynspg----------------------------------------------------
 
-\nlst{namdyn_spg}
+\begin{listing}
+  \nlst{namdyn_spg}
+  \caption{\texttt{namdyn\_spg}}
+  \label{lst:namdyn_spg}
+\end{listing}
 %------------------------------------------------------------------------------------------------------------
 
@@ -884 +897 @@
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts}
-    \caption{
-      \protect\label{fig:DYN_spg_ts}
-      Schematic of the split-explicit time stepping scheme for the external and internal modes.
-      Time increases to the right. In this particular exemple,
-      a boxcar averaging window over $nn\_baro$ barotropic time steps is used ($nn\_bt\_flt=1$) and $nn\_baro=5$.
-      Internal mode time steps (which are also the model time steps) are denoted by $t-\rdt$, $t$ and $t+\rdt$.
-      Variables with $k$ superscript refer to instantaneous barotropic variables,
-      $< >$ and $<< >>$ operator refer to time filtered variables using respectively primary (red vertical bars) and
-      secondary weights (blue vertical bars).
-      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: \protect\np{ln\_bt\_fw}\forcode{=.true.},
-      \protect\np{ln\_bt\_av}\forcode{=.true.}.
-      b) Centred time integration: \protect\np{ln\_bt\_fw}\forcode{=.false.},
-      \protect\np{ln\_bt\_av}\forcode{=.true.}.
-      c) Forward time integration with no time filtering (POM-like scheme):
-      \protect\np{ln\_bt\_fw}\forcode{=.true.}, \protect\np{ln\_bt\_av}\forcode{=.false.}.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts}
+  \caption[Split-explicit time stepping scheme for the external and internal modes]{
+    Schematic of the split-explicit time stepping scheme for the external and internal modes.
+    Time increases to the right.
+    In this particular exemple,
+    a boxcar averaging window over \np{nn\_baro} barotropic time steps is used
+    (\np{nn\_bt\_flt}\forcode{=1}) and \np{nn\_baro}\forcode{=5}.
+    Internal mode time steps (which are also the model time steps) are denoted by
+    $t-\rdt$, $t$ and $t+\rdt$.
+    Variables with $k$ superscript refer to instantaneous barotropic variables,
+    $< >$ and $<< >>$ operator refer to time filtered variables using respectively primary
+    (red vertical bars) and secondary weights (blue vertical bars).
+    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:
+    \protect\np{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln\_bt\_av}\forcode{=.true.}.
+    b) Centred time integration:
+    \protect\np{ln\_bt\_fw}\forcode{=.false.}, \protect\np{ln\_bt\_av}\forcode{=.true.}.
+    c) Forward time integration with no time filtering (POM-like scheme):
+    \protect\np{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln\_bt\_av}\forcode{=.false.}.}
+  \label{fig:DYN_spg_ts}
 \end{figure}
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >
@@ -1114 +1128 @@
 %------------------------------------------nam_dynldf----------------------------------------------------
 
-\nlst{namdyn_ldf}
+\begin{listing}
+  \nlst{namdyn_ldf}
+  \caption{\texttt{namdyn\_ldf}}
+  \label{lst:namdyn_ldf}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1245 +1263 @@
 %----------------------------------------------namzdf------------------------------------------------------
 
-\nlst{namzdf}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1332 +1349 @@
 by setting $\mathrm{ln\_wd\_dl} = \mathrm{.true.}$ and $\mathrm{ln\_wd\_il} = \mathrm{.false.}$.
 
-\nlst{namwad}
+\begin{listing}
+  \nlst{namwad}
+  \caption{\texttt{namwad}}
+  \label{lst:namwad}
+\end{listing}
 
 The following terminology is used. The depth of the topography (positive downwards)
@@ -1541 +1562 @@
 neighbouring $(i+1,j)$ and $(i,j)$ tracer points.  zcpx is calculated using two logicals
 variables, $\mathrm{ll\_tmp1}$ and $\mathrm{ll\_tmp2}$ which are evaluated for each grid
-column.  The three possible combinations are illustrated in figure \autoref{fig:DYN_WAD_dynhpg}.
+column.  The three possible combinations are illustrated in \autoref{fig:DYN_WAD_dynhpg}.
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!ht] \begin{center}
-\includegraphics[width=\textwidth]{Fig_WAD_dynhpg}
-\caption{
+\begin{figure}[!ht]
+  \centering
+  \includegraphics[width=\textwidth]{Fig_WAD_dynhpg}
+  \caption[Combinations controlling the limiting of the horizontal pressure gradient in
+  wetting and drying regimes]{
+    Three possible combinations of the logical variables controlling the
+    limiting of the horizontal pressure gradient in wetting and drying regimes}
   \label{fig:DYN_WAD_dynhpg}
-  Illustrations of the three possible combinations of the logical variables controlling the
-  limiting of the horizontal pressure gradient in wetting and drying regimes}
-\end{center}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -1625 +1647 @@
 %----------------------------------------------namdom----------------------------------------------------
 
-\nlst{namdom}
 %-------------------------------------------------------------------------------------------------------------
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

@@ -22 +22 @@
 %--------------------------------------------namlbc-------------------------------------------------------
 
-\nlst{namlbc}
+\begin{listing}
+  \nlst{namlbc}
+  \caption{\texttt{namlbc}}
+  \label{lst:namlbc}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -67 +71 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{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}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_LBC_uv}
+  \caption[Lateral boundary at $T$-level]{
+    Lateral boundary (thick line) at T-level.
+    The velocity normal to the boundary is set to zero.}
+  \label{fig:LBC_uv}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -96 +98 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!p]
-  \begin{center}
-    \includegraphics[width=\textwidth]{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 ($2<rn\_shlat$).
-      Implied "ghost" velocity inside land area is display in grey.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_LBC_shlat}
+  \caption[Lateral boundary conditions]{
+    Lateral boundary conditions
+    (a) free-slip                       (\protect\np{rn\_shlat}\forcode{=0});
+    (b) no-slip                         (\protect\np{rn\_shlat}\forcode{=2});
+    (c) "partial" free-slip (\forcode{0<}\protect\np{rn\_shlat}\forcode{<2}) and
+    (d) "strong" no-slip    (\forcode{2<}\protect\np{rn\_shlat}).
+    Implied "ghost" velocity inside land area is display in grey.}
+  \label{fig:LBC_shlat}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -207 +207 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LBC_jperio}
-    \caption{
-      \protect\label{fig:LBC_jperio}
-      setting of (a) east-west cyclic  (b) symmetric across the equator boundary conditions.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_LBC_jperio}
+  \caption[Setting of east-west cyclic and symmetric across the Equator boundary conditions]{
+    Setting of (a) east-west cyclic (b) symmetric across the Equator boundary conditions}
+  \label{fig:LBC_jperio}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -232 +230 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_North_Fold_T}
-    \caption{
-      \protect\label{fig:LBC_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 to the inner domain mask (see text).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_North_Fold_T}
+  \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{
+    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$),
+    as used in ORCA 2\deg, 1/4\deg and 1/12\deg.
+    Pink shaded area corresponds to the inner domain mask (see text).}
+  \label{fig:LBC_North_Fold_T}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -253 +249 @@
 %-----------------------------------------nammpp--------------------------------------------
 
-\nlst{nammpp}
+\begin{listing}
+  \nlst{nammpp}
+  \caption{\texttt{nammpp}}
+  \label{lst:nammpp}
+\end{listing}
 %-----------------------------------------------------------------------------------------------
 
@@ -291 +291 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_mpp}
-    \caption{
-      \protect\label{fig:LBC_mpp}
-      Positioning of a sub-domain when massively parallel processing is used.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_mpp}
+  \caption{Positioning of a sub-domain when massively parallel processing is used}
+  \label{fig:LBC_mpp}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -349 +346 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_mppini2}
-    \caption[Atlantic domain]{
-      \protect\label{fig:LBC_mppini2}
-      Example of Atlantic domain defined for the CLIPPER projet.
-      Initial grid is composed of 773 x 1236 horizontal points.
-      (a) the domain is split onto 9 \time 20 subdomains (jpni=9, jpnj=20).
-      52 subdomains are land areas.
-      (b) 52 subdomains are eliminated (white rectangles) and
-      the resulting number of processors really used during the computation is jpnij=128.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_mppini2}
+  \caption[Atlantic domain defined for the CLIPPER projet]{
+    Example of Atlantic domain defined for the CLIPPER projet.
+    Initial grid is composed of 773 x 1236 horizontal points.
+    (a) the domain is split onto 9 $times$ 20 subdomains (jpni=9, jpnj=20).
+    52 subdomains are land areas.
+    (b) 52 subdomains are eliminated (white rectangles) and
+    the resulting number of processors really used during the computation is jpnij=128.}
+  \label{fig:LBC_mppini2}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -373 +368 @@
 %-----------------------------------------nambdy--------------------------------------------
 
-\nlst{nambdy}
+\begin{listing}
+  \nlst{nambdy}
+  \caption{\texttt{nambdy}}
+  \label{lst:nambdy}
+\end{listing}
 %-----------------------------------------------------------------------------------------------
 %-----------------------------------------nambdy_dta--------------------------------------------
 
-\nlst{nambdy_dta}
+\begin{listing}
+  \nlst{nambdy_dta}
+  \caption{\texttt{nambdy\_dta}}
+  \label{lst:nambdy_dta}
+\end{listing}
 %-----------------------------------------------------------------------------------------------
 
@@ -594 +597 @@
 the boundary point is increasingly further away from the edge of the model domain.
 A set of $nbi$, $nbj$, and $nbr$ arrays is defined for each of the $T$, $U$ and $V$ grids.
-Figure \autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary.
+\autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary.
 
 The boundary geometry for each set may be defined in a namelist nambdy\_index or
@@ -607 +610 @@
 
 The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file.
-Figure \autoref{fig:LBC_nc_header} gives an example of the header information from such a file, based on the description of geometrical setup given above.
+\autoref{fig:LBC_nc_header} gives an example of the header information from such a file, based on the description of geometrical setup given above.
 The file should contain the index arrays for each of the $T$, $U$ and $V$ grids.
 The arrays must be in order of increasing $nbr$.
@@ -624 +627 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LBC_bdy_geom}
-    \caption {
-      \protect\label{fig:LBC_bdy_geom}
-      Example of geometry of unstructured open boundary
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_LBC_bdy_geom}
+  \caption[Geometry of unstructured open boundary]{Example of geometry of unstructured open boundary}
+  \label{fig:LBC_bdy_geom}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -664 +664 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LBC_nc_header}
-    \caption {
-      \protect\label{fig:LBC_nc_header}
-      Example of the header for a \protect\ifile{coordinates.bdy} file
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_LBC_nc_header}
+  \caption[Header for a \protect\ifile{coordinates.bdy} file]{
+    Example of the header for a \protect\ifile{coordinates.bdy} file}
+  \label{fig:LBC_nc_header}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -697 +695 @@
 %-----------------------------------------nambdy_tide--------------------------------------------
 
-\nlst{nambdy_tide}
+\begin{listing}
+  \nlst{nambdy_tide}
+  \caption{\texttt{nambdy\_tide}}
+  \label{lst:nambdy_tide}
+\end{listing}
 %-----------------------------------------------------------------------------------------------
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

@@ -23 +23 @@
 These three aspects of the lateral diffusion are set through namelist parameters
 (see the \nam{tra\_ldf} and \nam{dyn\_ldf} below).
-Note that this chapter describes the standard implementation of iso-neutral tracer mixing. 
+Note that this chapter describes the standard implementation of iso-neutral tracer mixing.
 Griffies's implementation, which is used if \np{ln\_traldf\_triad}\forcode{=.true.},
 is described in \autoref{apdx:TRIADS}
@@ -29 +29 @@
 %-----------------------------------namtra_ldf - namdyn_ldf--------------------------------------------
 
-\nlst{namtra_ldf} 
-
-\nlst{namdyn_ldf} 
 %--------------------------------------------------------------------------------------------------------------
 
@@ -45 +42 @@
 {No lateral mixing (\protect\np{ln\_traldf\_OFF}, \protect\np{ln\_dynldf\_OFF})}
 
-It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln\_traldf\_OFF}\forcode{=.true.}) and/or 
-momentum (\protect\np{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the 
+It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln\_traldf\_OFF}\forcode{=.true.}) and/or
+momentum (\protect\np{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the
 UBS advection scheme on momentum (\np{ln\_dynadv\_ubs}\forcode{=.true.},
 see \autoref{subsec:DYN_adv_ubs}) and can be useful for testing purposes.
@@ -52 +49 @@
 \subsection[Laplacian mixing (\forcode{ln_traldf_lap}, \forcode{ln_dynldf_lap})]
 {Laplacian mixing (\protect\np{ln\_traldf\_lap}, \protect\np{ln\_dynldf\_lap})}
-Setting \protect\np{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{=.true.} enables 
-a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine 
+Setting \protect\np{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{=.true.} enables
+a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine
 Laplacian and Bilaplacian operators for the same variable.
 
 \subsection[Bilaplacian mixing (\forcode{ln_traldf_blp}, \forcode{ln_dynldf_blp})]
 {Bilaplacian mixing (\protect\np{ln\_traldf\_blp}, \protect\np{ln\_dynldf\_blp})}
-Setting \protect\np{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{=.true.} enables 
-a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice. 
+Setting \protect\np{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{=.true.} enables
+a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice.
 We stress again that from \NEMO\ 4, the simultaneous use Laplacian and Bilaplacian operators is not allowed.
 
@@ -84 +81 @@
 $r_{1u}$, $r_{1w}$, $r_{2v}$, $r_{2w}$ (see \autoref{eq:TRA_ldf_iso}),
 while for momentum the slopes are  $r_{1t}$, $r_{1uw}$, $r_{2f}$, $r_{2uw}$ for $u$ and
-$r_{1f}$, $r_{1vw}$, $r_{2t}$, $r_{2vw}$ for $v$. 
+$r_{1f}$, $r_{1vw}$, $r_{2t}$, $r_{2vw}$ for $v$.
 
 %gm% add here afigure of the slope in i-direction
@@ -94 +91 @@
 Their discrete formulation is found by locally solving \autoref{eq:TRA_ldf_iso} when
 the diffusive fluxes in the three directions are set to zero and $T$ is assumed to be horizontally uniform,
-\ie\ a linear function of $z_T$, the depth of a $T$-point. 
+\ie\ a linear function of $z_T$, the depth of a $T$-point.
 %gm { Steven : My version is obviously wrong since I'm left with an arbitrary constant which is the local vertical temperature gradient}
 
@@ -113 +110 @@
 \end{equation}
 
-%gm%  caution I'm not sure the simplification was a good idea! 
+%gm%  caution I'm not sure the simplification was a good idea!
 
 These slopes are computed once in \rou{ldf\_slp\_init} when \np{ln\_sco}\forcode{=.true.},
-and either \np{ln\_traldf\_hor}\forcode{=.true.} or \np{ln\_dynldf\_hor}\forcode{=.true.}. 
+and either \np{ln\_traldf\_hor}\forcode{=.true.} or \np{ln\_dynldf\_hor}\forcode{=.true.}.
 
 \subsection{Slopes for tracer iso-neutral mixing}
@@ -145 +142 @@
 
 %gm% rewrite this as the explanation is not very clear !!!
-%In practice, \autoref{eq:LDF_slp_iso} is of little help in evaluating the neutral surface slopes. Indeed, for an unsimplified equation of state, the density has a strong dependancy on pressure (here approximated as the depth), therefore applying \autoref{eq:LDF_slp_iso} using the $in situ$ density, $\rho$, computed at T-points leads to a flattening of slopes as the depth increases. This is due to the strong increase of the $in situ$ density with depth. 
+%In practice, \autoref{eq:LDF_slp_iso} is of little help in evaluating the neutral surface slopes. Indeed, for an unsimplified equation of state, the density has a strong dependancy on pressure (here approximated as the depth), therefore applying \autoref{eq:LDF_slp_iso} using the $in situ$ density, $\rho$, computed at T-points leads to a flattening of slopes as the depth increases. This is due to the strong increase of the $in situ$ density with depth.
 
 %By definition, neutral surfaces are tangent to the local $in situ$ density \citep{mcdougall_JPO87}, therefore in \autoref{eq:LDF_slp_iso}, all the derivatives have to be evaluated at the same local pressure (which in decibars is approximated by the depth in meters).
 
-%In the $z$-coordinate, the derivative of the  \autoref{eq:LDF_slp_iso} numerator is evaluated at the same depth \nocite{as what?} ($T$-level, which is the same as the $u$- and $v$-levels), so  the $in situ$ density can be used for its evaluation. 
+%In the $z$-coordinate, the derivative of the  \autoref{eq:LDF_slp_iso} numerator is evaluated at the same depth \nocite{as what?} ($T$-level, which is the same as the $u$- and $v$-levels), so  the $in situ$ density can be used for its evaluation.
 
 As the mixing is performed along neutral surfaces, the gradient of $\rho$ in \autoref{eq:LDF_slp_iso} has to
@@ -164 +161 @@
   This is not the case for the vertical derivatives: $\delta_{k+1/2}[\rho]$ is replaced by $-\rho N^2/g$,
   where $N^2$ is the local Brunt-Vais\"{a}l\"{a} frequency evaluated following \citet{mcdougall_JPO87}
-  (see \autoref{subsec:TRA_bn2}). 
+  (see \autoref{subsec:TRA_bn2}).
 
 \item[$z$-coordinate with partial step: ]
@@ -179 +176 @@
   will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes.
 
-%gm% 
+%gm%
   Note: The solution for $s$-coordinate passes trough the use of different (and better) expression for
   the constraint on iso-neutral fluxes.
@@ -240 +237 @@
 
 Nevertheless, this iso-neutral operator does not ensure that variance cannot increase,
-contrary to the \citet{griffies.gnanadesikan.ea_JPO98} operator which has that property. 
+contrary to the \citet{griffies.gnanadesikan.ea_JPO98} operator which has that property.
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LDF_ZDF1}
-    \caption {
-      \protect\label{fig:LDF_ZDF1}
-      averaging procedure for isopycnal slope computation.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_LDF_ZDF1}
+  \caption{Averaging procedure for isopycnal slope computation}
+  \label{fig:LDF_ZDF1}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
-%There are three additional questions about the slope calculation. 
-%First the expression for the rotation tensor has been obtain assuming the "small slope" approximation, so a bound has to be imposed on slopes. 
-%Second, numerical stability issues also require a bound on slopes. 
+%There are three additional questions about the slope calculation.
+%First the expression for the rotation tensor has been obtain assuming the "small slope" approximation, so a bound has to be imposed on slopes.
+%Second, numerical stability issues also require a bound on slopes.
 %Third, the question of boundary condition specified on slopes...
 
@@ -263 +257 @@
 
 
-% In addition and also for numerical stability reasons \citep{cox_OM87, griffies_bk04}, 
-% the slopes are bounded by $1/100$ everywhere. This limit is decreasing linearly 
-% to zero fom $70$ meters depth and the surface (the fact that the eddies "feel" the 
+% In addition and also for numerical stability reasons \citep{cox_OM87, griffies_bk04},
+% the slopes are bounded by $1/100$ everywhere. This limit is decreasing linearly
+% to zero fom $70$ meters depth and the surface (the fact that the eddies "feel" the
 % surface motivates this flattening of isopycnals near the surface).
 
@@ -277 +271 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_eiv_slp}
-    \caption{
-      \protect\label{fig:LDF_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,
-      which has to be adjusted at the surface boundary
-      \ie\ it must tend to zero at the surface since there is no mixing across the air-sea interface:
-      wall boundary condition).
-      Nevertheless, the profile between the surface zero value and the interior iso-neutral one is unknown,
-      and especially the value at the base of the mixed layer;
-      \textit{(b)} profile of slope using a linear tapering of the slope near the surface and
-      imposing a maximum slope of 1/100;
-      \textit{(c)} profile of slope actually used in \NEMO: a linear decrease of the slope from
-      zero at the surface to its ocean interior value computed just below the mixed layer.
-      Note the huge change in the slope at the base of the mixed layer between \textit{(b)} and \textit{(c)}.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_eiv_slp}
+  \caption[Vertical profile of the slope used for lateral mixing in the mixed layer]{
+    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,
+    which has to be adjusted at the surface boundary
+    \ie\ it must tend to zero at the surface since there is no mixing across the air-sea interface:
+    wall boundary condition).
+    Nevertheless,
+    the profile between the surface zero value and the interior iso-neutral one is unknown,
+    and especially the value at the base of the mixed layer;
+    \textit{(b)} profile of slope using a linear tapering of the slope near the surface and
+    imposing a maximum slope of 1/100;
+    \textit{(c)} profile of slope actually used in \NEMO:
+    a linear decrease of the slope from zero at the surface to
+    its ocean interior value computed just below the mixed layer.
+    Note the huge change in the slope at the base of the mixed layer between
+    \textit{(b)} and \textit{(c)}.}
+  \label{fig:LDF_eiv_slp}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -326 +321 @@
 (see \autoref{sec:LBC_coast}).
 
-   
+
 % ================================================================
 % Lateral Mixing Coefficients
@@ -334 +329 @@
 \label{sec:LDF_coef}
 
-The specification of the space variation of the coefficient is made in modules \mdl{ldftra} and \mdl{ldfdyn}. 
+The specification of the space variation of the coefficient is made in modules \mdl{ldftra} and \mdl{ldfdyn}.
 The way the mixing coefficients are set in the reference version can be described as follows:
 
@@ -340 +335 @@
 { Mixing coefficients read from file (\protect\np{nn\_aht\_ijk\_t}\forcode{=-20, -30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=-20, -30})}
 
-Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model, 
+Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model,
 the laplacian viscosity operator uses $A^l$~= 4.10$^4$ m$^2$/s poleward of 20$^{\circ}$ north and south and
-decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}. 
-Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05. 
+decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}.
+Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05.
 The provided fields can either be 2d (\np{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn\_aht\_ijk\_t}\forcode{=-30},  \np{nn\_ahm\_ijk\_t}\forcode{=-30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}).
 
 %-------------------------------------------------TABLE---------------------------------------------------
 \begin{table}[htb]
-  \begin{center}
-    \begin{tabular}{|l|l|l|l|}
-      \hline
-      Namelist parameter                        & Input filename                               & dimensions & variable names                      \\  \hline
-      \np{nn\_ahm\_ijk\_t}\forcode{=-20}      & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline
-      \np{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$         & \forcode{ahtu_2d, ahtv_2d}    \\   \hline
-      \np{nn\_ahm\_ijk\_t}\forcode{=-30}      & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline
-      \np{nn\_aht\_ijk\_t}\forcode{=-30}      & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline
-    \end{tabular}
-    \caption{
-      \protect\label{tab:LDF_files}
-      Description of expected input files if mixing coefficients are read from NetCDF files.
-    }
-  \end{center}
+  \centering
+  \begin{tabular}{|l|l|l|l|}
+    \hline
+    Namelist parameter                       & Input filename                               & dimensions & variable names                      \\  \hline
+    \np{nn\_ahm\_ijk\_t}\forcode{=-20}     & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline
+    \np{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$           & \forcode{ahtu_2d, ahtv_2d}    \\   \hline
+    \np{nn\_ahm\_ijk\_t}\forcode{=-30}        & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline
+    \np{nn\_aht\_ijk\_t}\forcode{=-30}     & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline
+  \end{tabular}
+  \caption{Description of expected input files if mixing coefficients are read from NetCDF files}
+  \label{tab:LDF_files}
 \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -421 +413 @@
 The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases above,
 \ie\ a hyperbolic tangent variation with depth associated with a grid size dependence of
-the magnitude of the coefficient. 
+the magnitude of the coefficient.
 
 \subsection[Velocity dependent mixing coefficients (\forcode{nn_aht_ijk_t=31}, \forcode{nn_ahm_ijk_t=31})]
@@ -433 +425 @@
     \begin{aligned}
       & \frac{1}{12} \lvert U \rvert e          & \text{for laplacian operator } \\
-      & \frac{1}{12} \lvert U \rvert e^3             & \text{for bilaplacian operator } 
+      & \frac{1}{12} \lvert U \rvert e^3             & \text{for bilaplacian operator }
     \end{aligned}
   \right.
@@ -441 +433 @@
 {Deformation rate dependent viscosities (\protect\np{nn\_ahm\_ijk\_t}\forcode{=32})}
 
-This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a 
+This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a
 characteristic time scale $T_{smag}$ the deformation rate and for the lengthscale $L_{smag}$ the maximum wavenumber possible on the horizontal grid, e.g.:
 
@@ -459 +451 @@
     \begin{aligned}
       & C^2  T_{smag}^{-1}  L_{smag}^2       & \text{for laplacian operator } \\
-      & \frac{C^2}{8} T_{smag}^{-1} L_{smag}^4        & \text{for bilaplacian operator } 
+      & \frac{C^2}{8} T_{smag}^{-1} L_{smag}^4        & \text{for bilaplacian operator }
     \end{aligned}
   \right.
@@ -469 +461 @@
     \begin{aligned}
       & C_{min} \frac{1}{2}   \lvert U \rvert  e    < A_{smag} < C_{max} \frac{e^2}{   8\rdt}                 & \text{for laplacian operator } \\
-      & C_{min} \frac{1}{12} \lvert U \rvert  e^3 < A_{smag} < C_{max} \frac{e^4}{64 \rdt}                 & \text{for bilaplacian operator } 
+      & C_{min} \frac{1}{12} \lvert U \rvert  e^3 < A_{smag} < C_{max} \frac{e^4}{64 \rdt}                 & \text{for bilaplacian operator }
     \end{aligned}
 \end{equation}
@@ -482 +474 @@
 divergent components of the horizontal current (see \autoref{subsec:MB_ldf}).
 Although the eddy coefficient could be set to different values in these two terms,
-this option is not currently available. 
+this option is not currently available.
 
 (2) with an horizontally varying viscosity, the quadratic integral constraints on enstrophy and on the square of
@@ -498 +490 @@
 %--------------------------------------------namtra_eiv---------------------------------------------------
 
-\nlst{namtra_eiv}
+\begin{listing}
+  \nlst{namtra_eiv}
+  \caption{\texttt{namtra\_eiv}}
+  \label{lst:namtra_eiv}
+\end{listing}
 
 %--------------------------------------------------------------------------------------------------------------
@@ -530 +526 @@
 and the sum \autoref{eq:LDF_slp_geo} + \autoref{eq:LDF_slp_iso} in $s$-coordinates.
 
-If isopycnal mixing is used in the standard way, \ie\ \np{ln\_traldf\_triad}\forcode{=.false.}, the eddy induced velocity is given by: 
+If isopycnal mixing is used in the standard way, \ie\ \np{ln\_traldf\_triad}\forcode{=.false.}, the eddy induced velocity is given by:
 \begin{equation}
   \label{eq:LDF_eiv}
@@ -539 +535 @@
   \end{split}
 \end{equation}
-where $A^{eiv}$ is the eddy induced velocity coefficient whose value is set through \np{nn\_aei\_ijk\_t} \nam{tra\_eiv} namelist parameter. 
+where $A^{eiv}$ is the eddy induced velocity coefficient whose value is set through \np{nn\_aei\_ijk\_t} \nam{tra\_eiv} namelist parameter.
 The three components of the eddy induced velocity are computed in \rou{ldf\_eiv\_trp} and
 added to the eulerian velocity in \rou{tra\_adv} where tracer advection is performed.
@@ -547 +543 @@
 previous releases of OPA \citep{madec.delecluse.ea_NPM98}.
 This is particularly useful for passive tracers where \emph{positivity} of the advection scheme is of
-paramount importance. 
+paramount importance.
 
 At the surface, lateral and bottom boundaries, the eddy induced velocity,
-and thus the advective eddy fluxes of heat and salt, are set to zero. 
-The value of the eddy induced mixing coefficient and its space variation is controlled in a similar way as for lateral mixing coefficient described in the preceding subsection (\np{nn\_aei\_ijk\_t}, \np{rn\_Ue}, \np{rn\_Le} namelist parameters). 
+and thus the advective eddy fluxes of heat and salt, are set to zero.
+The value of the eddy induced mixing coefficient and its space variation is controlled in a similar way as for lateral mixing coefficient described in the preceding subsection (\np{nn\_aei\_ijk\_t}, \np{rn\_Ue}, \np{rn\_Le} namelist parameters).
 \colorbox{yellow}{CASE \np{nn\_aei\_ijk\_t} = 21 to be added}
 
@@ -566 +562 @@
 %--------------------------------------------namtra_eiv---------------------------------------------------
 
-\nlst{namtra_mle}
+\begin{listing}
+  \nlst{namtra_mle}
+  \caption{\texttt{namtra\_mle}}
+  \label{lst:namtra_mle}
+\end{listing}
 
 %--------------------------------------------------------------------------------------------------------------

NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

@@ -119 +119 @@
 %------------------------------------------namobs--------------------------------------------------------
 
-\nlst{namobs}
+\begin{listing}
+  \nlst{namobs}
+  \caption{\texttt{namobs}}
+  \label{lst:namobs}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -695 +699 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_OBS_avg_rec}
-    \caption{
-      \protect\label{fig:OBS_avgrec}
-      Weights associated with each model grid box (blue lines and numbers)
-      for an observation at -170.5\deg{E}, 56.0\deg{N} with a rectangular footprint of 1\deg x 1\deg.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_OBS_avg_rec}
+  \caption[Observational weights with a rectangular footprint]{
+    Weights associated with each model grid box (blue lines and numbers)
+    for an observation at -170.5\deg{E}, 56.0\deg{N} with a rectangular footprint of 1\deg\ x 1\deg.}
+  \label{fig:OBS_avgrec}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+% >>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_OBS_avg_rad}
-    \caption{
-      \protect\label{fig:OBS_avgrad}
-      Weights associated with each model grid box (blue lines and numbers)
-      for an observation at -170.5\deg{E}, 56.0\deg{N} with a radial footprint with diameter 1\deg.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_OBS_avg_rad}
+  \caption[Observational weights with a radial footprint]{
+    Weights associated with each model grid box (blue lines and numbers)
+    for an observation at -170.5\deg{E}, 56.0\deg{N} with a radial footprint with diameter 1\deg.}
+  \label{fig:OBS_avgrad}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -788 +788 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ASM_obsdist_local}
-    \caption{
-      \protect\label{fig:OBS_local}
-      Example of the distribution of observations with the geographical distribution of observational data.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ASM_obsdist_local}
+  \caption[Observations with the geographical distribution]{
+    Example of the distribution of observations with
+    the geographical distribution of observational data}
+  \label{fig:OBS_local}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -817 +816 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ASM_obsdist_global}
-    \caption{
-      \protect\label{fig:OBS_global}
-      Example of the distribution of observations with the round-robin distribution of observational data.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ASM_obsdist_global}
+  \caption[Observations with the round-robin distribution]{
+    Example of the distribution of observations with
+    the round-robin distribution of observational data.}
+  \label{fig:OBS_global}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -1150 +1148 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    % \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main}
-    \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main}
-    \caption{
-      \protect\label{fig:OBS_dataplotmain}
-      Main window of dataplot.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main}
+  \caption{Main window of dataplot}
+  \label{fig:OBS_dataplotmain}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -1166 +1160 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    % \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof}
-    \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof}
-    \caption{
-      \protect\label{fig:OBS_dataplotprofile}
-      Profile plot from dataplot produced by right clicking on a point in the main window.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof}
+  \caption[Profile plot from dataplot]{
+    Profile plot from dataplot produced by right clicking on a point in the main window}
+  \label{fig:OBS_dataplotprofile}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>

NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

@@ -14 +14 @@
 %---------------------------------------namsbc--------------------------------------------------
 
-\nlst{namsbc}
+\begin{listing}
+  \nlst{namsbc}
+  \caption{\texttt{namsbc}}
+  \label{lst:namsbc}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -183 +187 @@
 %-------------------------------------------------TABLE---------------------------------------------------
 \begin{table}[tb]
-  \begin{center}
-    \begin{tabular}{|l|l|l|l|}
-      \hline
-      Variable description                         & Model variable  & Units  & point                 \\\hline
-      i-component of the surface current  & ssu\_m               & $m.s^{-1}$     & U     \\\hline
-      j-component of the surface current  & ssv\_m               & $m.s^{-1}$     & V     \\ \hline
-      Sea surface temperature                & sst\_m               & \r{}$K$              & T     \\\hline
-      Sea surface salinty                          & sss\_m               & $psu$              & T     \\   \hline
-    \end{tabular}
-    \caption{
-      \protect\label{tab:SBC_ssm}
-      Ocean variables provided by the ocean to the surface module (SBC).
-      The variable are averaged over \np{nn\_fsbc} time-step,
-      \ie\ the frequency of computation of surface fluxes.
-    }
-  \end{center}
+  \centering
+  \begin{tabular}{|l|l|l|l|}
+    \hline
+    Variable description                           & Model variable  & Units  & point                 \\
+    \hline
+    i-component of the surface current & ssu\_m               & $m.s^{-1}$     & U     \\
+    \hline
+    j-component of the surface current & ssv\_m               & $m.s^{-1}$     & V     \\
+    \hline
+    Sea surface temperature                  & sst\_m               & \r{}$K$              & T     \\\hline
+    Sea surface salinty                         & sss\_m               & $psu$              & T     \\   \hline
+  \end{tabular}
+  \caption[Ocean variables provided to the surface module)]{
+    Ocean variables provided to the surface module (\texttt{SBC}).
+    The variable are averaged over \protect\np{nn\_fsbc} time-step,
+    \ie\ the frequency of computation of surface fluxes.}
+  \label{tab:SBC_ssm}
 \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -269 +274 @@
 %--------------------------------------------------TABLE--------------------------------------------------
   \begin{table}[htbp]
-    \begin{center}
-      \begin{tabular}{|l|c|c|c|}
-        \hline
-                                        &  daily or weekLL     &  monthly           &  yearly        \\   \hline
-        \np{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\   \hline
-        \np{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\   \hline
-      \end{tabular}
-    \end{center}
-    \caption{
-      \protect\label{tab:SBC_fldread}
-      naming nomenclature for climatological or interannual input file(s), as a function of the open/close frequency.
+    \centering
+    \begin{tabular}{|l|c|c|c|}
+      \hline
+                                  &  daily or weekLL     &  monthly           &  yearly        \\
+      \hline
+      \np{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\
+      \hline
+      \np{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\
+      \hline
+    \end{tabular}
+    \caption[Naming nomenclature for climatological or interannual input file]{
+      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
       (\ie\ 'sun','sat','fri','thu','wed','tue','mon').
-      The 'YYYY', 'MM' and 'DD' should be replaced by the actual year/month/day, always coded with 4 or 2 digits.
-      Note that (1) in mpp, if the file is split over each subdomain, the suffix '.nc' is replaced by '\_PPPP.nc',
+      The 'YYYY', 'MM' and 'DD' should be replaced by the actual year/month/day,
+      always coded with 4 or 2 digits.
+      Note that (1) in mpp, if the file is split over each subdomain,
+      the suffix '.nc' is replaced by '\_PPPP.nc',
       where 'PPPP' is the process number coded with 4 digits;
       (2) when using AGRIF, the prefix '\_N' is added to files, where 'N' is the child grid number.
     }
+    \label{tab:SBC_fldread}
   \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -519 +529 @@
 %---------------------------------------namsbc_sas--------------------------------------------------
 
-\nlst{namsbc_sas}
+\begin{listing}
+  \nlst{namsbc_sas}
+  \caption{\texttt{namsbc\_sas}}
+  \label{lst:namsbc_sas}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -604 +618 @@
 %------------------------------------------namsbc_flx----------------------------------------------------
 
-\nlst{namsbc_flx}
+\begin{listing}
+  \nlst{namsbc_flx}
+  \caption{\texttt{namsbc\_flx}}
+  \label{lst:namsbc_flx}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -627 +645 @@
 %---------------------------------------namsbc_blk--------------------------------------------------
 
-\nlst{namsbc_blk}
+\begin{listing}
+  \nlst{namsbc_blk}
+  \caption{\texttt{namsbc\_blk}}
+  \label{lst:namsbc_blk}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -649 +671 @@
 %--------------------------------------------------TABLE--------------------------------------------------
 \begin{table}[htbp]
+  \centering
+  \begin{tabular}{|l|c|c|c|}
+    \hline
+    Variable description                 & Model variable & Units              & point \\
+    \hline
+    i-component of the 10m air velocity  & utau           & $m.s^{-1}$         & T     \\
+    \hline
+    j-component of the 10m air velocity  & vtau           & $m.s^{-1}$         & T     \\
+    \hline
+    10m air temperature                  & tair           & \r{}$K$            & T     \\
+    \hline
+    Specific humidity                    & humi           & \%                 & T     \\
+    \hline
+    Incoming long wave radiation         & qlw            & $W.m^{-2}$         & T     \\
+    \hline
+    Incoming short wave radiation        & qsr            & $W.m^{-2}$         & T     \\
+    \hline
+    Total precipitation (liquid + solid) & precip         & $Kg.m^{-2}.s^{-1}$ & T     \\
+    \hline
+    Solid precipitation                  & snow           & $Kg.m^{-2}.s^{-1}$ & T     \\
+    \hline
+    Mean sea-level pressure              & slp            & $hPa$              & T     \\
+    \hline
+    \end{tabular}
   \label{tab:SBC_BULK}
-  \begin{center}
-    \begin{tabular}{|l|c|c|c|}
-      \hline
-      Variable description                           & Model variable   & Units                         & point \\   \hline
-      i-component of the 10m air velocity   & utau                   & $m.s^{-1}$                   & T         \\   \hline
-      j-component of the 10m air velocity   & vtau                & $m.s^{-1}$                   & T         \\   \hline
-      10m air temperature                      & tair                & \r{}$K$                        & T       \\   \hline
-      Specific humidity                        & humi           & \%                             & T      \\   \hline
-      Incoming long wave radiation          & qlw                & $W.m^{-2}$            & T        \\   \hline
-      Incoming short wave radiation          & qsr               & $W.m^{-2}$            & T        \\   \hline
-      Total precipitation (liquid + solid)         & precip            & $Kg.m^{-2}.s^{-1}$      & T      \\   \hline
-      Solid precipitation                           & snow               & $Kg.m^{-2}.s^{-1}$       & T      \\   \hline
-      Mean sea-level pressure                     & slp                     & $hPa$                          & T       \\ \hline
-    \end{tabular}
-  \end{center}
 \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -768 +799 @@
 %------------------------------------------namsbc_cpl----------------------------------------------------
 
-\nlst{namsbc_cpl}
+\begin{listing}
+  \nlst{namsbc_cpl}
+  \caption{\texttt{namsbc\_cpl}}
+  \label{lst:namsbc_cpl}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -807 +842 @@
 %------------------------------------------namsbc_apr----------------------------------------------------
 
-\nlst{namsbc_apr}
+\begin{listing}
+  \nlst{namsbc_apr}
+  \caption{\texttt{namsbc\_apr}}
+  \label{lst:namsbc_apr}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -847 +886 @@
 %------------------------------------------nam_tide---------------------------------------
 
-\nlst{nam_tide}
+\begin{listing}
+  \nlst{nam_tide}
+  \caption{\texttt{nam\_tide}}
+  \label{lst:nam_tide}
+\end{listing}
 %-----------------------------------------------------------------------------------------
 
@@ -899 +942 @@
 %------------------------------------------namsbc_rnf----------------------------------------------------
 
-\nlst{namsbc_rnf}
+\begin{listing}
+  \nlst{namsbc_rnf}
+  \caption{\texttt{namsbc\_rnf}}
+  \label{lst:namsbc_rnf}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1025 +1072 @@
 %------------------------------------------namsbc_isf----------------------------------------------------
 
-\nlst{namsbc_isf}
+\begin{listing}
+  \nlst{namsbc_isf}
+  \caption{\texttt{namsbc\_isf}}
+  \label{lst:namsbc_isf}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------
 
@@ -1126 +1177 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_SBC_isf}
-    \caption{
-      \protect\label{fig:SBC_isf}
-      Illustration the location where the fwf is injected and whether or not the fwf is interactif or not depending of \np{nn\_isf}.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_SBC_isf}
+  \caption[Ice shelf location and fresh water flux definition]{
+    Illustration of the location where the fwf is injected and
+    whether or not the fwf is interactif or not depending of \protect\np{nn\_isf}.}
+  \label{fig:SBC_isf}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -1145 +1195 @@
 %------------------------------------------namsbc_iscpl----------------------------------------------------
 
-\nlst{namsbc_iscpl}
+\begin{listing}
+  \nlst{namsbc_iscpl}
+  \caption{\texttt{namsbc\_iscpl}}
+  \label{lst:namsbc_iscpl}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------
 
@@ -1210 +1264 @@
 %------------------------------------------namberg----------------------------------------------------
 
-\nlst{namberg}
+\begin{listing}
+  \nlst{namberg}
+  \caption{\texttt{namberg}}
+  \label{lst:namberg}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1280 +1338 @@
 %------------------------------------------namsbc_wave--------------------------------------------------------
 
-\nlst{namsbc_wave}
+\begin{listing}
+  \nlst{namsbc_wave}
+  \caption{\texttt{namsbc\_wave}}
+  \label{lst:namsbc_wave}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1483 +1545 @@
 %------------------------------------------namsbc-------------------------------------------------------------
 %
-\nlst{namsbc}
+
 %-------------------------------------------------------------------------------------------------------------
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{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 as
-      the mean value of the analytical cycle (blue line) over a time step,
-      not as the mid time step value of the analytically cycle (red square).
-      From \citet{bernie.guilyardi.ea_CD07}.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_SBC_diurnal}
+  \caption[Reconstruction of the diurnal cycle variation of short wave flux]{
+    Example of reconstruction of the diurnal cycle variation of short wave flux from
+    daily mean values.
+    The reconstructed diurnal cycle (black line) is chosen as
+    the mean value of the analytical cycle (blue line) over a time step,
+    not as the mid time step value of the analytically cycle (red square).
+    From \citet{bernie.guilyardi.ea_CD07}.}
+  \label{fig:SBC_diurnal}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -1525 +1586 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{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).
-      The display is on (i,j) plane.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_SBC_dcy}
+  \caption[Reconstruction of the diurnal cycle variation of short wave flux on an ORCA2 grid]{
+    Example of reconstruction 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).
+    The display is on (i,j) plane.}
+  \label{fig:SBC_dcy}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -1569 +1628 @@
 %------------------------------------------namsbc_ssr----------------------------------------------------
 
-\nlst{namsbc_ssr}
+\begin{listing}
+  \nlst{namsbc_ssr}
+  \caption{\texttt{namsbc\_ssr}}
+  \label{lst:namsbc_ssr}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

@@ -176 +176 @@
 %---------------------------------------namsto--------------------------------------------------
 
-\nlst{namsto}
+\begin{listing}
+  \nlst{namsto}
+  \caption{\texttt{namsto}}
+  \label{lst:namsto}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

@@ -65 +65 @@
 %------------------------------------------namtra_adv-----------------------------------------------------
 
-\nlst{namtra_adv}
+\begin{listing}
+  \nlst{namtra_adv}
+  \caption{\texttt{namtra\_adv}}
+  \label{lst:namtra_adv}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -90 +94 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_adv_scheme}
-    \caption{
-      \protect\label{fig:TRA_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 points.
-      Upsteam biased scheme (ups):
-      the upstream value is used and the black area is exchanged.
-      Piecewise parabolic method (ppm):
-      a parabolic interpolation is used and the black and dark grey areas are exchanged.
-      Monotonic upstream scheme for conservative laws (muscl):
-      a parabolic interpolation is used and black, dark grey and grey areas are exchanged.
-      Second order scheme (cen2):
-      the mean value is used and black, dark grey, grey and light grey areas are exchanged.
-      Note that this illustration does not include the flux limiter used in ppm and muscl schemes.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_adv_scheme}
+  \caption[Ways to evaluate the tracer value and the amount of tracer exchanged]{
+    Schematic representation of some ways used to evaluate the tracer value at $u$-point and
+    the amount of tracer exchanged between two neighbouring grid points.
+    Upsteam biased scheme (ups):
+    the upstream value is used and the black area is exchanged.
+    Piecewise parabolic method (ppm):
+    a parabolic interpolation is used and the black and dark grey areas are exchanged.
+    Monotonic upstream scheme for conservative laws (muscl):
+    a parabolic interpolation is used and black, dark grey and grey areas are exchanged.
+    Second order scheme (cen2):
+    the mean value is used and black, dark grey, grey and light grey areas are exchanged.
+    Note that this illustration does not include the flux limiter used in ppm and muscl schemes.}
+  \label{fig:TRA_adv_scheme}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -435 +437 @@
 %-----------------------------------------nam_traldf------------------------------------------------------
 
-\nlst{namtra_ldf}
+\begin{listing}
+  \nlst{namtra_ldf}
+  \caption{\texttt{namtra\_ldf}}
+  \label{lst:namtra_ldf}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -640 +646 @@
 %--------------------------------------------namzdf---------------------------------------------------------
 
-\nlst{namzdf}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -759 +764 @@
 %--------------------------------------------namqsr--------------------------------------------------------
 
-\nlst{namtra_qsr}
+\begin{listing}
+  \nlst{namtra_qsr}
+  \caption{\texttt{namtra\_qsr}}
+  \label{lst:namtra_qsr}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -857 +866 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_TRA_Irradiance}
-    \caption{
-      \protect\label{fig:TRA_qsr_irradiance}
-      Penetration profile of the downward solar irradiance calculated by four models.
-      Two waveband chlorophyll-independent formulation (blue),
-      a chlorophyll-dependent monochromatic formulation (green),
-      4 waveband RGB formulation (red),
-      61 waveband Morel (1988) formulation (black) for a chlorophyll concentration of
-      (a) Chl=0.05 mg/m$^3$ and (b) Chl=0.5 mg/m$^3$.
-      From \citet{lengaigne.menkes.ea_CD07}.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_TRA_Irradiance}
+  \caption[Penetration profile of the downward solar irradiance calculated by four models]{
+    Penetration profile of the downward solar irradiance calculated by four models.
+    Two waveband chlorophyll-independent formulation (blue),
+    a chlorophyll-dependent monochromatic formulation (green),
+    4 waveband RGB formulation (red),
+    61 waveband Morel (1988) formulation (black) for a chlorophyll concentration of
+    (a) Chl=0.05 mg/m$^3$ and (b) Chl=0.5 mg/m$^3$.
+    From \citet{lengaigne.menkes.ea_CD07}.}
+  \label{fig:TRA_qsr_irradiance}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -881 +888 @@
 %--------------------------------------------nambbc--------------------------------------------------------
 
-\nlst{nambbc}
+\begin{listing}
+  \nlst{nambbc}
+  \caption{\texttt{nambbc}}
+  \label{lst:nambbc}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_TRA_geoth}
-    \caption{
-      \protect\label{fig:TRA_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_N92}.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_TRA_geoth}
+  \caption[Geothermal heat flux]{
+    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_N92}.}
+  \label{fig:TRA_geothermal}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -920 +929 @@
 %--------------------------------------------nambbl---------------------------------------------------------
 
-\nlst{nambbl}
+\begin{listing}
+  \nlst{nambbl}
+  \caption{\texttt{nambbl}}
+  \label{lst:nambbl}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -999 +1012 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_BBL_adv}
-    \caption{
-      \protect\label{fig:TRA_bbl}
-      Advective/diffusive Bottom Boundary Layer.
-      The BBL parameterisation is activated when $\rho^i_{kup}$ is larger than $\rho^{i + 1}_{kdnw}$.
-      Red arrows indicate the additional overturning circulation due to the advective BBL.
-      The transport of the downslope flow is defined either as the transport of the bottom ocean cell (black arrow),
-      or as a function of the along slope density gradient.
-      The green arrow indicates the diffusive BBL flux directly connecting $kup$ and $kdwn$ ocean bottom cells.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_BBL_adv}
+  \caption[Advective/diffusive bottom boundary layer]{
+    Advective/diffusive Bottom Boundary Layer.
+    The BBL parameterisation is activated when $\rho^i_{kup}$ is larger than $\rho^{i + 1}_{kdnw}$.
+    Red arrows indicate the additional overturning circulation due to the advective BBL.
+    The transport of the downslope flow is defined either
+    as the transport of the bottom ocean cell (black arrow),
+    or as a function of the along slope density gradient.
+    The green arrow indicates the diffusive BBL flux directly connecting
+    $kup$ and $kdwn$ ocean bottom cells.}
+  \label{fig:TRA_bbl}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -1085 +1098 @@
 %--------------------------------------------namtra_dmp-------------------------------------------------
 
-\nlst{namtra_dmp}
+\begin{listing}
+  \nlst{namtra_dmp}
+  \caption{\texttt{namtra\_dmp}}
+  \label{lst:namtra_dmp}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -1140 +1157 @@
 \label{sec:TRA_nxt}
 %--------------------------------------------namdom-----------------------------------------------------
-
-\nlst{namdom}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -1179 +1194 @@
 %--------------------------------------------nameos-----------------------------------------------------
 
-\nlst{nameos}
+\begin{listing}
+  \nlst{nameos}
+  \caption{\texttt{nameos}}
+  \label{lst:nameos}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -1283 +1302 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{table}[!tb]
-  \begin{center}
-    \begin{tabular}{|l|l|l|l|}
-      \hline
-      coeff.      & computer name   & S-EOS           & description                      \\
-      \hline
-      $a_0$       & \np{rn\_a0}     & $1.6550~10^{-1}$ & linear thermal expansion coeff. \\
-      \hline
-      $b_0$       & \np{rn\_b0}     & $7.6554~10^{-1}$ & linear haline  expansion coeff. \\
-      \hline
-      $\lambda_1$ & \np{rn\_lambda1}& $5.9520~10^{-2}$ & cabbeling coeff. in $T^2$       \\
-      \hline
-      $\lambda_2$ & \np{rn\_lambda2}& $5.4914~10^{-4}$ & cabbeling coeff. in $S^2$       \\
-      \hline
-      $\nu$       & \np{rn\_nu}     & $2.4341~10^{-3}$ & cabbeling coeff. in $T \, S$    \\
-      \hline
-      $\mu_1$     & \np{rn\_mu1}    & $1.4970~10^{-4}$ & thermobaric coeff. in T         \\
-      \hline
-      $\mu_2$     & \np{rn\_mu2}    & $1.1090~10^{-5}$ & thermobaric coeff. in S         \\
-      \hline
-    \end{tabular}
-    \caption{
-      \protect\label{tab:TRA_SEOS}
-      Standard value of S-EOS coefficients.
-    }
-\end{center}
+  \centering
+  \begin{tabular}{|l|l|l|l|}
+    \hline
+    coeff.     & computer name   & S-EOS           & description                      \\
+    \hline
+    $a_0$       & \np{rn\_a0}     & $1.6550~10^{-1}$ & linear thermal expansion coeff. \\
+    \hline
+    $b_0$         & \np{rn\_b0}     & $7.6554~10^{-1}$ & linear haline  expansion coeff. \\
+    \hline
+    $\lambda_1$   & \np{rn\_lambda1}& $5.9520~10^{-2}$ & cabbeling coeff. in $T^2$       \\
+    \hline
+    $\lambda_2$   & \np{rn\_lambda2}& $5.4914~10^{-4}$ & cabbeling coeff. in $S^2$       \\
+    \hline
+    $\nu$       & \np{rn\_nu}     & $2.4341~10^{-3}$ & cabbeling coeff. in $T \, S$      \\
+    \hline
+    $\mu_1$     & \np{rn\_mu1}   & $1.4970~10^{-4}$ & thermobaric coeff. in T         \\
+    \hline
+    $\mu_2$     & \np{rn\_mu2}   & $1.1090~10^{-5}$ & thermobaric coeff. in S         \\
+    \hline
+  \end{tabular}
+  \caption{Standard value of S-EOS coefficients}
+  \label{tab:TRA_SEOS}
 \end{table}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -1391 +1407 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!p]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_partial_step_scheme}
-    \caption{
-      \protect\label{fig:TRA_Partial_step_scheme}
-      Discretisation of the horizontal difference and average of tracers in the $z$-partial step coordinate
-      (\protect\np{ln\_zps}\forcode{=.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.
-      The horizontal difference is then given by: $\delta_{i + 1/2} T_k = \widetilde T_k^{\, i + 1} -T_k^{\, i}$ and
-      the average by: $\overline T_k^{\, i + 1/2} = (\widetilde T_k^{\, i + 1/2} - T_k^{\, i}) / 2$.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_partial_step_scheme}
+  \caption[Discretisation of the horizontal difference and average of tracers in
+  the $z$-partial step coordinate]{
+    Discretisation of the horizontal difference and average of tracers in
+    the $z$-partial step coordinate (\protect\np{ln\_zps}\forcode{=.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.
+    The horizontal difference is then given by:
+    $\delta_{i + 1/2} T_k = \widetilde T_k^{\, i + 1} -T_k^{\, i}$ and
+    the average by:
+    $\overline T_k^{\, i + 1/2} = (\widetilde T_k^{\, i + 1/2} - T_k^{\, i}) / 2$.}
+  \label{fig:TRA_Partial_step_scheme}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>

NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

@@ -1 +1 @@
 \documentclass[../main/NEMO_manual]{subfiles}
+
+%% Custom aliases
+\newcommand{\cf}{\ensuremath{C\kern-0.14em f}}
 
 \begin{document}
@@ -45 +48 @@
 %--------------------------------------------namzdf--------------------------------------------------------
 
-\nlst{namzdf}
+\begin{listing}
+  \nlst{namzdf}
+  \caption{\texttt{namzdf}}
+  \label{lst:namzdf}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -80 +87 @@
 %--------------------------------------------namric---------------------------------------------------------
 
-\nlst{namzdf_ric}
+\begin{listing}
+  \nlst{namzdf_ric}
+  \caption{\texttt{namzdf\_ric}}
+  \label{lst:namzdf_ric}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -137 +148 @@
 %--------------------------------------------namzdf_tke--------------------------------------------------
 
-\nlst{namzdf_tke}
+\begin{listing}
+  \nlst{namzdf_tke}
+  \caption{\texttt{namzdf\_tke}}
+  \label{lst:namzdf_tke}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -238 +253 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_mixing_length}
-    \caption{
-      \protect\label{fig:ZDF_mixing_length}
-      Illustration of the mixing length computation.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_mixing_length}
+  \caption[Mixing length computation]{Illustration of the mixing length computation}
+  \label{fig:ZDF_mixing_length}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -421 +433 @@
 %--------------------------------------------namzdf_gls---------------------------------------------------------
 
-\nlst{namzdf_gls}
+\begin{listing}
+  \nlst{namzdf_gls}
+  \caption{\texttt{namzdf\_gls}}
+  \label{lst:namzdf_gls}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -475 +491 @@
 %--------------------------------------------------TABLE--------------------------------------------------
 \begin{table}[htbp]
-  \begin{center}
-    % \begin{tabular}{cp{70pt}cp{70pt}cp{70pt}cp{70pt}cp{70pt}cp{70pt}c}
-    \begin{tabular}{ccccc}
-      &   $k-kl$   & $k-\epsilon$ & $k-\omega$ &   generic   \\
-      % & \citep{mellor.yamada_RG82} &  \citep{rodi_JGR87}       & \citep{wilcox_AJ88} &                 \\
-      \hline
-      \hline
-      \np{nn\_clo}     & \textbf{0} &   \textbf{1}  &   \textbf{2}   &    \textbf{3}   \\
-      \hline
-      $( p , n , m )$          &   ( 0 , 1 , 1 )   & ( 3 , 1.5 , -1 )   & ( -1 , 0.5 , -1 )    &  ( 2 , 1 , -0.67 )  \\
-      $\sigma_k$      &    2.44         &     1.              &      2.                &      0.8          \\
-      $\sigma_\psi$  &    2.44         &     1.3            &      2.                 &       1.07       \\
-      $C_1$              &      0.9         &     1.44          &      0.555          &       1.           \\
-      $C_2$              &      0.5         &     1.92          &      0.833          &       1.22       \\
-      $C_3$              &      1.           &     1.              &      1.                &       1.           \\
-      $F_{wall}$        &      Yes        &       --             &     --                  &      --          \\
-      \hline
-      \hline
-    \end{tabular}
-    \caption{
-      \protect\label{tab:ZDF_GLS}
-      Set of predefined GLS parameters, or equivalently predefined turbulence models available with
-      \protect\np{ln\_zdfgls}\forcode{=.true.} and controlled by the \protect\np{nn\_clos} namelist variable in \protect\nam{zdf\_gls}.
-    }
-  \end{center}
+  \centering
+  % \begin{tabular}{cp{70pt}cp{70pt}cp{70pt}cp{70pt}cp{70pt}cp{70pt}c}
+  \begin{tabular}{ccccc}
+    &   $k-kl$   & $k-\epsilon$ & $k-\omega$ &   generic   \\
+    % & \citep{mellor.yamada_RG82} &  \citep{rodi_JGR87}       & \citep{wilcox_AJ88} &                 \\
+    \hline
+    \hline
+    \np{nn\_clo}     & \textbf{0} &   \textbf{1}  &   \textbf{2}   &    \textbf{3}   \\
+    \hline
+    $( p , n , m )$         &   ( 0 , 1 , 1 )   & ( 3 , 1.5 , -1 )   & ( -1 , 0.5 , -1 )    &  ( 2 , 1 , -0.67 )  \\
+    $\sigma_k$      &    2.44         &     1.              &      2.                &      0.8          \\
+    $\sigma_\psi$  &    2.44         &     1.3            &      2.                 &       1.07       \\
+    $C_1$              &      0.9         &     1.44          &      0.555          &       1.           \\
+    $C_2$              &      0.5         &     1.92          &      0.833          &       1.22       \\
+    $C_3$              &      1.           &     1.              &      1.                &       1.           \\
+    $F_{wall}$        &      Yes        &       --             &     --                  &      --          \\
+    \hline
+    \hline
+  \end{tabular}
+  \caption[Set of predefined GLS parameters or equivalently predefined turbulence models available]{
+    Set of predefined GLS parameters, or equivalently predefined turbulence models available with
+    \protect\np{ln\_zdfgls}\forcode{=.true.} and controlled by
+    the \protect\np{nn\_clos} namelist variable in \protect\nam{zdf\_gls}.}
+  \label{tab:ZDF_GLS}
 \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -542 +557 @@
 %--------------------------------------------namzdf_osm---------------------------------------------------------
 
-\nlst{namzdf_osm}
+\begin{listing}
+  \nlst{namzdf_osm}
+  \caption{\texttt{namzdf\_osm}}
+  \label{lst:namzdf_osm}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -556 +575 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ZDF_TKE_time_scheme}
-    \caption{
-      \protect\label{fig:ZDF_TKE_time_scheme}
-      Illustration of the subgrid kinetic energy integration in GLS and TKE schemes and its links to the momentum and tracer time integration.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ZDF_TKE_time_scheme}
+  \caption[Subgrid kinetic energy integration in GLS and TKE schemes]{
+    Illustration of the subgrid kinetic energy integration in GLS and TKE schemes and
+    its links to the momentum and tracer time integration.}
+  \label{fig:ZDF_TKE_time_scheme}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -676 +694 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!htb]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_npc}
-    \caption{
-      \protect\label{fig:ZDF_npc}
-      Example of an unstable density profile treated by the non penetrative convective adjustment algorithm.
-      $1^{st}$ step: the initial profile is checked from the surface to the bottom.
-      It is found to be unstable between levels 3 and 4.
-      They are mixed.
-      The resulting $\rho$ is still larger than $\rho$(5): levels 3 to 5 are mixed.
-      The resulting $\rho$ is still larger than $\rho$(6): levels 3 to 6 are mixed.
-      The $1^{st}$ step ends since the density profile is then stable below the level 3.
-      $2^{nd}$ step: the new $\rho$ profile is checked following the same procedure as in $1^{st}$ step:
-      levels 2 to 5 are mixed.
-      The new density profile is checked.
-      It is found stable: end of algorithm.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_npc}
+  \caption[Unstable density profile treated by the non penetrative convective adjustment algorithm]{
+    Example of an unstable density profile treated by
+    the non penetrative convective adjustment algorithm.
+    $1^{st}$ step: the initial profile is checked from the surface to the bottom.
+    It is found to be unstable between levels 3 and 4.
+    They are mixed.
+    The resulting $\rho$ is still larger than $\rho$(5): levels 3 to 5 are mixed.
+    The resulting $\rho$ is still larger than $\rho$(6): levels 3 to 6 are mixed.
+    The $1^{st}$ step ends since the density profile is then stable below the level 3.
+    $2^{nd}$ step: the new $\rho$ profile is checked following the same procedure as in $1^{st}$ step:
+    levels 2 to 5 are mixed.
+    The new density profile is checked.
+    It is found stable: end of algorithm.}
+  \label{fig:ZDF_npc}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -838 +855 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_zdfddm}
-    \caption{
-      \protect\label{fig:ZDF_ddm}
-      From \citet{merryfield.holloway.ea_JPO99} :
-      (a) Diapycnal diffusivities $A_f^{vT}$ and $A_f^{vS}$ for temperature and salt in regions of salt fingering.
-      Heavy curves denote $A^{\ast v} = 10^{-3}~m^2.s^{-1}$ and thin curves $A^{\ast v} = 10^{-4}~m^2.s^{-1}$;
-      (b) diapycnal diffusivities $A_d^{vT}$ and $A_d^{vS}$ for temperature and salt in regions of
-      diffusive convection.
-      Heavy curves denote the Federov parameterisation and thin curves the Kelley parameterisation.
-      The latter is not implemented in \NEMO.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_zdfddm}
+  \caption[Diapycnal diffusivities for temperature and salt in regions of salt fingering and
+  diffusive convection]{
+    From \citet{merryfield.holloway.ea_JPO99}:
+    (a) Diapycnal diffusivities $A_f^{vT}$ and $A_f^{vS}$ for temperature and salt in
+    regions of salt fingering.
+    Heavy curves denote $A^{\ast v} = 10^{-3}~m^2.s^{-1}$ and
+    thin curves $A^{\ast v} = 10^{-4}~m^2.s^{-1}$;
+    (b) diapycnal diffusivities $A_d^{vT}$ and $A_d^{vS}$ for temperature and salt in
+    regions of diffusive convection.
+    Heavy curves denote the Federov parameterisation and thin curves the Kelley parameterisation.
+    The latter is not implemented in \NEMO.}
+  \label{fig:ZDF_ddm}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -893 +911 @@
 %--------------------------------------------namdrg--------------------------------------------------------
 %
-\nlst{namdrg}
-\nlst{namdrg_top}
-\nlst{namdrg_bot}
+\begin{listing}
+  \nlst{namdrg}
+  \caption{\texttt{namdrg}}
+  \label{lst:namdrg}
+\end{listing}
+\begin{listing}
+  \nlst{namdrg_top}
+  \caption{\texttt{namdrg\_top}}
+  \label{lst:namdrg_top}
+\end{listing}
+\begin{listing}
+  \nlst{namdrg_bot}
+  \caption{\texttt{namdrg\_bot}}
+  \label{lst:namdrg_bot}
+\end{listing}
 
 %--------------------------------------------------------------------------------------------------------------
@@ -1175 +1205 @@
 %--------------------------------------------namzdf_iwm------------------------------------------
 %
-\nlst{namzdf_iwm}
+\begin{listing}
+  \nlst{namzdf_iwm}
+  \caption{\texttt{namzdf\_iwm}}
+  \label{lst:namzdf_iwm}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -1287 +1321 @@
 
 \begin{table}[htbp]
-  \begin{center}
-    % \begin{tabular}{cp{70pt}cp{70pt}cp{70pt}cp{70pt}}
-    \begin{tabular}{r|ccc}
-      \hline
-      spatial discretization &   2nd order centered   & 3rd order upwind & 4th order compact  \\
-      advective CFL criterion     & 0.904 &   0.472  &   0.522    \\
-      \hline
-    \end{tabular}
-    \caption{
-      \protect\label{tab:ZDF_zad_Aimp_CFLcrit}
-      The advective CFL criteria for a range of spatial discretizations for the Leap-Frog with Robert Asselin filter time-stepping
-      ($\nu=0.1$) as given in \citep{lemarie.debreu.ea_OM15}.
-    }
-  \end{center}
+  \centering
+  % \begin{tabular}{cp{70pt}cp{70pt}cp{70pt}cp{70pt}}
+  \begin{tabular}{r|ccc}
+    \hline
+    spatial discretization  & 2$^nd$ order centered & 3$^rd$ order upwind & 4$^th$ order compact \\
+    advective CFL criterion &                 0.904 &              0.472  &                0.522 \\
+    \hline
+  \end{tabular}
+  \caption[Advective CFL criteria for the leapfrog with Robert Asselin filter time-stepping]{
+    The advective CFL criteria for a range of spatial discretizations for
+    the leapfrog with Robert Asselin filter time-stepping
+    ($\nu=0.1$) as given in \citep{lemarie.debreu.ea_OM15}.}
+  \label{tab:ZDF_zad_Aimp_CFLcrit}
 \end{table}
 
@@ -1331 +1364 @@
 Cu_{cut} &= 2Cu_{max} - Cu_{min} \nonumber \\
 Fcu    &= 4Cu_{max}*(Cu_{max}-Cu_{min}) \nonumber \\
-C\kern-0.14em f &=
+\cf &=
      \begin{cases}
         0.0                                                        &\text{if $Cu \leq Cu_{min}$} \\
@@ -1340 +1373 @@
 
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_coeff}
-    \caption{
-      \protect\label{fig:ZDF_zad_Aimp_coeff}
-      The value of the partitioning coefficient ($C\kern-0.14em f$) used to partition vertical velocities into parts to
-      be treated implicitly and explicitly for a range of typical Courant numbers (\forcode{ln_zad_Aimp=.true.})
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_coeff}
+  \caption[Partitioning coefficient used to partition vertical velocities into parts]{
+    The value of the partitioning coefficient (\cf) used to partition vertical velocities into
+    parts to be treated implicitly and explicitly for a range of typical Courant numbers
+    (\forcode{ln_zad_Aimp=.true.}).}
+  \label{fig:ZDF_zad_Aimp_coeff}
 \end{figure}
 
@@ -1356 +1388 @@
 \begin{align}
   \label{eq:ZDF_Eqn_zad_Aimp_partition2}
-    w_{i_{ijk}} &= C\kern-0.14em f_{ijk} w_{n_{ijk}}     \nonumber \\
-    w_{n_{ijk}} &= (1-C\kern-0.14em f_{ijk}) w_{n_{ijk}}
+    w_{i_{ijk}} &= \cf_{ijk} w_{n_{ijk}}     \nonumber \\
+    w_{n_{ijk}} &= (1-\cf_{ijk}) w_{n_{ijk}}
 \end{align}
 
@@ -1363 +1395 @@
 the three cases from \autoref{eq:ZDF_Eqn_zad_Aimp_partition} can be considered as:
 fully-explicit; mixed explicit/implicit and mostly-implicit.  With the settings shown the
-coefficient ($C\kern-0.14em f$) varies as shown in \autoref{fig:ZDF_zad_Aimp_coeff}. Note with these values
+coefficient (\cf) varies as shown in \autoref{fig:ZDF_zad_Aimp_coeff}. Note with these values
 the $Cu_{cut}$ boundary between the mixed implicit-explicit treatment and 'mostly
 implicit' is 0.45 which is just below the stability limited given in
@@ -1381 +1413 @@
 
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_overflow_frames}
-    \caption{
-      \protect\label{fig:ZDF_zad_Aimp_overflow_frames}
-      A time-series of temperature vertical cross-sections for the OVERFLOW test case. These results are for the default
-      settings with \forcode{nn_rdt=10.0} and without adaptive implicit vertical advection (\forcode{ln_zad_Aimp=.false.}).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_overflow_frames}
+  \caption[OVERFLOW: time-series of temperature vertical cross-sections]{
+    A time-series of temperature vertical cross-sections for the OVERFLOW test case.
+    These results are for the default settings with \forcode{nn_rdt=10.0} and
+    without adaptive implicit vertical advection (\forcode{ln_zad_Aimp=.false.}).}
+  \label{fig:ZDF_zad_Aimp_overflow_frames}
 \end{figure}
 
 \subsection{Adaptive-implicit vertical advection in the OVERFLOW test-case}
+
 The \href{https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/guide/html/test\_cases.html\#overflow}{OVERFLOW test case}
 provides a simple illustration of the adaptive-implicit advection in action. The example here differs from the basic test case
@@ -1428 +1460 @@
 implicit and explicit components of the vertical velocity are available via XIOS as
 \texttt{wimp} and \texttt{wexp} respectively.  Likewise, the partitioning coefficient
-($C\kern-0.14em f$) is also available as \texttt{wi\_cff}. For a quick oversight of
+(\cf) is also available as \texttt{wi\_cff}. For a quick oversight of
 the schemes activity the global maximum values of the absolute implicit component
 of the vertical velocity and the partitioning coefficient are written to the netCDF
@@ -1460 +1492 @@
 
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_overflow_all_rdt}
-    \caption{
-      \protect\label{fig:ZDF_zad_Aimp_overflow_all_rdt}
-      Sample temperature vertical cross-sections from mid- and end-run using different values for \forcode{nn_rdt}
-      and with or without adaptive implicit vertical advection. Without the adaptive implicit vertical advection only
-      the run with the shortest timestep is able to run to completion. Note also that the colour-scale has been
-      chosen to confirm that temperatures remain within the original range of 10$^o$ to 20$^o$.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_overflow_all_rdt}
+  \caption[OVERFLOW: sample temperature vertical cross-sections from mid- and end-run]{
+    Sample temperature vertical cross-sections from mid- and end-run using
+    different values for \forcode{nn_rdt} and with or without adaptive implicit vertical advection.
+    Without the adaptive implicit vertical advection
+    only the run with the shortest timestep is able to run to completion.
+    Note also that the colour-scale has been chosen to confirm that
+    temperatures remain within the original range of 10$^o$ to 20$^o$.}
+  \label{fig:ZDF_zad_Aimp_overflow_all_rdt}
 \end{figure}
 
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_maxCf}
-    \caption{
-      \protect\label{fig:ZDF_zad_Aimp_maxCf}
-      The maximum partitioning coefficient during a series of test runs with increasing model timestep length.
-      At the larger timesteps, the vertical velocity is treated mostly implicitly at some location throughout
-      the run.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_maxCf}
+  \caption[OVERFLOW: maximum partitioning coefficient during a series of test runs]{
+    The maximum partitioning coefficient during a series of test runs with
+    increasing model timestep length.
+    At the larger timesteps,
+    the vertical velocity is treated mostly implicitly at some location throughout the run.}
+  \label{fig:ZDF_zad_Aimp_maxCf}
 \end{figure}
 
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_maxCf_loc}
-    \caption{
-      \protect\label{fig:ZDF_zad_Aimp_maxCf_loc}
-      The maximum partitioning coefficient for the  \forcode{nn_rdt=10.0s} case overlaid with  information on the gridcell i- and k-
-      locations of the maximum value.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_maxCf_loc}
+  \caption[OVERFLOW: maximum partitioning coefficient for the case overlaid]{
+    The maximum partitioning coefficient for the \forcode{nn_rdt=10.0} case overlaid with
+    information on the gridcell i- and k-locations of the maximum value.}
+  \label{fig:ZDF_zad_Aimp_maxCf_loc}
 \end{figure}
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

@@ -28 +28 @@
 %------------------------------------------namcfg----------------------------------------------------
 
-\nlst{namcfg}
+\begin{listing}
+  \nlst{namcfg}
+  \caption{\texttt{namcfg}}
+  \label{lst:namcfg}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -89 +93 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ORCA_NH_mesh}
-    \caption{
-      \protect\label{fig:CFGS_ORCA_msh}
-      ORCA mesh conception.
-      The departure from an isotropic Mercator grid start poleward of 20\deg{N}.
-      The two "north pole" are the foci of a series of embedded ellipses (blue curves) which
-      are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
-      Then, following \citet{madec.imbard_CD96}, the normal to the series of ellipses (red curves) is computed which
-      provides the j-lines of the mesh (pseudo longitudes).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ORCA_NH_mesh}
+  \caption[ORCA mesh conception]{
+    ORCA mesh conception.
+    The departure from an isotropic Mercator grid start poleward of 20\deg{N}.
+    The two "north pole" are the foci of a series of embedded ellipses (blue curves) which
+    are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
+    Then, following \citet{madec.imbard_CD96},
+    the normal to the series of ellipses (red curves) is computed which
+    provides the j-lines of the mesh (pseudo longitudes).}
+  \label{fig:CFGS_ORCA_msh}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -121 +124 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!tbp]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
-    \includegraphics[width=\textwidth]{Fig_ORCA_aniso}
-    \caption {
-      \protect\label{fig:CFGS_ORCA_e1e2}
-      \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
-      \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
-      for ORCA 0.5\deg ~mesh.
-      South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
-      Poleward of 20\deg{N}, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
-      vicinity of Victoria Island (Canadian Arctic Archipelago).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
+  \includegraphics[width=\textwidth]{Fig_ORCA_aniso}
+  \caption[Horizontal scale factors and ratio of anisotropy for ORCA 0.5\deg\ mesh]{
+    \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
+    \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
+    for ORCA 0.5\deg\ mesh.
+    South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
+    Poleward of 20\deg{N},
+    the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
+    vicinity of Victoria Island (Canadian Arctic Archipelago).}
+  \label{fig:CFGS_ORCA_e1e2}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -163 +165 @@
 %--------------------------------------------------TABLE--------------------------------------------------
 \begin{table}[!t]
-  \begin{center}
-    \begin{tabular}{p{4cm} c c c c}
-      Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\
-      \hline \hline
-%             4   \deg &              4   &          92 &          76 \\
-             2   \deg &              2   &         182 &         149 \\
-             1   \deg &              1   &         362 &         292 \\
-             0.5 \deg &              05  &         722 &         511 \\
-             0.25\deg &              025 &        1442 &        1021 \\
-      \hline \hline
-    \end{tabular}
-    \caption{
-      \protect\label{tab:CFGS_ORCA}
-      Domain size of ORCA family configurations.
-      The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.
-    }
-  \end{center}
+  \centering
+  \begin{tabular}{p{4cm} c c c c}
+    Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\
+    \hline \hline
+    % 4   \deg\ &              4   &          92 &          76 \\
+    2   \deg\ &              2   &         182 &         149 \\
+    1   \deg\ &              1   &         362 &         292 \\
+    0.5 \deg\ &              05  &         722 &         511 \\
+    0.25\deg\ &              025 &        1442 &        1021 \\
+    \hline \hline
+  \end{tabular}
+  \caption[Domain size of ORCA family configurations]{
+    Domain size of ORCA family configurations.
+    The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.}
+  \label{tab:CFGS_ORCA}
 \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -277 +277 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_GYRE}
-    \caption{
-      \protect\label{fig:CFGS_GYRE}
-      Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
-      From \citet{levy.klein.ea_OM10}.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_GYRE}
+  \caption[Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54]{
+    Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
+    From \citet{levy.klein.ea_OM10}.}
+  \label{fig:CFGS_GYRE}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>

NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

@@ -27 +27 @@
 balance the net evaporation occurring over the Mediterranean region.
 This problem occurs even in eddy permitting simulations.
-For example, in ORCA 1/4\deg several straits of the Indonesian archipelago (Ombai, Lombok...)
+For example, in ORCA 1/4\deg\ several straits of the Indonesian archipelago (Ombai, Lombok...)
 are much narrow than even a single ocean grid-point.
 
@@ -72 +72 @@
 \end{itemize}
 
-
 The second method is to increase the viscous boundary layer thickness by a local increase
 of the fmask value at the coast. This method can also be effective in wider passages.  The
@@ -86 +85 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!tbp]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_Gibraltar}
-    \includegraphics[width=\textwidth]{Fig_Gibraltar2}
-    \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 is reduced on both sides of the strait to account for
-      the real width of the strait (about 20 km).
-      Note that the scale factors of the strait $T$-point remains unchanged.
-      \textit{Bottom}: using viscous boundary layers.
-      The four fmask parameters along the strait coastlines are set to a value larger than 4,
-      \ie\ "strong" no-slip case (see \autoref{fig:LBC_shlat}) creating a large viscous boundary layer that
-      allows a reduced transport through the strait.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_Gibraltar}
+  \includegraphics[width=\textwidth]{Fig_Gibraltar2}
+  \caption[Two methods to defined the Gibraltar strait]{
+    Example of the Gibraltar strait defined in a 1\deg\ $\times$ 1\deg\ mesh.
+    \textit{Top}: using partially open cells.
+    The meridional scale factor at $v$-point is reduced on both sides of the strait to
+    account for the real width of the strait (about 20 km).
+    Note that the scale factors of the strait $T$-point remains unchanged.
+    \textit{Bottom}: using viscous boundary layers.
+    The four fmask parameters along the strait coastlines are set to a value larger than 4,
+    \ie\ "strong" no-slip case (see \autoref{fig:LBC_shlat}) creating a large viscous boundary layer
+    that allows a reduced transport through the strait.}
+  \label{fig:MISC_strait_hand}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -107 +104 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!tbp]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_closea_mask_example}
-    \caption{
-      \protect\label{fig:MISC_closea_mask_example}
-      Example of mask fields for the closea module. \textit{Left}: a
-      closea\_mask field; \textit{Right}: a closea\_mask\_rnf
-      field. In this example, if ln\_closea is set to .true., the mean
-      freshwater flux over each of the American Great Lakes will be
-      set to zero, and the total residual for all the lakes, if
-      negative, will be put into the St Laurence Seaway in the area
-      shown.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_closea_mask_example}
+  \caption[Mask fields for the \protect\mdl{closea} module]{
+    Example of mask fields for the \protect\mdl{closea} module.
+    \textit{Left}: a closea\_mask field;
+    \textit{Right}: a closea\_mask\_rnf field.
+    In this example, if \protect\np{ln\_closea} is set to \forcode{.true.},
+    the mean freshwater flux over each of the American Great Lakes will be set to zero,
+    and the total residual for all the lakes, if negative, will be put into
+    the St Laurence Seaway in the area shown.}
+  \label{fig:MISC_closea_mask_example}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -351 +346 @@
 %--------------------------------------------namctl-------------------------------------------------------
 
-\nlst{namctl}
+\begin{listing}
+  \nlst{namctl}
+  \caption{\texttt{namctl}}
+  \label{lst:namctl}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 

NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

@@ -130 +130 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_I_ocean_bc}
-    \caption{
-      \protect\label{fig:MB_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.
-      Both $H$ and $\eta$ are referenced to $z = 0$.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_I_ocean_bc}
+  \caption[Ocean boundary conditions]{
+    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.
+    Both $H$ and $\eta$ are referenced to $z = 0$.}
+  \label{fig:MB_ocean_bc}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -333 +331 @@
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!tb]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_I_earth_referential}
-    \caption{
-      \protect\label{fig:MB_referential}
-      the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear
-      coordinate system $(i,j,k)$.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_I_earth_referential}
+  \caption[Geographical and curvilinear coordinate systems]{
+    the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear
+    coordinate system $(i,j,k)$.}
+  \label{fig:MB_referential}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -749 +745 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!b]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_z_zstar}
-    \caption{
-      \protect\label{fig:MB_z_zstar}
-      (a) $z$-coordinate in linear free-surface case ;
-      (b) $z$-coordinate in non-linear free surface case ;
-      (c) re-scaled height coordinate
-      (become popular as the \zstar-coordinate \citep{adcroft.campin_OM04}).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_z_zstar}
+  \caption[Curvilinear z-coordinate systems (\{non-\}linear free-surface cases and re-scaled \zstar)]{
+    (a) $z$-coordinate in linear free-surface case ;
+    (b) $z$-coordinate in non-linear free surface case ;
+    (c) re-scaled height coordinate
+    (become popular as the \zstar-coordinate \citep{adcroft.campin_OM04}).}
+  \label{fig:MB_z_zstar}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>

NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

@@ -140 +140 @@
 %--------------------------------------------namdom----------------------------------------------------
 
-\nlst{namdom}
 %--------------------------------------------------------------------------------------------------------------
 The split-explicit free surface formulation used in OPA follows the one proposed by \citet{Griffies2004?}.
@@ -149 +148 @@
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts}
-    \caption{
-      \protect\label{fig:MBZ_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 $t-\Delta t$, $t, t+\Delta t$, and $t+2\Delta t$.
-      The curved line represents a leap-frog time step,
-      and the smaller barotropic time steps $N \Delta t=2\Delta t$ are denoted by the zig-zag line.
-      The vertically integrated forcing \textbf{M}(t) computed at
-      baroclinic time step t represents the interaction between the barotropic and baroclinic motions.
-      While keeping the total depth, tracer, and freshwater forcing fields fixed,
-      a leap-frog integration carries the surface height and vertically integrated velocity from
-      t to $t+2 \Delta t$ using N barotropic time steps of length $\Delta t$.
-      Time averaging the barotropic fields over the N+1 time steps (endpoints included)
-      centers the vertically integrated velocity at the baroclinic timestep $t+\Delta t$.
-      A baroclinic leap-frog time step carries the surface height to $t+\Delta t$ using the convergence of
-      the time averaged vertically integrated velocity taken from baroclinic time step t.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts}
+  \caption[Schematic of the split-explicit time stepping scheme for
+  the barotropic and baroclinic modes, after \citet{Griffies2004?}]{
+    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 $t-\Delta t$, $t, t+\Delta t$, and $t+2\Delta t$.
+    The curved line represents a leap-frog time step,
+    and the smaller barotropic time steps $N \Delta t=2\Delta t$ are denoted by the zig-zag line.
+    The vertically integrated forcing \textbf{M}(t) computed at
+    baroclinic time step t represents the interaction between the barotropic and baroclinic motions.
+    While keeping the total depth, tracer, and freshwater forcing fields fixed,
+    a leap-frog integration carries the surface height and vertically integrated velocity from
+    t to $t+2 \Delta t$ using N barotropic time steps of length $\Delta t$.
+    Time averaging the barotropic fields over the N+1 time steps (endpoints included)
+    centers the vertically integrated velocity at the baroclinic timestep $t+\Delta t$.
+    A baroclinic leap-frog time step carries the surface height to $t+\Delta t$ using
+    the convergence of the time averaged vertically integrated velocity taken from
+    baroclinic time step t.}
+  \label{fig:MBZ_dyn_dynspg_ts}
 \end{figure}
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >

NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

@@ -186 +186 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_TimeStepping_flowchart_v4}
-    \caption{
-      \protect\label{fig:TD_TimeStep_flowchart}
-      Sketch of the leapfrog time stepping sequence in \NEMO\ with split-explicit free surface. The latter combined
-       with non-linear free surface requires the dynamical tendency being updated prior tracers tendency to ensure
-       conservation. Note the use of time integrated fluxes issued from the barotropic loop  in subsequent calculations
-       of tracer advection and in the continuity equation. Details about the time-splitting scheme can be found
-       in \autoref{subsec:DYN_spg_ts}.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_TimeStepping_flowchart_v4}
+  \caption[Leapfrog time stepping sequence with split-explicit free surface]{
+    Sketch of the leapfrog time stepping sequence in \NEMO\ with split-explicit free surface.
+    The latter combined with non-linear free surface requires the dynamical tendency being
+    updated prior tracers tendency to ensure conservation.
+    Note the use of time integrated fluxes issued from the barotropic loop in
+    subsequent calculations of tracer advection and in the continuity equation.
+    Details about the time-splitting scheme can be found in \autoref{subsec:DYN_spg_ts}.}
+  \label{fig:TD_TimeStep_flowchart}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -248 +247 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_MLF_forcing}
-    \caption{
-      \protect\label{fig:TD_MLF_forcing}
-      Illustration of forcing integration methods.
-      (top) ''Traditional'' formulation:
-      the forcing is defined at the same time as the variable to which it is applied
-      (integer value of the time step index) and it is applied over a $2 \rdt$ period.
-      (bottom)  modified formulation:
-      the forcing is defined in the middle of the time (integer and a half value of the time step index) and
-      the mean of two successive forcing values ($n - 1 / 2$, $n + 1 / 2$) is applied over a $2 \rdt$ period.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_MLF_forcing}
+  \caption[Forcing integration methods for modified leapfrog (top and bottom)]{
+    Illustration of forcing integration methods.
+    (top) ''Traditional'' formulation:
+    the forcing is defined at the same time as the variable to which it is applied
+    (integer value of the time step index) and it is applied over a $2 \rdt$ period.
+    (bottom)  modified formulation:
+    the forcing is defined in the middle of the time
+    (integer and a half value of the time step index) and
+    the mean of two successive forcing values ($n - 1 / 2$, $n + 1 / 2$) is applied over
+    a $2 \rdt$ period.}
+  \label{fig:TD_MLF_forcing}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -271 +270 @@
 
 %--------------------------------------------namrun-------------------------------------------
-\nlst{namrun}
+\begin{listing}
+  \nlst{namrun}
+  \caption{\texttt{namrun}}
+  \label{lst:namrun}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -317 +320 @@
 %--------------------------------------------namrun-------------------------------------------
 
-\nlst{namdom}
 %--------------------------------------------------------------------------------------------------------------