Changeset 11558


Ignore:
Timestamp:
2019-09-17T17:04:06+02:00 (13 months 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
  1. 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:
23 edited

Legend:

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

    r11543 r11558  
    4343%--------------------------------------------namdom------------------------------------------------------- 
    4444 
    45 \nlst{namdom_domcfg} 
     45\begin{listing} 
     46  \nlst{namdom_domcfg} 
     47  \caption{\texttt{namdom\_domcfg}} 
     48  \label{lst:namdom_domcfg} 
     49\end{listing} 
    4650%-------------------------------------------------------------------------------------------------------------- 
    4751 
     
    103107\section{Vertical grid} 
    104108\label{sec:DOMCFG_vert} 
     109 
    105110\subsection{Vertical reference coordinate} 
    106111\label{sec:DOMCFG_zref} 
     
    108113%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    109114\begin{figure}[!tb] 
    110   \begin{center} 
    111     \includegraphics[width=\textwidth]{Fig_zgr} 
    112     \caption{ 
    113       \protect\label{fig:DOMCFG_zgr} 
    114       Default vertical mesh for ORCA2: 30 ocean levels (L30). 
    115       Vertical level functions for (a) T-point depth and (b) the associated scale factor for the $z$-coordinate case. 
    116     } 
    117   \end{center} 
     115  \centering 
     116  \includegraphics[width=\textwidth]{Fig_zgr} 
     117  \caption[DOMAINcfg: default vertical mesh for ORCA2]{ 
     118    Default vertical mesh for ORCA2: 30 ocean levels (L30). 
     119    Vertical level functions for (a) T-point depth and (b) the associated scale factor for 
     120    the $z$-coordinate case.} 
     121  \label{fig:DOMCFG_zgr} 
    118122\end{figure} 
    119123%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    225229%% %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    226230\begin{table} 
    227   \begin{center} 
    228     \begin{tabular}{c||r|r|r|r} 
    229       \hline 
    230       \textbf{LEVEL} & \textbf{gdept\_1d} & \textbf{gdepw\_1d} & \textbf{e3t\_1d } & \textbf{e3w\_1d} \\ 
    231    \hline 
    232       1              & \textbf{     5.00} &               0.00 & \textbf{   10.00} &            10.00 \\ 
    233       \hline 
    234       2              & \textbf{    15.00} &              10.00 & \textbf{   10.00} &            10.00 \\ 
    235       \hline 
    236       3              & \textbf{    25.00} &              20.00 & \textbf{   10.00} &            10.00 \\ 
    237       \hline 
    238       4              & \textbf{    35.01} &              30.00 & \textbf{   10.01} &            10.00 \\ 
    239       \hline 
    240       5              & \textbf{    45.01} &              40.01 & \textbf{   10.01} &            10.01 \\ 
    241       \hline 
    242       6              & \textbf{    55.03} &              50.02 & \textbf{   10.02} &            10.02 \\ 
    243       \hline 
    244       7              & \textbf{    65.06} &              60.04 & \textbf{   10.04} &            10.03 \\ 
    245       \hline 
    246       8              & \textbf{    75.13} &              70.09 & \textbf{   10.09} &            10.06 \\ 
    247       \hline 
    248       9              & \textbf{    85.25} &              80.18 & \textbf{   10.17} &            10.12 \\ 
    249       \hline 
    250       10             & \textbf{    95.49} &              90.35 & \textbf{   10.33} &            10.24 \\ 
    251       \hline 
    252       11             & \textbf{   105.97} &             100.69 & \textbf{   10.65} &            10.47 \\ 
    253       \hline 
    254       12             & \textbf{   116.90} &             111.36 & \textbf{   11.27} &            10.91 \\ 
    255       \hline 
    256       13             & \textbf{   128.70} &             122.65 & \textbf{   12.47} &            11.77 \\ 
    257       \hline 
    258       14             & \textbf{   142.20} &             135.16 & \textbf{   14.78} &            13.43 \\ 
    259       \hline 
    260       15             & \textbf{   158.96} &             150.03 & \textbf{   19.23} &            16.65 \\ 
    261       \hline 
    262       16             & \textbf{   181.96} &             169.42 & \textbf{   27.66} &            22.78 \\ 
    263       \hline 
    264       17             & \textbf{   216.65} &             197.37 & \textbf{   43.26} &            34.30 \\ 
    265       \hline 
    266       18             & \textbf{   272.48} &             241.13 & \textbf{   70.88} &            55.21 \\ 
    267       \hline 
    268       19             & \textbf{   364.30} &             312.74 & \textbf{  116.11} &            90.99 \\ 
    269       \hline 
    270       20             & \textbf{   511.53} &             429.72 & \textbf{  181.55} &           146.43 \\ 
    271       \hline 
    272       21             & \textbf{   732.20} &             611.89 & \textbf{  261.03} &           220.35 \\ 
    273       \hline 
    274       22             & \textbf{  1033.22} &             872.87 & \textbf{  339.39} &           301.42 \\ 
    275       \hline 
    276       23             & \textbf{  1405.70} &            1211.59 & \textbf{  402.26} &           373.31 \\ 
    277       \hline 
    278       24             & \textbf{  1830.89} &            1612.98 & \textbf{  444.87} &           426.00 \\ 
    279       \hline 
    280       25             & \textbf{  2289.77} &            2057.13 & \textbf{  470.55} &           459.47 \\ 
    281       \hline 
    282       26             & \textbf{  2768.24} &            2527.22 & \textbf{  484.95} &           478.83 \\ 
    283       \hline 
    284       27             & \textbf{  3257.48} &            3011.90 & \textbf{  492.70} &           489.44 \\ 
    285       \hline 
    286       28             & \textbf{  3752.44} &            3504.46 & \textbf{  496.78} &           495.07 \\ 
    287       \hline 
    288       29             & \textbf{  4250.40} &            4001.16 & \textbf{  498.90} &           498.02 \\ 
    289       \hline 
    290       30             & \textbf{  4749.91} &            4500.02 & \textbf{  500.00} &           499.54 \\ 
    291       \hline 
    292       31             & \textbf{  5250.23} &            5000.00 & \textbf{  500.56} &           500.33 \\ 
    293       \hline 
    294     \end{tabular} 
    295   \end{center} 
    296   \caption{ 
    297     \protect\label{tab:DOMCFG_orca_zgr} 
    298     Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration as computed from 
    299     \autoref{eq:DOMCFG_zgr_ana_2} using the coefficients given in \autoref{eq:DOMCFG_zgr_coef} 
    300   } 
     231  \centering 
     232  \begin{tabular}{c||r|r|r|r} 
     233    \hline 
     234    \textbf{LEVEL} & \textbf{gdept\_1d} & \textbf{gdepw\_1d} & \textbf{e3t\_1d } & \textbf{e3w\_1d} \\ 
     235    \hline 
     236    1              & \textbf{     5.00} &               0.00 & \textbf{   10.00} &            10.00 \\ 
     237    \hline 
     238    2              & \textbf{    15.00} &              10.00 & \textbf{   10.00} &            10.00 \\ 
     239    \hline 
     240    3              & \textbf{    25.00} &              20.00 & \textbf{   10.00} &            10.00 \\ 
     241    \hline 
     242    4              & \textbf{    35.01} &              30.00 & \textbf{   10.01} &            10.00 \\ 
     243    \hline 
     244    5              & \textbf{    45.01} &              40.01 & \textbf{   10.01} &            10.01 \\ 
     245    \hline 
     246    6              & \textbf{    55.03} &              50.02 & \textbf{   10.02} &            10.02 \\ 
     247    \hline 
     248    7              & \textbf{    65.06} &              60.04 & \textbf{   10.04} &            10.03 \\ 
     249    \hline 
     250    8              & \textbf{    75.13} &              70.09 & \textbf{   10.09} &            10.06 \\ 
     251    \hline 
     252    9              & \textbf{    85.25} &              80.18 & \textbf{   10.17} &            10.12 \\ 
     253    \hline 
     254    10             & \textbf{    95.49} &              90.35 & \textbf{   10.33} &            10.24 \\ 
     255    \hline 
     256    11             & \textbf{   105.97} &             100.69 & \textbf{   10.65} &            10.47 \\ 
     257    \hline 
     258    12             & \textbf{   116.90} &             111.36 & \textbf{   11.27} &            10.91 \\ 
     259    \hline 
     260    13             & \textbf{   128.70} &             122.65 & \textbf{   12.47} &            11.77 \\ 
     261    \hline 
     262    14             & \textbf{   142.20} &             135.16 & \textbf{   14.78} &            13.43 \\ 
     263    \hline 
     264    15             & \textbf{   158.96} &             150.03 & \textbf{   19.23} &            16.65 \\ 
     265    \hline 
     266    16             & \textbf{   181.96} &             169.42 & \textbf{   27.66} &            22.78 \\ 
     267    \hline 
     268    17             & \textbf{   216.65} &             197.37 & \textbf{   43.26} &            34.30 \\ 
     269    \hline 
     270    18             & \textbf{   272.48} &             241.13 & \textbf{   70.88} &            55.21 \\ 
     271    \hline 
     272    19             & \textbf{   364.30} &             312.74 & \textbf{  116.11} &            90.99 \\ 
     273    \hline 
     274    20             & \textbf{   511.53} &             429.72 & \textbf{  181.55} &           146.43 \\ 
     275    \hline 
     276    21             & \textbf{   732.20} &             611.89 & \textbf{  261.03} &           220.35 \\ 
     277    \hline 
     278    22             & \textbf{  1033.22} &             872.87 & \textbf{  339.39} &           301.42 \\ 
     279    \hline 
     280    23             & \textbf{  1405.70} &            1211.59 & \textbf{  402.26} &           373.31 \\ 
     281    \hline 
     282    24             & \textbf{  1830.89} &            1612.98 & \textbf{  444.87} &           426.00 \\ 
     283    \hline 
     284    25             & \textbf{  2289.77} &            2057.13 & \textbf{  470.55} &           459.47 \\ 
     285    \hline 
     286    26             & \textbf{  2768.24} &            2527.22 & \textbf{  484.95} &           478.83 \\ 
     287    \hline 
     288    27             & \textbf{  3257.48} &            3011.90 & \textbf{  492.70} &           489.44 \\ 
     289    \hline 
     290    28             & \textbf{  3752.44} &            3504.46 & \textbf{  496.78} &           495.07 \\ 
     291    \hline 
     292    29             & \textbf{  4250.40} &            4001.16 & \textbf{  498.90} &           498.02 \\ 
     293    \hline 
     294    30             & \textbf{  4749.91} &            4500.02 & \textbf{  500.00} &           499.54 \\ 
     295    \hline 
     296    31             & \textbf{  5250.23} &            5000.00 & \textbf{  500.56} &           500.33 \\ 
     297    \hline 
     298  \end{tabular} 
     299  \caption[Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration]{ 
     300    Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration as 
     301    computed from \autoref{eq:DOMCFG_zgr_ana_2} using 
     302    the coefficients given in \autoref{eq:DOMCFG_zgr_coef}} 
     303  \label{tab:DOMCFG_orca_zgr} 
    301304\end{table} 
    302305%%%YY 
     
    405408%------------------------------------------nam_zgr_sco--------------------------------------------------- 
    406409% 
    407 \nlst{namzgr_sco_domcfg} 
     410\begin{listing} 
     411  \nlst{namzgr_sco_domcfg} 
     412  \caption{\texttt{namzgr\_sco\_domcfg}} 
     413  \label{lst:namzgr_sco_domcfg} 
     414\end{listing} 
    408415%-------------------------------------------------------------------------------------------------------------- 
    409416Options are defined in \nam{zgr\_sco} (\texttt{DOMAINcfg} only). 
     
    463470%% %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    464471\begin{figure}[!ht] 
    465   \begin{center} 
    466     \includegraphics[width=\textwidth]{Fig_sco_function} 
    467     \caption{ 
    468       \protect\label{fig:DOMCFG_sco_function} 
    469       Examples of the stretching function applied to a seamount; 
    470       from left to right: surface, surface and bottom, and bottom intensified resolutions 
    471     } 
    472   \end{center} 
     472  \centering 
     473  \includegraphics[width=\textwidth]{Fig_sco_function} 
     474  \caption[DOMAINcfg: examples of the stretching function applied to a seamount]{ 
     475    Examples of the stretching function applied to a seamount; 
     476    from left to right: surface, surface and bottom, and bottom intensified resolutions} 
     477  \label{fig:DOMCFG_sco_function} 
    473478\end{figure} 
    474479%% %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    516521%% %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    517522\begin{figure}[!ht] 
     523  \centering 
    518524  \includegraphics[width=\textwidth]{Fig_DOM_compare_coordinates_surface} 
    519   \caption{ 
     525  \caption[DOMAINcfg: comparison of $s$- and $z$-coordinate]{ 
    520526    A comparison of the \citet{song.haidvogel_JCP94} $S$-coordinate (solid lines), 
    521527    a 50 level $Z$-coordinate (contoured surfaces) and 
    522528    the \citet{siddorn.furner_OM13} $S$-coordinate (dashed lines) in the surface $100~m$ for 
    523529    a idealised bathymetry that goes from $50~m$ to $5500~m$ depth. 
    524     For clarity every third coordinate surface is shown. 
    525   } 
     530    For clarity every third coordinate surface is shown.} 
    526531  \label{fig:DOMCFG_fig_compare_coordinates_surface} 
    527532\end{figure} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex

    r11544 r11558  
    307307%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    308308\begin{figure}[!ht] 
    309   \begin{center} 
    310     \includegraphics[width=\textwidth]{Fig_ISO_triad} 
    311     \caption{ 
    312       \protect\label{fig:ALGOS_ISO_triad} 
    313       Triads used in the Griffies's like iso-neutral diffision scheme for 
    314       $u$-component (upper panel) and $w$-component (lower panel). 
    315     } 
    316   \end{center} 
     309  \centering 
     310  \includegraphics[width=\textwidth]{Fig_ISO_triad} 
     311  \caption[Triads used in the Griffies's like iso-neutral diffision scheme for 
     312    $u$- and $w$-components)]{ 
     313    Triads used in the Griffies's like iso-neutral diffision scheme for 
     314    $u$-component (upper panel) and $w$-component (lower panel).} 
     315  \label{fig:ALGOS_ISO_triad} 
    317316\end{figure} 
    318317%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

    r11543 r11558  
    7070Indeed, for the special case $k=z$ and thus $e_3 =1$, 
    7171we introduce an arbitrary vertical coordinate $s = s (i,j,z)$ as in \autoref{apdx:SCOORD} and 
    72 use \autoref{eq:SCOORD_s_slope} and \autoref{eq:SCOORD_s_chain_rule}. 
     72use \autoref{eq:SCOORD_s_slope} and \autoref{eq:SCOORD_s_chain_rule1}. 
    7373Since no cross horizontal derivative $\partial _i \partial _j $ appears in \autoref{eq:DIFFOPERS_1}, 
    7474the ($i$,$z$) and ($j$,$z$) planes are independent. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex

    r11543 r11558  
    411411With the EEN scheme, the vorticity terms are represented as: 
    412412\begin{equation} 
    413   \label{eq:INVARIANTS_dynvor_een} 
     413  \label{eq:INVARIANTS_dynvor_een1} 
    414414  \left\{ { 
    415415      \begin{aligned} 
     
    952952With the EEN scheme, the vorticity terms are represented as: 
    953953\begin{equation} 
    954   \label{eq:INVARIANTS_dynvor_een} 
     954  \label{eq:INVARIANTS_dynvor_een2} 
    955955  \left\{ { 
    956956      \begin{aligned} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex

    r11543 r11558  
    6363Using the first form and considering a change $\delta i$ with $j, z$ and $t$ held constant, shows that 
    6464\begin{equation} 
    65   \label{eq:SCOORD_s_chain_rule} 
     65  \label{eq:SCOORD_s_chain_rule1} 
    6666      \left. {\frac{\partial \bullet }{\partial i}} \right|_{j,z,t}  = 
    6767      \left. {\frac{\partial \bullet }{\partial i}} \right|_{j,s,t} 
     
    102102the model equations in the curvilinear $s-$coordinate system are: 
    103103\begin{equation} 
    104   \label{eq:SCOORD_s_chain_rule} 
     104  \label{eq:SCOORD_s_chain_rule2} 
    105105  \begin{aligned} 
    106106    &\left. {\frac{\partial \bullet }{\partial t}} \right|_z  = 
     
    128128\label{sec:SCOORD_continuity} 
    129129 
    130 Using (\autoref{eq:SCOORD_s_chain_rule}) and 
     130Using (\autoref{eq:SCOORD_s_chain_rule1}) and 
    131131the fact that the horizontal scale factors $e_1$ and $e_2$ do not depend on the vertical coordinate, 
    132132the divergence of the velocity relative to the ($i$,$j$,$z$) coordinate system is transformed as follows in order to 
     
    272272        +  w \;\frac{\partial u}{\partial z}      \\ 
    273273        % 
    274       \intertext{introducing the chain rule (\autoref{eq:SCOORD_s_chain_rule}) } 
     274      \intertext{introducing the chain rule (\autoref{eq:SCOORD_s_chain_rule1}) } 
    275275      % 
    276276      &= \left. {\frac{\partial u }{\partial t}} \right|_z 
     
    317317\end{subequations} 
    318318% 
    319 Applying the time derivative chain rule (first equation of (\autoref{eq:SCOORD_s_chain_rule})) to $u$ and 
     319Applying the time derivative chain rule (first equation of (\autoref{eq:SCOORD_s_chain_rule1})) to $u$ and 
    320320using (\autoref{eq:SCOORD_w_in_s}) provides the expression of the last term of the right hand side, 
    321321\[ 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex

    r11543 r11558  
    2626%-----------------------------------------nam_traldf------------------------------------------------------ 
    2727 
    28 \nlst{namtra_ldf} 
    2928%--------------------------------------------------------------------------------------------------------- 
    3029 
     
    202201% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    203202\begin{figure}[tb] 
    204   \begin{center} 
    205     \includegraphics[width=\textwidth]{Fig_GRIFF_triad_fluxes} 
    206     \caption{ 
    207       \protect\label{fig:TRIADS_ISO_triad} 
    208       (a) Arrangement of triads $S_i$ and tracer gradients to 
    209       give lateral tracer flux from box $i,k$ to $i+1,k$ 
    210       (b) Triads $S'_i$ and tracer gradients to give vertical tracer flux from 
    211       box $i,k$ to $i,k+1$. 
    212     } 
    213   \end{center} 
     203  \centering 
     204  \includegraphics[width=\textwidth]{Fig_GRIFF_triad_fluxes} 
     205  \caption[Triads arrangement and tracer gradients to give lateral and vertical tracer fluxes]{ 
     206    (a) Arrangement of triads $S_i$ and tracer gradients to 
     207    give lateral tracer flux from box $i,k$ to $i+1,k$ 
     208    (b) Triads $S'_i$ and tracer gradients to give vertical tracer flux from 
     209    box $i,k$ to $i,k+1$.} 
     210  \label{fig:TRIADS_ISO_triad} 
    214211\end{figure} 
    215212% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    266263% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    267264\begin{figure}[tb] 
    268   \begin{center} 
    269     \includegraphics[width=\textwidth]{Fig_GRIFF_qcells} 
    270     \caption{ 
    271       \protect\label{fig:TRIADS_qcells} 
    272       Triad notation for quarter cells. $T$-cells are inside boxes, 
    273       while the  $i+\fractext{1}{2},k$ $u$-cell is shaded in green and 
    274       the $i,k+\fractext{1}{2}$ $w$-cell is shaded in pink. 
    275     } 
    276   \end{center} 
     265  \centering 
     266  \includegraphics[width=\textwidth]{Fig_GRIFF_qcells} 
     267  \caption[Triad notation for quarter cells]{ 
     268    Triad notation for quarter cells. 
     269    $T$-cells are inside boxes, 
     270    while the $i+\fractext{1}{2},k$ $u$-cell is shaded in green and 
     271    the $i,k+\fractext{1}{2}$ $w$-cell is shaded in pink.} 
     272  \label{fig:TRIADS_qcells} 
    277273\end{figure} 
    278274% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    659655% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    660656\begin{figure}[h] 
    661   \begin{center} 
    662     \includegraphics[width=\textwidth]{Fig_GRIFF_bdry_triads} 
    663     \caption{ 
    664       \protect\label{fig:TRIADS_bdry_triads} 
    665       (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer points (black dots), 
    666       and $i+1/2,1$ $u$-point (blue square). 
    667       Triad slopes \triad{i}{1}{R}{1/2}{-1/2} (magenta) and \triad{i+1}{1}{R}{-1/2}{-1/2} (blue) poking through 
    668       the ocean surface are masked (faded in figure). 
    669       However, the lateral $_{11}$ contributions towards \triad[u]{i}{1}{F}{1/2}{-1/2} and 
    670       \triad[u]{i+1}{1}{F}{-1/2}{-1/2} (yellow line) are still applied, 
    671       giving diapycnal diffusive fluxes. 
    672       \newline 
    673       (b) Both near bottom triad slopes \triad{i}{k}{R}{1/2}{1/2} and 
    674       \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, 
    675       \ie\ the $i,k+1$ $u$-point is masked. 
    676       The associated lateral fluxes (grey-black dashed line) are masked if 
    677       \protect\np{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked, 
    678       giving bottom mixing, if \protect\np{ln\_botmix\_triad}\forcode{ = .true.} 
    679     } 
    680   \end{center} 
     657  \centering 
     658  \includegraphics[width=\textwidth]{Fig_GRIFF_bdry_triads} 
     659  \caption[Boundary triads]{ 
     660    (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer points (black dots), 
     661    and $i+1/2,1$ $u$-point (blue square). 
     662    Triad slopes \triad{i}{1}{R}{1/2}{-1/2} (magenta) and 
     663    \triad{i+1}{1}{R}{-1/2}{-1/2} (blue) poking through the ocean surface are masked 
     664    (faded in figure). 
     665    However, 
     666    the lateral $_{11}$ contributions towards \triad[u]{i}{1}{F}{1/2}{-1/2} and 
     667    \triad[u]{i+1}{1}{F}{-1/2}{-1/2} (yellow line) are still applied, 
     668    giving diapycnal diffusive fluxes. 
     669    \newline 
     670    (b) Both near bottom triad slopes \triad{i}{k}{R}{1/2}{1/2} and 
     671    \triad{i+1}{k}{R}{-1/2}{1/2} are masked when 
     672    either of the $i,k+1$ or $i+1,k+1$ tracer points is masked, 
     673    \ie\ the $i,k+1$ $u$-point is masked. 
     674    The associated lateral fluxes (grey-black dashed line) are masked if 
     675    \protect\np{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked, 
     676    giving bottom mixing, if \protect\np{ln\_botmix\_triad}\forcode{ = .true.}} 
     677  \label{fig:TRIADS_bdry_triads} 
    681678\end{figure} 
    682679% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    811808% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    812809\begin{figure}[h] 
    813 %  \fcapside { 
    814   \caption{ 
    815     \protect\label{fig:TRIADS_MLB_triad} 
     810  \centering 
     811  \includegraphics[width=\textwidth]{Fig_GRIFF_MLB_triads} 
     812  \caption[Definition of mixed-layer depth and calculation of linearly tapered triads]{ 
    816813    Definition of mixed-layer depth and calculation of linearly tapered triads. 
    817     The figure shows a water column at a given $i,j$ (simplified to $i$), with the ocean surface at the top. 
     814    The figure shows a water column at a given $i,j$ (simplified to $i$), 
     815    with the ocean surface at the top. 
    818816    Tracer points are denoted by bullets, and black lines the edges of the tracer cells; 
    819817    $k$ increases upwards. 
    820818    \newline 
    821     \hspace{5 em} 
    822     We define the mixed-layer by setting the vertical index of the tracer point immediately below the mixed layer, 
    823     $k_{\mathrm{ML}}$, as the maximum $k$ (shallowest tracer point) such that 
     819    We define the mixed-layer by setting the vertical index of the tracer point immediately below 
     820    the mixed layer, $k_{\mathrm{ML}}$, as the maximum $k$ (shallowest tracer point) such that 
    824821    ${\rho_0}_{i,k}>{\rho_0}_{i,k_{10}}+\Delta\rho_c$, 
    825822    where $i,k_{10}$ is the tracer gridbox within which the depth reaches 10~m. 
     
    830827    Triads with different $i_p,k_p$, denoted by different colours, 
    831828    (\eg\ the green triad $i_p=1/2,k_p=-1/2$) are tapered to the appropriate basal triad.} 
    832   % } 
    833   \includegraphics[width=\textwidth]{Fig_GRIFF_MLB_triads} 
     829  \label{fig:TRIADS_MLB_triad} 
    834830\end{figure} 
    835831% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

    r11543 r11558  
    149149%------------------------------------------nam_asminc----------------------------------------------------- 
    150150% 
    151 \nlst{nam_asminc} 
     151\begin{listing} 
     152  \nlst{nam_asminc} 
     153  \caption{\texttt{nam\_asminc}} 
     154  \label{lst:nam_asminc} 
     155\end{listing} 
    152156%------------------------------------------------------------------------------------------------------------- 
    153157 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

    r11543 r11558  
    174174\xmlline|<variable id="using_server" type="bool"></variable>| 
    175175 
    176 The {\ttfamily using\_server} setting determines whether or not the server will be used in \textit{attached mode} 
    177 (as a library) [{\ttfamily> false <}] or in \textit{detached mode} 
    178 (as an external executable on N additional, dedicated cpus) [{\ttfamily > true <}]. 
    179 The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications. 
     176The \texttt{using\_server} setting determines whether or not the server will be used in 
     177\textit{attached mode} 
     178(as a library) [\texttt{> false <}] or in \textit{detached mode} 
     179(as an external executable on N additional, dedicated cpus) [\texttt{ > true <}]. 
     180The \textit{attached mode} is simpler to use but much less efficient for 
     181massively parallel applications. 
    180182The type of each file can be either ''multiple\_file'' or ''one\_file''. 
    181183 
     
    218220 
    219221\begin{table} 
    220   \scriptsize 
    221222  \begin{tabularx}{\textwidth}{|lXl|} 
    222223    \hline 
     
    341342 
    342343\begin{table} 
    343   \scriptsize 
    344344  \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 
    345345    \hline 
     
    373373 
    374374\begin{table} 
    375   \scriptsize 
    376375  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 
    377376    \hline 
     
    398397 
    399398\begin{table} 
    400   \scriptsize 
    401399  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 
    402400    \hline 
     
    418416 
    419417\begin{table} 
    420   \scriptsize 
    421418  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 
    422419    \hline 
     
    634631 
    635632\begin{table} 
    636   \scriptsize 
    637633  \begin{tabularx}{\textwidth}{|lX|} 
    638634    \hline 
     
    695691 
    696692\begin{table} 
    697   \scriptsize 
    698693  \begin{tabular}{|l|c|c|} 
    699694    \hline 
     
    894889 
    895890\begin{table} 
    896   \scriptsize 
    897891  \begin{tabularx}{\textwidth}{|l|X|X|l|X|} 
    898892    \hline 
     
    917911    \hline 
    918912  \end{tabularx} 
    919   \caption{Context tags} 
     913  \caption{XIOS: context tags} 
    920914\end{table} 
    921915 
    922916\begin{table} 
    923   \scriptsize 
    924917  \begin{tabularx}{\textwidth}{|l|X|X|X|l|} 
    925918    \hline 
     
    952945    \hline 
    953946  \end{tabularx} 
    954   \caption{Field tags ("\ttfamily{field\_*}")} 
     947  \caption{XIOS: field tags ("\texttt{field\_*}")} 
    955948\end{table} 
    956949 
    957950\begin{table} 
    958   \scriptsize 
    959951  \begin{tabularx}{\textwidth}{|l|X|X|X|l|} 
    960952    \hline 
     
    988980    \hline 
    989981  \end{tabularx} 
    990   \caption{File tags ("\ttfamily{file\_*}")} 
     982  \caption{XIOS: file tags ("\texttt{file\_*}")} 
    991983\end{table} 
    992984 
    993985\begin{table} 
    994   \scriptsize 
    995986  \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 
    996987    \hline 
     
    10211012    \hline 
    10221013  \end{tabularx} 
    1023   \caption{Axis tags ("\ttfamily{axis\_*}")} 
     1014  \caption{XIOS: axis tags ("\texttt{axis\_*}")} 
    10241015\end{table} 
    10251016 
    10261017\begin{table} 
    1027   \scriptsize 
    10281018  \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 
    10291019    \hline 
     
    10541044    \hline 
    10551045  \end{tabularx} 
    1056   \caption{Domain tags ("\ttfamily{domain\_*)}"} 
     1046  \caption{XIOS: domain tags ("\texttt{domain\_*)}"} 
    10571047\end{table} 
    10581048 
    10591049\begin{table} 
    1060   \scriptsize 
    10611050  \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 
    10621051    \hline 
     
    10871076    \hline 
    10881077  \end{tabularx} 
    1089   \caption{Grid tags ("\ttfamily{grid\_*}")} 
     1078  \caption{XIOS: grid tags ("\texttt{grid\_*}")} 
    10901079\end{table} 
    10911080 
     
    10931082 
    10941083\begin{table} 
    1095   \scriptsize 
    10961084  \begin{tabularx}{\textwidth}{|l|X|l|l|} 
    10971085    \hline 
     
    11281116    \hline 
    11291117  \end{tabularx} 
    1130   \caption{Reference attributes ("\ttfamily{*\_ref}")} 
     1118  \caption{XIOS: reference attributes ("\texttt{*\_ref}")} 
    11311119\end{table} 
    11321120 
    11331121\begin{table} 
    1134   \scriptsize 
    11351122  \begin{tabularx}{\textwidth}{|l|X|l|l|} 
    11361123    \hline 
     
    11641151    \hline 
    11651152  \end{tabularx} 
    1166   \caption{Domain attributes ("\ttfamily{zoom\_*}")} 
     1153  \caption{XIOS: domain attributes ("\texttt{zoom\_*}")} 
    11671154\end{table} 
    11681155 
    11691156\begin{table} 
    1170   \scriptsize 
    11711157  \begin{tabularx}{\textwidth}{|l|X|l|l|} 
    11721158    \hline 
     
    12191205    \hline 
    12201206  \end{tabularx} 
    1221   \caption{File attributes} 
     1207  \caption{XIOS: file attributes} 
    12221208\end{table} 
    12231209 
    12241210\begin{table} 
    1225   \scriptsize 
    12261211  \begin{tabularx}{\textwidth}{|l|X|l|l|} 
    12271212    \hline 
     
    12681253    \hline 
    12691254  \end{tabularx} 
    1270   \caption{Field attributes} 
     1255  \caption{XIOS: field attributes} 
    12711256\end{table} 
    12721257 
    12731258\begin{table} 
    1274   \scriptsize 
    12751259  \begin{tabularx}{\textwidth}{|l|X|X|X|} 
    12761260    \hline 
     
    13271311    \hline 
    13281312  \end{tabularx} 
    1329   \caption{Miscellaneous attributes} 
     1313  \caption{XIOS: miscellaneous attributes} 
    13301314\end{table} 
    13311315 
     
    13661350%------------------------------------------namnc4---------------------------------------------------- 
    13671351 
    1368 \nlst{namnc4} 
     1352\begin{listing} 
     1353  \nlst{namnc4} 
     1354  \caption{\texttt{namnc4}} 
     1355  \label{lst:namnc4} 
     1356\end{listing} 
    13691357%------------------------------------------------------------------------------------------------------------- 
    13701358 
     
    14041392\end{forlines} 
    14051393 
    1406 \noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\ttfamily 46x38x1} respectively in 
    1407 the mono-processor case (\ie\ global domain of {\small\ttfamily 182x149x31}). 
     1394\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\texttt 46x38x1} respectively in 
     1395the mono-processor case (\ie\ global domain of {\small\texttt 182x149x31}). 
    14081396An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in 
    14091397table \autoref{tab:DIA_NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with 
     
    14141402%------------------------------------------TABLE---------------------------------------------------- 
    14151403\begin{table} 
    1416   \scriptsize 
    14171404  \centering 
    14181405  \begin{tabular}{lrrr} 
     
    14461433    ORCA2\_2d\_grid\_W\_0007.nc & 4416    & 1368     & 70\%      \\ 
    14471434  \end{tabular} 
    1448   \caption{ 
    1449     \protect\label{tab:DIA_NC4} 
    1450     Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression 
    1451   } 
     1435  \caption{Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression} 
     1436  \label{tab:DIA_NC4} 
    14521437\end{table} 
    14531438%---------------------------------------------------------------------------------------------------- 
     
    14711456%------------------------------------------namtrd---------------------------------------------------- 
    14721457 
    1473 \nlst{namtrd} 
     1458\begin{listing} 
     1459  \nlst{namtrd} 
     1460  \caption{\texttt{namtrd}} 
     1461  \label{lst:namtrd} 
     1462\end{listing} 
    14741463%------------------------------------------------------------------------------------------------------------- 
    14751464 
     
    15181507%--------------------------------------------namflo------------------------------------------------------- 
    15191508 
    1520 \nlst{namflo} 
     1509\begin{listing} 
     1510  \nlst{namflo} 
     1511  \caption{\texttt{namflo}} 
     1512  \label{lst:namflo} 
     1513\end{listing} 
    15211514%-------------------------------------------------------------------------------------------------------------- 
    15221515 
     
    15361529In case of Ariane convention, input filename is \textit{init\_float\_ariane}. 
    15371530Its format is: \\ 
    1538 {\scriptsize \texttt{I J K nisobfl itrash}} 
     1531{ \texttt{I J K nisobfl itrash}} 
    15391532 
    15401533\noindent with: 
     
    15481541\noindent Example: \\ 
    15491542\noindent 
    1550 {\scriptsize 
     1543{ 
    15511544  \texttt{ 
    15521545    100.00000  90.00000  -1.50000 1.00000   0.00000   \\ 
     
    15591552In the other case (longitude and latitude), input filename is init\_float. 
    15601553Its format is: \\ 
    1561 {\scriptsize \texttt{Long Lat depth nisobfl ngrpfl itrash}} 
     1554{ \texttt{Long Lat depth nisobfl ngrpfl itrash}} 
    15621555 
    15631556\noindent with: 
     
    15731566\noindent Example: \\ 
    15741567\noindent 
    1575 {\scriptsize 
     1568{ 
    15761569  \texttt{ 
    15771570    20.0 0.0 0.0 0 1 1    \\ 
     
    16221615%------------------------------------------nam_diaharm---------------------------------------------------- 
    16231616% 
    1624 \nlst{nam_diaharm} 
     1617\begin{listing} 
     1618  \nlst{nam_diaharm} 
     1619  \caption{\texttt{nam\_diaharm}} 
     1620  \label{lst:nam_diaharm} 
     1621\end{listing} 
    16251622%---------------------------------------------------------------------------------------------------------- 
    16261623 
     
    16701667%------------------------------------------nam_diadct---------------------------------------------------- 
    16711668 
    1672 \nlst{nam_diadct} 
     1669\begin{listing} 
     1670  \nlst{nam_diadct} 
     1671  \caption{\texttt{nam\_diadct}} 
     1672  \label{lst:nam_diadct} 
     1673\end{listing} 
    16731674%------------------------------------------------------------------------------------------------------------- 
    16741675 
     
    17041705 
    17051706Each section is defined by: \\ 
    1706 \noindent {\scriptsize \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\ 
     1707\noindent { \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\ 
    17071708with: 
    17081709 
     
    17211722 
    17221723\noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\ 
    1723 {\scriptsize 
     1724{ 
    17241725  \texttt{ 
    17251726    long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\ 
     
    17541755 and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\ 
    17551756 \noindent 
    1756  {\scriptsize 
     1757 { 
    17571758   \texttt{ 
    17581759     -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage \\ 
     
    17691770 
    17701771The output format is: \\ 
    1771 {\scriptsize 
     1772{ 
    17721773  \texttt{ 
    17731774    date, time-step number, section number,                \\ 
     
    17911792 
    17921793\begin{table} 
    1793   \scriptsize 
    17941794  \begin{tabular}{|l|l|l|l|l|} 
    17951795    \hline 
     
    20112011%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    20122012\begin{figure}[!t] 
    2013   \begin{center} 
    2014     \includegraphics[width=\textwidth]{Fig_mask_subasins} 
    2015     \caption{ 
    2016       \protect\label{fig:DIA_mask_subasins} 
    2017       Decomposition of the World Ocean (here ORCA2) into sub-basin used in to 
    2018       compute the heat and salt transports as well as the meridional stream-function: 
    2019       Atlantic basin (red), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green). 
    2020       Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay are removed from the sub-basins. 
    2021       Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line. 
    2022     } 
    2023   \end{center} 
     2013  \centering 
     2014  \includegraphics[width=\textwidth]{Fig_mask_subasins} 
     2015  \caption[Decomposition of the World Ocean to compute transports as well as 
     2016  the meridional stream-function]{ 
     2017    Decomposition of the World Ocean (here ORCA2) into sub-basin used in to 
     2018    compute the heat and salt transports as well as the meridional stream-function: 
     2019    Atlantic basin (red), Pacific basin (green), 
     2020    Indian basin (blue), Indo-Pacific basin (blue+green). 
     2021    Note that semi-enclosed seas (Red, Med and Baltic seas) as well as 
     2022    Hudson Bay are removed from the sub-basins. 
     2023    Note also that the Arctic Ocean has been split into Atlantic and 
     2024    Pacific basins along the North fold line. 
     2025  } 
     2026  \label{fig:DIA_mask_subasins} 
    20242027\end{figure} 
    20252028%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    20492052%------------------------------------------namptr----------------------------------------- 
    20502053 
    2051 \nlst{namptr} 
     2054\begin{listing} 
     2055  \nlst{namptr} 
     2056  \caption{\texttt{namptr}} 
     2057  \label{lst:namptr} 
     2058\end{listing} 
    20522059%----------------------------------------------------------------------------------------- 
    20532060 
     
    20592066%------------------------------------------nam_dia25h------------------------------------- 
    20602067 
    2061 \nlst{nam_dia25h} 
     2068\begin{listing} 
     2069  \nlst{nam_dia25h} 
     2070  \caption{\texttt{nam\_dia25h}} 
     2071  \label{lst:nam_dia25h} 
     2072\end{listing} 
    20622073%----------------------------------------------------------------------------------------- 
    20632074 
     
    20742085%------------------------------------------nam_diatmb----------------------------------------------------- 
    20752086 
    2076 \nlst{nam_diatmb} 
     2087\begin{listing} 
     2088  \nlst{nam_diatmb} 
     2089  \caption{\texttt{nam\_diatmb}} 
     2090  \label{lst:nam_diatmb} 
     2091\end{listing} 
    20772092%---------------------------------------------------------------------------------------------------------- 
    20782093 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

    r11544 r11558  
    3838Both the cool skin and warm layer models are controlled through the namelist \nam{diu}: 
    3939 
    40 \nlst{namdiu} 
     40\begin{listing} 
     41  \nlst{namdiu} 
     42  \caption{\texttt{namdiu}} 
     43  \label{lst:namdiu} 
     44\end{listing} 
     45 
    4146This namelist contains only two variables: 
    4247\begin{description} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11552 r11558  
    88\label{chap:DOM} 
    99 
    10 %\chaptertoc 
     10\chaptertoc 
    1111 
    1212% Missing things: 
     
    5757%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    5858\begin{figure}[!tb] 
    59   \begin{center} 
    60     \includegraphics[width=\textwidth]{Fig_cell} 
    61     \caption{ 
    62       \protect\label{fig:DOM_cell} 
    63       Arrangement of variables. 
    64       $t$ indicates scalar points where temperature, salinity, density, pressure and 
    65       horizontal divergence are defined. 
    66       $(u,v,w)$ indicates vector points, and $f$ indicates vorticity points where both relative and 
    67       planetary vorticities are defined. 
    68     } 
    69   \end{center} 
     59  \centering 
     60  \includegraphics[width=\textwidth]{Fig_cell} 
     61  \caption[Arrangement of variables in the unit cell of space domain]{ 
     62    Arrangement of variables in the unit cell of space domain. 
     63    $t$ indicates scalar points where 
     64    temperature, salinity, density, pressure and horizontal divergence are defined. 
     65    $(u,v,w)$ indicates vector points, 
     66    and $f$ indicates vorticity points where 
     67    both relative and planetary vorticities are defined.} 
     68  \label{fig:DOM_cell} 
    7069\end{figure} 
    7170%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    102101%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    103102\begin{table}[!tb] 
    104   \begin{center} 
    105     \begin{tabular}{|p{46pt}|p{56pt}|p{56pt}|p{56pt}|} 
    106       \hline 
    107       t  & $i      $ & $j      $ & $k      $ \\ 
    108       \hline 
    109       u  & $i + 1/2$ & $j      $ & $k      $ \\ 
    110       \hline 
    111       v  & $i      $ & $j + 1/2$ & $k      $ \\ 
    112       \hline 
    113       w  & $i      $ & $j      $ & $k + 1/2$ \\ 
    114       \hline 
    115       f  & $i + 1/2$ & $j + 1/2$ & $k      $ \\ 
    116       \hline 
    117       uw & $i + 1/2$ & $j      $ & $k + 1/2$ \\ 
    118       \hline 
    119       vw & $i      $ & $j + 1/2$ & $k + 1/2$ \\ 
    120       \hline 
    121       fw & $i + 1/2$ & $j + 1/2$ & $k + 1/2$ \\ 
    122       \hline 
    123     \end{tabular} 
    124     \caption{ 
    125       \protect\label{tab:DOM_cell} 
    126       Location of grid-points as a function of integer or integer and a half value of the column, line or level. 
    127       This indexing is only used for the writing of the semi -discrete equations. 
    128       In the code, the indexing uses integer values only and is positive downwards in the vertical with $k=1$ at the surface. 
    129       (see \autoref{subsec:DOM_Num_Index}) 
    130     } 
    131   \end{center} 
     103  \centering 
     104  \begin{tabular}{|p{46pt}|p{56pt}|p{56pt}|p{56pt}|} 
     105    \hline 
     106    t & $i      $ & $j      $ & $k      $ \\ 
     107    \hline 
     108    u & $i + 1/2$ & $j      $ & $k      $ \\ 
     109    \hline 
     110    v & $i      $ & $j + 1/2$ & $k      $ \\ 
     111    \hline 
     112    w & $i      $ & $j      $ & $k + 1/2$ \\ 
     113    \hline 
     114    f & $i + 1/2$ & $j + 1/2$ & $k      $ \\ 
     115    \hline 
     116    uw   & $i + 1/2$ & $j      $ & $k + 1/2$ \\ 
     117    \hline 
     118    vw   & $i      $ & $j + 1/2$ & $k + 1/2$ \\ 
     119    \hline 
     120    fw   & $i + 1/2$ & $j + 1/2$ & $k + 1/2$ \\ 
     121    \hline 
     122  \end{tabular} 
     123  \caption[Location of grid-points]{ 
     124    Location of grid-points as a function of integer or 
     125    integer and a half value of the column, line or level. 
     126    This indexing is only used for the writing of the semi -discrete equations. 
     127    In the code, the indexing uses integer values only and 
     128    is positive downwards in the vertical with $k=1$ at the surface. 
     129    (see \autoref{subsec:DOM_Num_Index})} 
     130  \label{tab:DOM_cell} 
    132131\end{table} 
    133132%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    148147%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    149148\begin{figure}[!t] 
    150   \begin{center} 
    151     \includegraphics[width=\textwidth]{Fig_zgr_e3} 
    152     \caption{ 
    153       \protect\label{fig:DOM_zgr_e3} 
    154       Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical, 
    155       and (b) analytically derived grid-point position and scale factors. 
    156       For both grids here, the same $w$-point depth has been chosen but 
    157       in (a) the $t$-points are set half way between $w$-points while 
    158       in (b) they are defined from an analytical function: 
    159       $z(k) = 5 \, (k - 1/2)^3 - 45 \, (k - 1/2)^2 + 140 \, (k - 1/2) - 150$. 
    160       Note the resulting difference between the value of the grid-size $\Delta_k$ and 
    161       those of the scale factor $e_k$. 
    162     } 
    163   \end{center} 
     149  \centering 
     150  \includegraphics[width=\textwidth]{Fig_zgr_e3} 
     151  \caption[Comparison of grid-point position, vertical grid-size and scale factors]{ 
     152    Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical, 
     153    and (b) analytically derived grid-point position and scale factors. 
     154    For both grids here, the same $w$-point depth has been chosen but 
     155    in (a) the $t$-points are set half way between $w$-points while 
     156    in (b) they are defined from an analytical function: 
     157    $z(k) = 5 \, (k - 1/2)^3 - 45 \, (k - 1/2)^2 + 140 \, (k - 1/2) - 150$. 
     158    Note the resulting difference between the value of the grid-size $\Delta_k$ and 
     159    those of the scale factor $e_k$.} 
     160  \label{fig:DOM_zgr_e3} 
    164161\end{figure} 
    165162%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    266263%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    267264\begin{figure}[!tb] 
    268   \begin{center} 
    269     \includegraphics[width=\textwidth]{Fig_index_hor} 
    270     \caption{ 
    271       \protect\label{fig:DOM_index_hor} 
    272       Horizontal integer indexing used in the \fortran\ code. 
    273       The dashed area indicates the cell in which variables contained in arrays have the same $i$- and $j$-indices 
    274     } 
    275   \end{center} 
     265  \centering 
     266  \includegraphics[width=\textwidth]{Fig_index_hor} 
     267  \caption[Horizontal integer indexing]{ 
     268    Horizontal integer indexing used in the \fortran\ code. 
     269    The dashed area indicates the cell in which 
     270    variables contained in arrays have the same $i$- and $j$-indices} 
     271  \label{fig:DOM_index_hor} 
    276272\end{figure} 
    277273%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    321317%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    322318\begin{figure}[!pt] 
    323   \begin{center} 
    324     \includegraphics[width=\textwidth]{Fig_index_vert} 
    325     \caption{ 
    326       \protect\label{fig:DOM_index_vert} 
    327       Vertical integer indexing used in the \fortran\ code. 
    328       Note that the $k$-axis is oriented downward. 
    329       The dashed area indicates the cell in which variables contained in arrays have a common $k$-index. 
    330     } 
    331   \end{center} 
     319  \centering 
     320  \includegraphics[width=\textwidth]{Fig_index_vert} 
     321  \caption[Vertical integer indexing]{ 
     322    Vertical integer indexing used in the \fortran\ code. 
     323    Note that the $k$-axis is oriented downward. 
     324    The dashed area indicates the cell in which 
     325    variables contained in arrays have a common $k$-index.} 
     326  \label{fig:DOM_index_vert} 
    332327\end{figure} 
    333328%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    338333\section{Spatial domain configuration} 
    339334\label{subsec:DOM_config} 
    340  
    341 \nlst{namcfg} 
    342335 
    343336Two typical methods are available to specify the spatial domain configuration; 
     
    468461\label{subsec:DOM_zgr} 
    469462%-----------------------------------------namdom------------------------------------------- 
    470 \nlst{namdom} 
     463\begin{listing} 
     464  \nlst{namdom} 
     465  \caption{\texttt{namdom}} 
     466  \label{lst:namdom} 
     467\end{listing} 
    471468%------------------------------------------------------------------------------------------------------------- 
    472469 
     
    482479%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    483480\begin{figure}[!tb] 
    484   \begin{center} 
    485     \includegraphics[width=\textwidth]{Fig_z_zps_s_sps} 
    486     \caption{ 
    487       \protect\label{fig:DOM_z_zps_s_sps} 
    488       The ocean bottom as seen by the model: 
    489       (a) $z$-coordinate with full step, 
    490       (b) $z$-coordinate with partial step, 
    491       (c) $s$-coordinate: terrain following representation, 
    492       (d) hybrid $s-z$ coordinate, 
    493       (e) hybrid $s-z$ coordinate with partial step, and 
    494       (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}\forcode{=.false.}). 
    495       Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e). 
    496     } 
    497   \end{center} 
     481  \centering 
     482  \includegraphics[width=\textwidth]{Fig_z_zps_s_sps} 
     483  \caption[Ocean bottom regarding coordinate systems ($z$, $s$ and hybrid $s-z$)]{ 
     484    The ocean bottom as seen by the model: 
     485    (a) $z$-coordinate with full step, 
     486    (b) $z$-coordinate with partial step, 
     487    (c) $s$-coordinate: terrain following representation, 
     488    (d) hybrid $s-z$ coordinate, 
     489    (e) hybrid $s-z$ coordinate with partial step, and 
     490    (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}\forcode{=.false.}). 
     491    Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).} 
     492  \label{fig:DOM_z_zps_s_sps} 
    498493\end{figure} 
    499494%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    654649\label{subsec:DOM_meshmask} 
    655650 
    656 \nlst{namcfg} 
    657  
    658651Most of the arrays relating to a particular ocean model configuration discussed in this chapter 
    659652(grid-point position, scale factors) 
     
    665658checking or confirmation is required. 
    666659 
    667 \nlst{namdom} 
    668  
    669660Alternatively, all the arrays relating to a particular ocean model configuration 
    670661(grid-point position, scale factors, depths and masks) 
     
    680671\label{sec:DOM_DTA_tsd} 
    681672%-----------------------------------------namtsd------------------------------------------- 
    682 \nlst{namtsd} 
     673\begin{listing} 
     674  \nlst{namtsd} 
     675  \caption{\texttt{namtsd}} 
     676  \label{lst:namtsd} 
     677\end{listing} 
    683678%------------------------------------------------------------------------------------------ 
    684679 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11552 r11558  
    166166%-----------------------------------------nam_dynadv---------------------------------------------------- 
    167167 
    168 \nlst{namdyn_adv} 
     168\begin{listing} 
     169  \nlst{namdyn_adv} 
     170  \caption{\texttt{namdyn\_adv}} 
     171  \label{lst:namdyn_adv} 
     172\end{listing} 
    169173%------------------------------------------------------------------------------------------------------------- 
    170174 
     
    185189%------------------------------------------nam_dynvor---------------------------------------------------- 
    186190 
    187 \nlst{namdyn_vor} 
     191\begin{listing} 
     192  \nlst{namdyn_vor} 
     193  \caption{\texttt{namdyn\_vor}} 
     194  \label{lst:namdyn_vor} 
     195\end{listing} 
    188196%------------------------------------------------------------------------------------------------------------- 
    189197 
     
    308316%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    309317\begin{figure}[!ht] 
    310   \begin{center} 
    311     \includegraphics[width=\textwidth]{Fig_DYN_een_triad} 
    312     \caption{ 
    313       \protect\label{fig:DYN_een_triad} 
    314       Triads used in the energy and enstrophy conserving scheme (een) for 
    315       $u$-component (upper panel) and $v$-component (lower panel). 
    316     } 
    317   \end{center} 
     318  \centering 
     319  \includegraphics[width=\textwidth]{Fig_DYN_een_triad} 
     320  \caption[Triads used in the energy and enstrophy conserving scheme (EEN)]{ 
     321    Triads used in the energy and enstrophy conserving scheme (EEN) for 
     322    $u$-component (upper panel) and $v$-component (lower panel).} 
     323  \label{fig:DYN_een_triad} 
    318324\end{figure} 
    319325% >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    416422%------------------------------------------nam_dynadv---------------------------------------------------- 
    417423 
    418 \nlst{namdyn_adv} 
    419424%------------------------------------------------------------------------------------------------------------- 
    420425 
     
    564569%------------------------------------------nam_dynhpg--------------------------------------------------- 
    565570 
    566 \nlst{namdyn_hpg} 
     571\begin{listing} 
     572  \nlst{namdyn_hpg} 
     573  \caption{\texttt{namdyn\_hpg}} 
     574  \label{lst:namdyn_hpg} 
     575\end{listing} 
    567576%------------------------------------------------------------------------------------------------------------- 
    568577 
     
    778787%-----------------------------------------nam_dynspg---------------------------------------------------- 
    779788 
    780 \nlst{namdyn_spg} 
     789\begin{listing} 
     790  \nlst{namdyn_spg} 
     791  \caption{\texttt{namdyn\_spg}} 
     792  \label{lst:namdyn_spg} 
     793\end{listing} 
    781794%------------------------------------------------------------------------------------------------------------ 
    782795 
     
    884897%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    885898\begin{figure}[!t] 
    886   \begin{center} 
    887     \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts} 
    888     \caption{ 
    889       \protect\label{fig:DYN_spg_ts} 
    890       Schematic of the split-explicit time stepping scheme for the external and internal modes. 
    891       Time increases to the right. In this particular exemple, 
    892       a boxcar averaging window over $nn\_baro$ barotropic time steps is used ($nn\_bt\_flt=1$) and $nn\_baro=5$. 
    893       Internal mode time steps (which are also the model time steps) are denoted by $t-\rdt$, $t$ and $t+\rdt$. 
    894       Variables with $k$ superscript refer to instantaneous barotropic variables, 
    895       $< >$ and $<< >>$ operator refer to time filtered variables using respectively primary (red vertical bars) and 
    896       secondary weights (blue vertical bars). 
    897       The former are used to obtain time filtered quantities at $t+\rdt$ while 
    898       the latter are used to obtain time averaged transports to advect tracers. 
    899       a) Forward time integration: \protect\np{ln\_bt\_fw}\forcode{=.true.}, 
    900       \protect\np{ln\_bt\_av}\forcode{=.true.}. 
    901       b) Centred time integration: \protect\np{ln\_bt\_fw}\forcode{=.false.}, 
    902       \protect\np{ln\_bt\_av}\forcode{=.true.}. 
    903       c) Forward time integration with no time filtering (POM-like scheme): 
    904       \protect\np{ln\_bt\_fw}\forcode{=.true.}, \protect\np{ln\_bt\_av}\forcode{=.false.}. 
    905     } 
    906   \end{center} 
     899  \centering 
     900  \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts} 
     901  \caption[Split-explicit time stepping scheme for the external and internal modes]{ 
     902    Schematic of the split-explicit time stepping scheme for the external and internal modes. 
     903    Time increases to the right. 
     904    In this particular exemple, 
     905    a boxcar averaging window over \np{nn\_baro} barotropic time steps is used 
     906    (\np{nn\_bt\_flt}\forcode{=1}) and \np{nn\_baro}\forcode{=5}. 
     907    Internal mode time steps (which are also the model time steps) are denoted by 
     908    $t-\rdt$, $t$ and $t+\rdt$. 
     909    Variables with $k$ superscript refer to instantaneous barotropic variables, 
     910    $< >$ and $<< >>$ operator refer to time filtered variables using respectively primary 
     911    (red vertical bars) and secondary weights (blue vertical bars). 
     912    The former are used to obtain time filtered quantities at $t+\rdt$ while 
     913    the latter are used to obtain time averaged transports to advect tracers. 
     914    a) Forward time integration: 
     915    \protect\np{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln\_bt\_av}\forcode{=.true.}. 
     916    b) Centred time integration: 
     917    \protect\np{ln\_bt\_fw}\forcode{=.false.}, \protect\np{ln\_bt\_av}\forcode{=.true.}. 
     918    c) Forward time integration with no time filtering (POM-like scheme): 
     919    \protect\np{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln\_bt\_av}\forcode{=.false.}.} 
     920  \label{fig:DYN_spg_ts} 
    907921\end{figure} 
    908922%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
     
    11141128%------------------------------------------nam_dynldf---------------------------------------------------- 
    11151129 
    1116 \nlst{namdyn_ldf} 
     1130\begin{listing} 
     1131  \nlst{namdyn_ldf} 
     1132  \caption{\texttt{namdyn\_ldf}} 
     1133  \label{lst:namdyn_ldf} 
     1134\end{listing} 
    11171135%------------------------------------------------------------------------------------------------------------- 
    11181136 
     
    12451263%----------------------------------------------namzdf------------------------------------------------------ 
    12461264 
    1247 \nlst{namzdf} 
    12481265%------------------------------------------------------------------------------------------------------------- 
    12491266 
     
    13321349by setting $\mathrm{ln\_wd\_dl} = \mathrm{.true.}$ and $\mathrm{ln\_wd\_il} = \mathrm{.false.}$. 
    13331350 
    1334 \nlst{namwad} 
     1351\begin{listing} 
     1352  \nlst{namwad} 
     1353  \caption{\texttt{namwad}} 
     1354  \label{lst:namwad} 
     1355\end{listing} 
    13351356 
    13361357The following terminology is used. The depth of the topography (positive downwards) 
     
    15411562neighbouring $(i+1,j)$ and $(i,j)$ tracer points.  zcpx is calculated using two logicals 
    15421563variables, $\mathrm{ll\_tmp1}$ and $\mathrm{ll\_tmp2}$ which are evaluated for each grid 
    1543 column.  The three possible combinations are illustrated in figure \autoref{fig:DYN_WAD_dynhpg}. 
     1564column.  The three possible combinations are illustrated in \autoref{fig:DYN_WAD_dynhpg}. 
    15441565 
    15451566%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    1546 \begin{figure}[!ht] \begin{center} 
    1547 \includegraphics[width=\textwidth]{Fig_WAD_dynhpg} 
    1548 \caption{ 
     1567\begin{figure}[!ht] 
     1568  \centering 
     1569  \includegraphics[width=\textwidth]{Fig_WAD_dynhpg} 
     1570  \caption[Combinations controlling the limiting of the horizontal pressure gradient in 
     1571  wetting and drying regimes]{ 
     1572    Three possible combinations of the logical variables controlling the 
     1573    limiting of the horizontal pressure gradient in wetting and drying regimes} 
    15491574  \label{fig:DYN_WAD_dynhpg} 
    1550   Illustrations of the three possible combinations of the logical variables controlling the 
    1551   limiting of the horizontal pressure gradient in wetting and drying regimes} 
    1552 \end{center} 
    15531575\end{figure} 
    15541576%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    16251647%----------------------------------------------namdom---------------------------------------------------- 
    16261648 
    1627 \nlst{namdom} 
    16281649%------------------------------------------------------------------------------------------------------------- 
    16291650 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11552 r11558  
    2222%--------------------------------------------namlbc------------------------------------------------------- 
    2323 
    24 \nlst{namlbc} 
     24\begin{listing} 
     25  \nlst{namlbc} 
     26  \caption{\texttt{namlbc}} 
     27  \label{lst:namlbc} 
     28\end{listing} 
    2529%-------------------------------------------------------------------------------------------------------------- 
    2630 
     
    6771%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    6872\begin{figure}[!t] 
    69   \begin{center} 
    70     \includegraphics[width=\textwidth]{Fig_LBC_uv} 
    71     \caption{ 
    72       \protect\label{fig:LBC_uv} 
    73       Lateral boundary (thick line) at T-level. 
    74       The velocity normal to the boundary is set to zero. 
    75     } 
    76   \end{center} 
     73  \centering 
     74  \includegraphics[width=\textwidth]{Fig_LBC_uv} 
     75  \caption[Lateral boundary at $T$-level]{ 
     76    Lateral boundary (thick line) at T-level. 
     77    The velocity normal to the boundary is set to zero.} 
     78  \label{fig:LBC_uv} 
    7779\end{figure} 
    7880%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    9698%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    9799\begin{figure}[!p] 
    98   \begin{center} 
    99     \includegraphics[width=\textwidth]{Fig_LBC_shlat} 
    100     \caption{ 
    101       \protect\label{fig:LBC_shlat} 
    102       lateral boundary condition 
    103       (a) free-slip ($rn\_shlat=0$); 
    104       (b) no-slip ($rn\_shlat=2$); 
    105       (c) "partial" free-slip ($0<rn\_shlat<2$) and 
    106       (d) "strong" no-slip ($2<rn\_shlat$). 
    107       Implied "ghost" velocity inside land area is display in grey. 
    108     } 
    109   \end{center} 
     100  \centering 
     101  \includegraphics[width=\textwidth]{Fig_LBC_shlat} 
     102  \caption[Lateral boundary conditions]{ 
     103    Lateral boundary conditions 
     104    (a) free-slip                       (\protect\np{rn\_shlat}\forcode{=0}); 
     105    (b) no-slip                         (\protect\np{rn\_shlat}\forcode{=2}); 
     106    (c) "partial" free-slip (\forcode{0<}\protect\np{rn\_shlat}\forcode{<2}) and 
     107    (d) "strong" no-slip    (\forcode{2<}\protect\np{rn\_shlat}). 
     108    Implied "ghost" velocity inside land area is display in grey.} 
     109  \label{fig:LBC_shlat} 
    110110\end{figure} 
    111111%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    207207%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    208208\begin{figure}[!t] 
    209   \begin{center} 
    210     \includegraphics[width=\textwidth]{Fig_LBC_jperio} 
    211     \caption{ 
    212       \protect\label{fig:LBC_jperio} 
    213       setting of (a) east-west cyclic  (b) symmetric across the equator boundary conditions. 
    214     } 
    215   \end{center} 
     209  \centering 
     210  \includegraphics[width=\textwidth]{Fig_LBC_jperio} 
     211  \caption[Setting of east-west cyclic and symmetric across the Equator boundary conditions]{ 
     212    Setting of (a) east-west cyclic (b) symmetric across the Equator boundary conditions} 
     213  \label{fig:LBC_jperio} 
    216214\end{figure} 
    217215%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    232230%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    233231\begin{figure}[!t] 
    234   \begin{center} 
    235     \includegraphics[width=\textwidth]{Fig_North_Fold_T} 
    236     \caption{ 
    237       \protect\label{fig:LBC_North_Fold_T} 
    238       North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$), 
    239       as used in ORCA 2, 1/4, and 1/12. 
    240       Pink shaded area corresponds to the inner domain mask (see text). 
    241     } 
    242   \end{center} 
     232  \centering 
     233  \includegraphics[width=\textwidth]{Fig_North_Fold_T} 
     234  \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{ 
     235    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$), 
     236    as used in ORCA 2\deg, 1/4\deg and 1/12\deg. 
     237    Pink shaded area corresponds to the inner domain mask (see text).} 
     238  \label{fig:LBC_North_Fold_T} 
    243239\end{figure} 
    244240%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    253249%-----------------------------------------nammpp-------------------------------------------- 
    254250 
    255 \nlst{nammpp} 
     251\begin{listing} 
     252  \nlst{nammpp} 
     253  \caption{\texttt{nammpp}} 
     254  \label{lst:nammpp} 
     255\end{listing} 
    256256%----------------------------------------------------------------------------------------------- 
    257257 
     
    291291%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    292292\begin{figure}[!t] 
    293   \begin{center} 
    294     \includegraphics[width=\textwidth]{Fig_mpp} 
    295     \caption{ 
    296       \protect\label{fig:LBC_mpp} 
    297       Positioning of a sub-domain when massively parallel processing is used. 
    298     } 
    299   \end{center} 
     293  \centering 
     294  \includegraphics[width=\textwidth]{Fig_mpp} 
     295  \caption{Positioning of a sub-domain when massively parallel processing is used} 
     296  \label{fig:LBC_mpp} 
    300297\end{figure} 
    301298%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    349346%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    350347\begin{figure}[!ht] 
    351   \begin{center} 
    352     \includegraphics[width=\textwidth]{Fig_mppini2} 
    353     \caption[Atlantic domain]{ 
    354       \protect\label{fig:LBC_mppini2} 
    355       Example of Atlantic domain defined for the CLIPPER projet. 
    356       Initial grid is composed of 773 x 1236 horizontal points. 
    357       (a) the domain is split onto 9 \time 20 subdomains (jpni=9, jpnj=20). 
    358       52 subdomains are land areas. 
    359       (b) 52 subdomains are eliminated (white rectangles) and 
    360       the resulting number of processors really used during the computation is jpnij=128. 
    361     } 
    362   \end{center} 
     348  \centering 
     349  \includegraphics[width=\textwidth]{Fig_mppini2} 
     350  \caption[Atlantic domain defined for the CLIPPER projet]{ 
     351    Example of Atlantic domain defined for the CLIPPER projet. 
     352    Initial grid is composed of 773 x 1236 horizontal points. 
     353    (a) the domain is split onto 9 $times$ 20 subdomains (jpni=9, jpnj=20). 
     354    52 subdomains are land areas. 
     355    (b) 52 subdomains are eliminated (white rectangles) and 
     356    the resulting number of processors really used during the computation is jpnij=128.} 
     357  \label{fig:LBC_mppini2} 
    363358\end{figure} 
    364359%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    373368%-----------------------------------------nambdy-------------------------------------------- 
    374369 
    375 \nlst{nambdy} 
     370\begin{listing} 
     371  \nlst{nambdy} 
     372  \caption{\texttt{nambdy}} 
     373  \label{lst:nambdy} 
     374\end{listing} 
    376375%----------------------------------------------------------------------------------------------- 
    377376%-----------------------------------------nambdy_dta-------------------------------------------- 
    378377 
    379 \nlst{nambdy_dta} 
     378\begin{listing} 
     379  \nlst{nambdy_dta} 
     380  \caption{\texttt{nambdy\_dta}} 
     381  \label{lst:nambdy_dta} 
     382\end{listing} 
    380383%----------------------------------------------------------------------------------------------- 
    381384 
     
    594597the boundary point is increasingly further away from the edge of the model domain. 
    595598A set of $nbi$, $nbj$, and $nbr$ arrays is defined for each of the $T$, $U$ and $V$ grids. 
    596 Figure \autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary. 
     599\autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary. 
    597600 
    598601The boundary geometry for each set may be defined in a namelist nambdy\_index or 
     
    607610 
    608611The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file. 
    609 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. 
     612\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. 
    610613The file should contain the index arrays for each of the $T$, $U$ and $V$ grids. 
    611614The arrays must be in order of increasing $nbr$. 
     
    624627%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    625628\begin{figure}[!t] 
    626   \begin{center} 
    627     \includegraphics[width=\textwidth]{Fig_LBC_bdy_geom} 
    628     \caption { 
    629       \protect\label{fig:LBC_bdy_geom} 
    630       Example of geometry of unstructured open boundary 
    631     } 
    632   \end{center} 
     629  \centering 
     630  \includegraphics[width=\textwidth]{Fig_LBC_bdy_geom} 
     631  \caption[Geometry of unstructured open boundary]{Example of geometry of unstructured open boundary} 
     632  \label{fig:LBC_bdy_geom} 
    633633\end{figure} 
    634634%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    664664%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    665665\begin{figure}[!t] 
    666   \begin{center} 
    667     \includegraphics[width=\textwidth]{Fig_LBC_nc_header} 
    668     \caption { 
    669       \protect\label{fig:LBC_nc_header} 
    670       Example of the header for a \protect\ifile{coordinates.bdy} file 
    671     } 
    672   \end{center} 
     666  \centering 
     667  \includegraphics[width=\textwidth]{Fig_LBC_nc_header} 
     668  \caption[Header for a \protect\ifile{coordinates.bdy} file]{ 
     669    Example of the header for a \protect\ifile{coordinates.bdy} file} 
     670  \label{fig:LBC_nc_header} 
    673671\end{figure} 
    674672%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    697695%-----------------------------------------nambdy_tide-------------------------------------------- 
    698696 
    699 \nlst{nambdy_tide} 
     697\begin{listing} 
     698  \nlst{nambdy_tide} 
     699  \caption{\texttt{nambdy\_tide}} 
     700  \label{lst:nambdy_tide} 
     701\end{listing} 
    700702%----------------------------------------------------------------------------------------------- 
    701703 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11543 r11558  
    2323These three aspects of the lateral diffusion are set through namelist parameters 
    2424(see the \nam{tra\_ldf} and \nam{dyn\_ldf} below). 
    25 Note that this chapter describes the standard implementation of iso-neutral tracer mixing.  
     25Note that this chapter describes the standard implementation of iso-neutral tracer mixing. 
    2626Griffies's implementation, which is used if \np{ln\_traldf\_triad}\forcode{=.true.}, 
    2727is described in \autoref{apdx:TRIADS} 
     
    2929%-----------------------------------namtra_ldf - namdyn_ldf-------------------------------------------- 
    3030 
    31 \nlst{namtra_ldf}  
    32  
    33 \nlst{namdyn_ldf}  
    3431%-------------------------------------------------------------------------------------------------------------- 
    3532 
     
    4542{No lateral mixing (\protect\np{ln\_traldf\_OFF}, \protect\np{ln\_dynldf\_OFF})} 
    4643 
    47 It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln\_traldf\_OFF}\forcode{=.true.}) and/or  
    48 momentum (\protect\np{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the  
     44It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln\_traldf\_OFF}\forcode{=.true.}) and/or 
     45momentum (\protect\np{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the 
    4946UBS advection scheme on momentum (\np{ln\_dynadv\_ubs}\forcode{=.true.}, 
    5047see \autoref{subsec:DYN_adv_ubs}) and can be useful for testing purposes. 
     
    5249\subsection[Laplacian mixing (\forcode{ln_traldf_lap}, \forcode{ln_dynldf_lap})] 
    5350{Laplacian mixing (\protect\np{ln\_traldf\_lap}, \protect\np{ln\_dynldf\_lap})} 
    54 Setting \protect\np{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{=.true.} enables  
    55 a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine  
     51Setting \protect\np{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{=.true.} enables 
     52a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine 
    5653Laplacian and Bilaplacian operators for the same variable. 
    5754 
    5855\subsection[Bilaplacian mixing (\forcode{ln_traldf_blp}, \forcode{ln_dynldf_blp})] 
    5956{Bilaplacian mixing (\protect\np{ln\_traldf\_blp}, \protect\np{ln\_dynldf\_blp})} 
    60 Setting \protect\np{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{=.true.} enables  
    61 a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice.  
     57Setting \protect\np{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{=.true.} enables 
     58a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice. 
    6259We stress again that from \NEMO\ 4, the simultaneous use Laplacian and Bilaplacian operators is not allowed. 
    6360 
     
    8481$r_{1u}$, $r_{1w}$, $r_{2v}$, $r_{2w}$ (see \autoref{eq:TRA_ldf_iso}), 
    8582while for momentum the slopes are  $r_{1t}$, $r_{1uw}$, $r_{2f}$, $r_{2uw}$ for $u$ and 
    86 $r_{1f}$, $r_{1vw}$, $r_{2t}$, $r_{2vw}$ for $v$.  
     83$r_{1f}$, $r_{1vw}$, $r_{2t}$, $r_{2vw}$ for $v$. 
    8784 
    8885%gm% add here afigure of the slope in i-direction 
     
    9491Their discrete formulation is found by locally solving \autoref{eq:TRA_ldf_iso} when 
    9592the diffusive fluxes in the three directions are set to zero and $T$ is assumed to be horizontally uniform, 
    96 \ie\ a linear function of $z_T$, the depth of a $T$-point.  
     93\ie\ a linear function of $z_T$, the depth of a $T$-point. 
    9794%gm { Steven : My version is obviously wrong since I'm left with an arbitrary constant which is the local vertical temperature gradient} 
    9895 
     
    113110\end{equation} 
    114111 
    115 %gm%  caution I'm not sure the simplification was a good idea!  
     112%gm%  caution I'm not sure the simplification was a good idea! 
    116113 
    117114These slopes are computed once in \rou{ldf\_slp\_init} when \np{ln\_sco}\forcode{=.true.}, 
    118 and either \np{ln\_traldf\_hor}\forcode{=.true.} or \np{ln\_dynldf\_hor}\forcode{=.true.}.  
     115and either \np{ln\_traldf\_hor}\forcode{=.true.} or \np{ln\_dynldf\_hor}\forcode{=.true.}. 
    119116 
    120117\subsection{Slopes for tracer iso-neutral mixing} 
     
    145142 
    146143%gm% rewrite this as the explanation is not very clear !!! 
    147 %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.  
     144%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. 
    148145 
    149146%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). 
    150147 
    151 %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.  
     148%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. 
    152149 
    153150As the mixing is performed along neutral surfaces, the gradient of $\rho$ in \autoref{eq:LDF_slp_iso} has to 
     
    164161  This is not the case for the vertical derivatives: $\delta_{k+1/2}[\rho]$ is replaced by $-\rho N^2/g$, 
    165162  where $N^2$ is the local Brunt-Vais\"{a}l\"{a} frequency evaluated following \citet{mcdougall_JPO87} 
    166   (see \autoref{subsec:TRA_bn2}).  
     163  (see \autoref{subsec:TRA_bn2}). 
    167164 
    168165\item[$z$-coordinate with partial step: ] 
     
    179176  will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes. 
    180177 
    181 %gm%  
     178%gm% 
    182179  Note: The solution for $s$-coordinate passes trough the use of different (and better) expression for 
    183180  the constraint on iso-neutral fluxes. 
     
    240237 
    241238Nevertheless, this iso-neutral operator does not ensure that variance cannot increase, 
    242 contrary to the \citet{griffies.gnanadesikan.ea_JPO98} operator which has that property.  
     239contrary to the \citet{griffies.gnanadesikan.ea_JPO98} operator which has that property. 
    243240 
    244241%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    245242\begin{figure}[!ht] 
    246   \begin{center} 
    247     \includegraphics[width=\textwidth]{Fig_LDF_ZDF1} 
    248     \caption { 
    249       \protect\label{fig:LDF_ZDF1} 
    250       averaging procedure for isopycnal slope computation. 
    251     } 
    252   \end{center} 
     243  \centering 
     244  \includegraphics[width=\textwidth]{Fig_LDF_ZDF1} 
     245  \caption{Averaging procedure for isopycnal slope computation} 
     246  \label{fig:LDF_ZDF1} 
    253247\end{figure} 
    254248%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    255249 
    256 %There are three additional questions about the slope calculation.  
    257 %First the expression for the rotation tensor has been obtain assuming the "small slope" approximation, so a bound has to be imposed on slopes.  
    258 %Second, numerical stability issues also require a bound on slopes.  
     250%There are three additional questions about the slope calculation. 
     251%First the expression for the rotation tensor has been obtain assuming the "small slope" approximation, so a bound has to be imposed on slopes. 
     252%Second, numerical stability issues also require a bound on slopes. 
    259253%Third, the question of boundary condition specified on slopes... 
    260254 
     
    263257 
    264258 
    265 % In addition and also for numerical stability reasons \citep{cox_OM87, griffies_bk04},  
    266 % the slopes are bounded by $1/100$ everywhere. This limit is decreasing linearly  
    267 % to zero fom $70$ meters depth and the surface (the fact that the eddies "feel" the  
     259% In addition and also for numerical stability reasons \citep{cox_OM87, griffies_bk04}, 
     260% the slopes are bounded by $1/100$ everywhere. This limit is decreasing linearly 
     261% to zero fom $70$ meters depth and the surface (the fact that the eddies "feel" the 
    268262% surface motivates this flattening of isopycnals near the surface). 
    269263 
     
    277271%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    278272\begin{figure}[!ht] 
    279   \begin{center} 
    280     \includegraphics[width=\textwidth]{Fig_eiv_slp} 
    281     \caption{ 
    282       \protect\label{fig:LDF_eiv_slp} 
    283       Vertical profile of the slope used for lateral mixing in the mixed layer: 
    284       \textit{(a)} in the real ocean the slope is the iso-neutral slope in the ocean interior, 
    285       which has to be adjusted at the surface boundary 
    286       \ie\ it must tend to zero at the surface since there is no mixing across the air-sea interface: 
    287       wall boundary condition). 
    288       Nevertheless, the profile between the surface zero value and the interior iso-neutral one is unknown, 
    289       and especially the value at the base of the mixed layer; 
    290       \textit{(b)} profile of slope using a linear tapering of the slope near the surface and 
    291       imposing a maximum slope of 1/100; 
    292       \textit{(c)} profile of slope actually used in \NEMO: a linear decrease of the slope from 
    293       zero at the surface to its ocean interior value computed just below the mixed layer. 
    294       Note the huge change in the slope at the base of the mixed layer between \textit{(b)} and \textit{(c)}. 
    295     } 
    296   \end{center} 
     273  \centering 
     274  \includegraphics[width=\textwidth]{Fig_eiv_slp} 
     275  \caption[Vertical profile of the slope used for lateral mixing in the mixed layer]{ 
     276    Vertical profile of the slope used for lateral mixing in the mixed layer: 
     277    \textit{(a)} in the real ocean the slope is the iso-neutral slope in the ocean interior, 
     278    which has to be adjusted at the surface boundary 
     279    \ie\ it must tend to zero at the surface since there is no mixing across the air-sea interface: 
     280    wall boundary condition). 
     281    Nevertheless, 
     282    the profile between the surface zero value and the interior iso-neutral one is unknown, 
     283    and especially the value at the base of the mixed layer; 
     284    \textit{(b)} profile of slope using a linear tapering of the slope near the surface and 
     285    imposing a maximum slope of 1/100; 
     286    \textit{(c)} profile of slope actually used in \NEMO: 
     287    a linear decrease of the slope from zero at the surface to 
     288    its ocean interior value computed just below the mixed layer. 
     289    Note the huge change in the slope at the base of the mixed layer between 
     290    \textit{(b)} and \textit{(c)}.} 
     291  \label{fig:LDF_eiv_slp} 
    297292\end{figure} 
    298293%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    326321(see \autoref{sec:LBC_coast}). 
    327322 
    328     
     323 
    329324% ================================================================ 
    330325% Lateral Mixing Coefficients 
     
    334329\label{sec:LDF_coef} 
    335330 
    336 The specification of the space variation of the coefficient is made in modules \mdl{ldftra} and \mdl{ldfdyn}.  
     331The specification of the space variation of the coefficient is made in modules \mdl{ldftra} and \mdl{ldfdyn}. 
    337332The way the mixing coefficients are set in the reference version can be described as follows: 
    338333 
     
    340335{ Mixing coefficients read from file (\protect\np{nn\_aht\_ijk\_t}\forcode{=-20, -30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=-20, -30})} 
    341336 
    342 Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model,  
     337Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model, 
    343338the laplacian viscosity operator uses $A^l$~= 4.10$^4$ m$^2$/s poleward of 20$^{\circ}$ north and south and 
    344 decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}.  
    345 Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05.  
     339decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}. 
     340Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05. 
    346341The 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}). 
    347342 
    348343%-------------------------------------------------TABLE--------------------------------------------------- 
    349344\begin{table}[htb] 
    350   \begin{center} 
    351     \begin{tabular}{|l|l|l|l|} 
    352       \hline 
    353       Namelist parameter                        & Input filename                               & dimensions & variable names                      \\  \hline 
    354       \np{nn\_ahm\_ijk\_t}\forcode{=-20}      & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline 
    355       \np{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$         & \forcode{ahtu_2d, ahtv_2d}    \\   \hline 
    356       \np{nn\_ahm\_ijk\_t}\forcode{=-30}      & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline 
    357       \np{nn\_aht\_ijk\_t}\forcode{=-30}      & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline 
    358     \end{tabular} 
    359     \caption{ 
    360       \protect\label{tab:LDF_files} 
    361       Description of expected input files if mixing coefficients are read from NetCDF files. 
    362     } 
    363   \end{center} 
     345  \centering 
     346  \begin{tabular}{|l|l|l|l|} 
     347    \hline 
     348    Namelist parameter                       & Input filename                               & dimensions & variable names                      \\  \hline 
     349    \np{nn\_ahm\_ijk\_t}\forcode{=-20}     & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline 
     350    \np{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$           & \forcode{ahtu_2d, ahtv_2d}    \\   \hline 
     351    \np{nn\_ahm\_ijk\_t}\forcode{=-30}        & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline 
     352    \np{nn\_aht\_ijk\_t}\forcode{=-30}     & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline 
     353  \end{tabular} 
     354  \caption{Description of expected input files if mixing coefficients are read from NetCDF files} 
     355  \label{tab:LDF_files} 
    364356\end{table} 
    365357%-------------------------------------------------------------------------------------------------------------- 
     
    421413The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases above, 
    422414\ie\ a hyperbolic tangent variation with depth associated with a grid size dependence of 
    423 the magnitude of the coefficient.  
     415the magnitude of the coefficient. 
    424416 
    425417\subsection[Velocity dependent mixing coefficients (\forcode{nn_aht_ijk_t=31}, \forcode{nn_ahm_ijk_t=31})] 
     
    433425    \begin{aligned} 
    434426      & \frac{1}{12} \lvert U \rvert e          & \text{for laplacian operator } \\ 
    435       & \frac{1}{12} \lvert U \rvert e^3             & \text{for bilaplacian operator }  
     427      & \frac{1}{12} \lvert U \rvert e^3             & \text{for bilaplacian operator } 
    436428    \end{aligned} 
    437429  \right. 
     
    441433{Deformation rate dependent viscosities (\protect\np{nn\_ahm\_ijk\_t}\forcode{=32})} 
    442434 
    443 This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a  
     435This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a 
    444436characteristic time scale $T_{smag}$ the deformation rate and for the lengthscale $L_{smag}$ the maximum wavenumber possible on the horizontal grid, e.g.: 
    445437 
     
    459451    \begin{aligned} 
    460452      & C^2  T_{smag}^{-1}  L_{smag}^2       & \text{for laplacian operator } \\ 
    461       & \frac{C^2}{8} T_{smag}^{-1} L_{smag}^4        & \text{for bilaplacian operator }  
     453      & \frac{C^2}{8} T_{smag}^{-1} L_{smag}^4        & \text{for bilaplacian operator } 
    462454    \end{aligned} 
    463455  \right. 
     
    469461    \begin{aligned} 
    470462      & C_{min} \frac{1}{2}   \lvert U \rvert  e    < A_{smag} < C_{max} \frac{e^2}{   8\rdt}                 & \text{for laplacian operator } \\ 
    471       & C_{min} \frac{1}{12} \lvert U \rvert  e^3 < A_{smag} < C_{max} \frac{e^4}{64 \rdt}                 & \text{for bilaplacian operator }  
     463      & C_{min} \frac{1}{12} \lvert U \rvert  e^3 < A_{smag} < C_{max} \frac{e^4}{64 \rdt}                 & \text{for bilaplacian operator } 
    472464    \end{aligned} 
    473465\end{equation} 
     
    482474divergent components of the horizontal current (see \autoref{subsec:MB_ldf}). 
    483475Although the eddy coefficient could be set to different values in these two terms, 
    484 this option is not currently available.  
     476this option is not currently available. 
    485477 
    486478(2) with an horizontally varying viscosity, the quadratic integral constraints on enstrophy and on the square of 
     
    498490%--------------------------------------------namtra_eiv--------------------------------------------------- 
    499491 
    500 \nlst{namtra_eiv} 
     492\begin{listing} 
     493  \nlst{namtra_eiv} 
     494  \caption{\texttt{namtra\_eiv}} 
     495  \label{lst:namtra_eiv} 
     496\end{listing} 
    501497 
    502498%-------------------------------------------------------------------------------------------------------------- 
     
    530526and the sum \autoref{eq:LDF_slp_geo} + \autoref{eq:LDF_slp_iso} in $s$-coordinates. 
    531527 
    532 If isopycnal mixing is used in the standard way, \ie\ \np{ln\_traldf\_triad}\forcode{=.false.}, the eddy induced velocity is given by:  
     528If isopycnal mixing is used in the standard way, \ie\ \np{ln\_traldf\_triad}\forcode{=.false.}, the eddy induced velocity is given by: 
    533529\begin{equation} 
    534530  \label{eq:LDF_eiv} 
     
    539535  \end{split} 
    540536\end{equation} 
    541 where $A^{eiv}$ is the eddy induced velocity coefficient whose value is set through \np{nn\_aei\_ijk\_t} \nam{tra\_eiv} namelist parameter.  
     537where $A^{eiv}$ is the eddy induced velocity coefficient whose value is set through \np{nn\_aei\_ijk\_t} \nam{tra\_eiv} namelist parameter. 
    542538The three components of the eddy induced velocity are computed in \rou{ldf\_eiv\_trp} and 
    543539added to the eulerian velocity in \rou{tra\_adv} where tracer advection is performed. 
     
    547543previous releases of OPA \citep{madec.delecluse.ea_NPM98}. 
    548544This is particularly useful for passive tracers where \emph{positivity} of the advection scheme is of 
    549 paramount importance.  
     545paramount importance. 
    550546 
    551547At the surface, lateral and bottom boundaries, the eddy induced velocity, 
    552 and thus the advective eddy fluxes of heat and salt, are set to zero.  
    553 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).  
     548and thus the advective eddy fluxes of heat and salt, are set to zero. 
     549The 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). 
    554550\colorbox{yellow}{CASE \np{nn\_aei\_ijk\_t} = 21 to be added} 
    555551 
     
    566562%--------------------------------------------namtra_eiv--------------------------------------------------- 
    567563 
    568 \nlst{namtra_mle} 
     564\begin{listing} 
     565  \nlst{namtra_mle} 
     566  \caption{\texttt{namtra\_mle}} 
     567  \label{lst:namtra_mle} 
     568\end{listing} 
    569569 
    570570%-------------------------------------------------------------------------------------------------------------- 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11552 r11558  
    119119%------------------------------------------namobs-------------------------------------------------------- 
    120120 
    121 \nlst{namobs} 
     121\begin{listing} 
     122  \nlst{namobs} 
     123  \caption{\texttt{namobs}} 
     124  \label{lst:namobs} 
     125\end{listing} 
    122126%------------------------------------------------------------------------------------------------------------- 
    123127 
     
    695699%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    696700\begin{figure} 
    697   \begin{center} 
    698     \includegraphics[width=\textwidth]{Fig_OBS_avg_rec} 
    699     \caption{ 
    700       \protect\label{fig:OBS_avgrec} 
    701       Weights associated with each model grid box (blue lines and numbers) 
    702       for an observation at -170.5\deg{E}, 56.0\deg{N} with a rectangular footprint of 1\deg x 1\deg. 
    703     } 
    704   \end{center} 
     701  \centering 
     702  \includegraphics[width=\textwidth]{Fig_OBS_avg_rec} 
     703  \caption[Observational weights with a rectangular footprint]{ 
     704    Weights associated with each model grid box (blue lines and numbers) 
     705    for an observation at -170.5\deg{E}, 56.0\deg{N} with a rectangular footprint of 1\deg\ x 1\deg.} 
     706  \label{fig:OBS_avgrec} 
    705707\end{figure} 
    706 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     708% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    707709 
    708710%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    709711\begin{figure} 
    710   \begin{center} 
    711     \includegraphics[width=\textwidth]{Fig_OBS_avg_rad} 
    712     \caption{ 
    713       \protect\label{fig:OBS_avgrad} 
    714       Weights associated with each model grid box (blue lines and numbers) 
    715       for an observation at -170.5\deg{E}, 56.0\deg{N} with a radial footprint with diameter 1\deg. 
    716     } 
    717   \end{center} 
     712  \centering 
     713  \includegraphics[width=\textwidth]{Fig_OBS_avg_rad} 
     714  \caption[Observational weights with a radial footprint]{ 
     715    Weights associated with each model grid box (blue lines and numbers) 
     716    for an observation at -170.5\deg{E}, 56.0\deg{N} with a radial footprint with diameter 1\deg.} 
     717  \label{fig:OBS_avgrad} 
    718718\end{figure} 
    719719%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    788788%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    789789\begin{figure} 
    790   \begin{center} 
    791     \includegraphics[width=\textwidth]{Fig_ASM_obsdist_local} 
    792     \caption{ 
    793       \protect\label{fig:OBS_local} 
    794       Example of the distribution of observations with the geographical distribution of observational data. 
    795     } 
    796   \end{center} 
     790  \centering 
     791  \includegraphics[width=\textwidth]{Fig_ASM_obsdist_local} 
     792  \caption[Observations with the geographical distribution]{ 
     793    Example of the distribution of observations with 
     794    the geographical distribution of observational data} 
     795  \label{fig:OBS_local} 
    797796\end{figure} 
    798797%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    817816%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    818817\begin{figure} 
    819   \begin{center} 
    820     \includegraphics[width=\textwidth]{Fig_ASM_obsdist_global} 
    821     \caption{ 
    822       \protect\label{fig:OBS_global} 
    823       Example of the distribution of observations with the round-robin distribution of observational data. 
    824     } 
    825   \end{center} 
     818  \centering 
     819  \includegraphics[width=\textwidth]{Fig_ASM_obsdist_global} 
     820  \caption[Observations with the round-robin distribution]{ 
     821    Example of the distribution of observations with 
     822    the round-robin distribution of observational data.} 
     823  \label{fig:OBS_global} 
    826824\end{figure} 
    827825%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    11501148%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11511149\begin{figure} 
    1152   \begin{center} 
    1153     % \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main} 
    1154     \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main} 
    1155     \caption{ 
    1156       \protect\label{fig:OBS_dataplotmain} 
    1157       Main window of dataplot. 
    1158     } 
    1159   \end{center} 
     1150  \centering 
     1151  \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main} 
     1152  \caption{Main window of dataplot} 
     1153  \label{fig:OBS_dataplotmain} 
    11601154\end{figure} 
    11611155%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    11661160%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11671161\begin{figure} 
    1168   \begin{center} 
    1169     % \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof} 
    1170     \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof} 
    1171     \caption{ 
    1172       \protect\label{fig:OBS_dataplotprofile} 
    1173       Profile plot from dataplot produced by right clicking on a point in the main window. 
    1174     } 
    1175   \end{center} 
     1162  \centering 
     1163  \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof} 
     1164  \caption[Profile plot from dataplot]{ 
     1165    Profile plot from dataplot produced by right clicking on a point in the main window} 
     1166  \label{fig:OBS_dataplotprofile} 
    11761167\end{figure} 
    11771168%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11551 r11558  
    1414%---------------------------------------namsbc-------------------------------------------------- 
    1515 
    16 \nlst{namsbc} 
     16\begin{listing} 
     17  \nlst{namsbc} 
     18  \caption{\texttt{namsbc}} 
     19  \label{lst:namsbc} 
     20\end{listing} 
    1721%-------------------------------------------------------------------------------------------------------------- 
    1822 
     
    183187%-------------------------------------------------TABLE--------------------------------------------------- 
    184188\begin{table}[tb] 
    185   \begin{center} 
    186     \begin{tabular}{|l|l|l|l|} 
    187       \hline 
    188       Variable description                         & Model variable  & Units  & point                 \\\hline 
    189       i-component of the surface current  & ssu\_m               & $m.s^{-1}$     & U     \\\hline 
    190       j-component of the surface current  & ssv\_m               & $m.s^{-1}$     & V     \\ \hline 
    191       Sea surface temperature                & sst\_m               & \r{}$K$              & T     \\\hline 
    192       Sea surface salinty                          & sss\_m               & $psu$              & T     \\   \hline 
    193     \end{tabular} 
    194     \caption{ 
    195       \protect\label{tab:SBC_ssm} 
    196       Ocean variables provided by the ocean to the surface module (SBC). 
    197       The variable are averaged over \np{nn\_fsbc} time-step, 
    198       \ie\ the frequency of computation of surface fluxes. 
    199     } 
    200   \end{center} 
     189  \centering 
     190  \begin{tabular}{|l|l|l|l|} 
     191    \hline 
     192    Variable description                           & Model variable  & Units  & point                 \\ 
     193    \hline 
     194    i-component of the surface current & ssu\_m               & $m.s^{-1}$     & U     \\ 
     195    \hline 
     196    j-component of the surface current & ssv\_m               & $m.s^{-1}$     & V     \\ 
     197    \hline 
     198    Sea surface temperature                  & sst\_m               & \r{}$K$              & T     \\\hline 
     199    Sea surface salinty                         & sss\_m               & $psu$              & T     \\   \hline 
     200  \end{tabular} 
     201  \caption[Ocean variables provided to the surface module)]{ 
     202    Ocean variables provided to the surface module (\texttt{SBC}). 
     203    The variable are averaged over \protect\np{nn\_fsbc} time-step, 
     204    \ie\ the frequency of computation of surface fluxes.} 
     205  \label{tab:SBC_ssm} 
    201206\end{table} 
    202207%-------------------------------------------------------------------------------------------------------------- 
     
    269274%--------------------------------------------------TABLE-------------------------------------------------- 
    270275  \begin{table}[htbp] 
    271     \begin{center} 
    272       \begin{tabular}{|l|c|c|c|} 
    273         \hline 
    274                                         &  daily or weekLL     &  monthly           &  yearly        \\   \hline 
    275         \np{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\   \hline 
    276         \np{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\   \hline 
    277       \end{tabular} 
    278     \end{center} 
    279     \caption{ 
    280       \protect\label{tab:SBC_fldread} 
    281       naming nomenclature for climatological or interannual input file(s), as a function of the open/close frequency. 
     276    \centering 
     277    \begin{tabular}{|l|c|c|c|} 
     278      \hline 
     279                                  &  daily or weekLL     &  monthly           &  yearly        \\ 
     280      \hline 
     281      \np{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\ 
     282      \hline 
     283      \np{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\ 
     284      \hline 
     285    \end{tabular} 
     286    \caption[Naming nomenclature for climatological or interannual input file]{ 
     287      Naming nomenclature for climatological or interannual input file, 
     288      as a function of the open/close frequency. 
    282289      The stem name is assumed to be 'fn'. 
    283290      For weekly files, the 'LLL' corresponds to the first three letters of the first day of the week 
    284291      (\ie\ 'sun','sat','fri','thu','wed','tue','mon'). 
    285       The 'YYYY', 'MM' and 'DD' should be replaced by the actual year/month/day, always coded with 4 or 2 digits. 
    286       Note that (1) in mpp, if the file is split over each subdomain, the suffix '.nc' is replaced by '\_PPPP.nc', 
     292      The 'YYYY', 'MM' and 'DD' should be replaced by the actual year/month/day, 
     293      always coded with 4 or 2 digits. 
     294      Note that (1) in mpp, if the file is split over each subdomain, 
     295      the suffix '.nc' is replaced by '\_PPPP.nc', 
    287296      where 'PPPP' is the process number coded with 4 digits; 
    288297      (2) when using AGRIF, the prefix '\_N' is added to files, where 'N' is the child grid number. 
    289298    } 
     299    \label{tab:SBC_fldread} 
    290300  \end{table} 
    291301%-------------------------------------------------------------------------------------------------------------- 
     
    519529%---------------------------------------namsbc_sas-------------------------------------------------- 
    520530 
    521 \nlst{namsbc_sas} 
     531\begin{listing} 
     532  \nlst{namsbc_sas} 
     533  \caption{\texttt{namsbc\_sas}} 
     534  \label{lst:namsbc_sas} 
     535\end{listing} 
    522536%-------------------------------------------------------------------------------------------------------------- 
    523537 
     
    604618%------------------------------------------namsbc_flx---------------------------------------------------- 
    605619 
    606 \nlst{namsbc_flx} 
     620\begin{listing} 
     621  \nlst{namsbc_flx} 
     622  \caption{\texttt{namsbc\_flx}} 
     623  \label{lst:namsbc_flx} 
     624\end{listing} 
    607625%------------------------------------------------------------------------------------------------------------- 
    608626 
     
    627645%---------------------------------------namsbc_blk-------------------------------------------------- 
    628646 
    629 \nlst{namsbc_blk} 
     647\begin{listing} 
     648  \nlst{namsbc_blk} 
     649  \caption{\texttt{namsbc\_blk}} 
     650  \label{lst:namsbc_blk} 
     651\end{listing} 
    630652%-------------------------------------------------------------------------------------------------------------- 
    631653 
     
    649671%--------------------------------------------------TABLE-------------------------------------------------- 
    650672\begin{table}[htbp] 
     673  \centering 
     674  \begin{tabular}{|l|c|c|c|} 
     675    \hline 
     676    Variable description                 & Model variable & Units              & point \\ 
     677    \hline 
     678    i-component of the 10m air velocity  & utau           & $m.s^{-1}$         & T     \\ 
     679    \hline 
     680    j-component of the 10m air velocity  & vtau           & $m.s^{-1}$         & T     \\ 
     681    \hline 
     682    10m air temperature                  & tair           & \r{}$K$            & T     \\ 
     683    \hline 
     684    Specific humidity                    & humi           & \%                 & T     \\ 
     685    \hline 
     686    Incoming long wave radiation         & qlw            & $W.m^{-2}$         & T     \\ 
     687    \hline 
     688    Incoming short wave radiation        & qsr            & $W.m^{-2}$         & T     \\ 
     689    \hline 
     690    Total precipitation (liquid + solid) & precip         & $Kg.m^{-2}.s^{-1}$ & T     \\ 
     691    \hline 
     692    Solid precipitation                  & snow           & $Kg.m^{-2}.s^{-1}$ & T     \\ 
     693    \hline 
     694    Mean sea-level pressure              & slp            & $hPa$              & T     \\ 
     695    \hline 
     696    \end{tabular} 
    651697  \label{tab:SBC_BULK} 
    652   \begin{center} 
    653     \begin{tabular}{|l|c|c|c|} 
    654       \hline 
    655       Variable description                           & Model variable   & Units                         & point \\   \hline 
    656       i-component of the 10m air velocity   & utau                   & $m.s^{-1}$                   & T         \\   \hline 
    657       j-component of the 10m air velocity   & vtau                & $m.s^{-1}$                   & T         \\   \hline 
    658       10m air temperature                      & tair                & \r{}$K$                        & T       \\   \hline 
    659       Specific humidity                        & humi           & \%                             & T      \\   \hline 
    660       Incoming long wave radiation          & qlw                & $W.m^{-2}$            & T        \\   \hline 
    661       Incoming short wave radiation          & qsr               & $W.m^{-2}$            & T        \\   \hline 
    662       Total precipitation (liquid + solid)         & precip            & $Kg.m^{-2}.s^{-1}$      & T      \\   \hline 
    663       Solid precipitation                           & snow               & $Kg.m^{-2}.s^{-1}$       & T      \\   \hline 
    664       Mean sea-level pressure                     & slp                     & $hPa$                          & T       \\ \hline 
    665     \end{tabular} 
    666   \end{center} 
    667698\end{table} 
    668699%-------------------------------------------------------------------------------------------------------------- 
     
    768799%------------------------------------------namsbc_cpl---------------------------------------------------- 
    769800 
    770 \nlst{namsbc_cpl} 
     801\begin{listing} 
     802  \nlst{namsbc_cpl} 
     803  \caption{\texttt{namsbc\_cpl}} 
     804  \label{lst:namsbc_cpl} 
     805\end{listing} 
    771806%------------------------------------------------------------------------------------------------------------- 
    772807 
     
    807842%------------------------------------------namsbc_apr---------------------------------------------------- 
    808843 
    809 \nlst{namsbc_apr} 
     844\begin{listing} 
     845  \nlst{namsbc_apr} 
     846  \caption{\texttt{namsbc\_apr}} 
     847  \label{lst:namsbc_apr} 
     848\end{listing} 
    810849%------------------------------------------------------------------------------------------------------------- 
    811850 
     
    847886%------------------------------------------nam_tide--------------------------------------- 
    848887 
    849 \nlst{nam_tide} 
     888\begin{listing} 
     889  \nlst{nam_tide} 
     890  \caption{\texttt{nam\_tide}} 
     891  \label{lst:nam_tide} 
     892\end{listing} 
    850893%----------------------------------------------------------------------------------------- 
    851894 
     
    899942%------------------------------------------namsbc_rnf---------------------------------------------------- 
    900943 
    901 \nlst{namsbc_rnf} 
     944\begin{listing} 
     945  \nlst{namsbc_rnf} 
     946  \caption{\texttt{namsbc\_rnf}} 
     947  \label{lst:namsbc_rnf} 
     948\end{listing} 
    902949%------------------------------------------------------------------------------------------------------------- 
    903950 
     
    10251072%------------------------------------------namsbc_isf---------------------------------------------------- 
    10261073 
    1027 \nlst{namsbc_isf} 
     1074\begin{listing} 
     1075  \nlst{namsbc_isf} 
     1076  \caption{\texttt{namsbc\_isf}} 
     1077  \label{lst:namsbc_isf} 
     1078\end{listing} 
    10281079%-------------------------------------------------------------------------------------------------------- 
    10291080 
     
    11261177%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11271178\begin{figure}[!t] 
    1128   \begin{center} 
    1129     \includegraphics[width=\textwidth]{Fig_SBC_isf} 
    1130     \caption{ 
    1131       \protect\label{fig:SBC_isf} 
    1132       Illustration the location where the fwf is injected and whether or not the fwf is interactif or not depending of \np{nn\_isf}. 
    1133     } 
    1134   \end{center} 
     1179  \centering 
     1180  \includegraphics[width=\textwidth]{Fig_SBC_isf} 
     1181  \caption[Ice shelf location and fresh water flux definition]{ 
     1182    Illustration of the location where the fwf is injected and 
     1183    whether or not the fwf is interactif or not depending of \protect\np{nn\_isf}.} 
     1184  \label{fig:SBC_isf} 
    11351185\end{figure} 
    11361186%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    11451195%------------------------------------------namsbc_iscpl---------------------------------------------------- 
    11461196 
    1147 \nlst{namsbc_iscpl} 
     1197\begin{listing} 
     1198  \nlst{namsbc_iscpl} 
     1199  \caption{\texttt{namsbc\_iscpl}} 
     1200  \label{lst:namsbc_iscpl} 
     1201\end{listing} 
    11481202%-------------------------------------------------------------------------------------------------------- 
    11491203 
     
    12101264%------------------------------------------namberg---------------------------------------------------- 
    12111265 
    1212 \nlst{namberg} 
     1266\begin{listing} 
     1267  \nlst{namberg} 
     1268  \caption{\texttt{namberg}} 
     1269  \label{lst:namberg} 
     1270\end{listing} 
    12131271%------------------------------------------------------------------------------------------------------------- 
    12141272 
     
    12801338%------------------------------------------namsbc_wave-------------------------------------------------------- 
    12811339 
    1282 \nlst{namsbc_wave} 
     1340\begin{listing} 
     1341  \nlst{namsbc_wave} 
     1342  \caption{\texttt{namsbc\_wave}} 
     1343  \label{lst:namsbc_wave} 
     1344\end{listing} 
    12831345%------------------------------------------------------------------------------------------------------------- 
    12841346 
     
    14831545%------------------------------------------namsbc------------------------------------------------------------- 
    14841546% 
    1485 \nlst{namsbc} 
     1547 
    14861548%------------------------------------------------------------------------------------------------------------- 
    14871549 
    14881550%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14891551\begin{figure}[!t] 
    1490   \begin{center} 
    1491     \includegraphics[width=\textwidth]{Fig_SBC_diurnal} 
    1492     \caption{ 
    1493       \protect\label{fig:SBC_diurnal} 
    1494       Example of recontruction of the diurnal cycle variation of short wave flux from daily mean values. 
    1495       The reconstructed diurnal cycle (black line) is chosen as 
    1496       the mean value of the analytical cycle (blue line) over a time step, 
    1497       not as the mid time step value of the analytically cycle (red square). 
    1498       From \citet{bernie.guilyardi.ea_CD07}. 
    1499     } 
    1500   \end{center} 
     1552  \centering 
     1553  \includegraphics[width=\textwidth]{Fig_SBC_diurnal} 
     1554  \caption[Reconstruction of the diurnal cycle variation of short wave flux]{ 
     1555    Example of reconstruction of the diurnal cycle variation of short wave flux from 
     1556    daily mean values. 
     1557    The reconstructed diurnal cycle (black line) is chosen as 
     1558    the mean value of the analytical cycle (blue line) over a time step, 
     1559    not as the mid time step value of the analytically cycle (red square). 
     1560    From \citet{bernie.guilyardi.ea_CD07}.} 
     1561  \label{fig:SBC_diurnal} 
    15011562\end{figure} 
    15021563%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    15251586%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    15261587\begin{figure}[!t] 
    1527   \begin{center} 
    1528     \includegraphics[width=\textwidth]{Fig_SBC_dcy} 
    1529     \caption{ 
    1530       \protect\label{fig:SBC_dcy} 
    1531       Example of recontruction of the diurnal cycle variation of short wave flux from 
    1532       daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm). 
    1533       The display is on (i,j) plane. 
    1534     } 
    1535   \end{center} 
     1588  \centering 
     1589  \includegraphics[width=\textwidth]{Fig_SBC_dcy} 
     1590  \caption[Reconstruction of the diurnal cycle variation of short wave flux on an ORCA2 grid]{ 
     1591    Example of reconstruction of the diurnal cycle variation of short wave flux from 
     1592    daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm). 
     1593    The display is on (i,j) plane.} 
     1594  \label{fig:SBC_dcy} 
    15361595\end{figure} 
    15371596%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    15691628%------------------------------------------namsbc_ssr---------------------------------------------------- 
    15701629 
    1571 \nlst{namsbc_ssr} 
     1630\begin{listing} 
     1631  \nlst{namsbc_ssr} 
     1632  \caption{\texttt{namsbc\_ssr}} 
     1633  \label{lst:namsbc_ssr} 
     1634\end{listing} 
    15721635%------------------------------------------------------------------------------------------------------------- 
    15731636 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

    r11544 r11558  
    176176%---------------------------------------namsto-------------------------------------------------- 
    177177 
    178 \nlst{namsto} 
     178\begin{listing} 
     179  \nlst{namsto} 
     180  \caption{\texttt{namsto}} 
     181  \label{lst:namsto} 
     182\end{listing} 
    179183%-------------------------------------------------------------------------------------------------------------- 
    180184 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11552 r11558  
    6565%------------------------------------------namtra_adv----------------------------------------------------- 
    6666 
    67 \nlst{namtra_adv} 
     67\begin{listing} 
     68  \nlst{namtra_adv} 
     69  \caption{\texttt{namtra\_adv}} 
     70  \label{lst:namtra_adv} 
     71\end{listing} 
    6872%------------------------------------------------------------------------------------------------------------- 
    6973 
     
    9094%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    9195\begin{figure}[!t] 
    92   \begin{center} 
    93     \includegraphics[width=\textwidth]{Fig_adv_scheme} 
    94     \caption{ 
    95       \protect\label{fig:TRA_adv_scheme} 
    96       Schematic representation of some ways used to evaluate the tracer value at $u$-point and 
    97       the amount of tracer exchanged between two neighbouring grid points. 
    98       Upsteam biased scheme (ups): 
    99       the upstream value is used and the black area is exchanged. 
    100       Piecewise parabolic method (ppm): 
    101       a parabolic interpolation is used and the black and dark grey areas are exchanged. 
    102       Monotonic upstream scheme for conservative laws (muscl): 
    103       a parabolic interpolation is used and black, dark grey and grey areas are exchanged. 
    104       Second order scheme (cen2): 
    105       the mean value is used and black, dark grey, grey and light grey areas are exchanged. 
    106       Note that this illustration does not include the flux limiter used in ppm and muscl schemes. 
    107     } 
    108   \end{center} 
     96  \centering 
     97  \includegraphics[width=\textwidth]{Fig_adv_scheme} 
     98  \caption[Ways to evaluate the tracer value and the amount of tracer exchanged]{ 
     99    Schematic representation of some ways used to evaluate the tracer value at $u$-point and 
     100    the amount of tracer exchanged between two neighbouring grid points. 
     101    Upsteam biased scheme (ups): 
     102    the upstream value is used and the black area is exchanged. 
     103    Piecewise parabolic method (ppm): 
     104    a parabolic interpolation is used and the black and dark grey areas are exchanged. 
     105    Monotonic upstream scheme for conservative laws (muscl): 
     106    a parabolic interpolation is used and black, dark grey and grey areas are exchanged. 
     107    Second order scheme (cen2): 
     108    the mean value is used and black, dark grey, grey and light grey areas are exchanged. 
     109    Note that this illustration does not include the flux limiter used in ppm and muscl schemes.} 
     110  \label{fig:TRA_adv_scheme} 
    109111\end{figure} 
    110112%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    435437%-----------------------------------------nam_traldf------------------------------------------------------ 
    436438 
    437 \nlst{namtra_ldf} 
     439\begin{listing} 
     440  \nlst{namtra_ldf} 
     441  \caption{\texttt{namtra\_ldf}} 
     442  \label{lst:namtra_ldf} 
     443\end{listing} 
    438444%------------------------------------------------------------------------------------------------------------- 
    439445 
     
    640646%--------------------------------------------namzdf--------------------------------------------------------- 
    641647 
    642 \nlst{namzdf} 
    643648%-------------------------------------------------------------------------------------------------------------- 
    644649 
     
    759764%--------------------------------------------namqsr-------------------------------------------------------- 
    760765 
    761 \nlst{namtra_qsr} 
     766\begin{listing} 
     767  \nlst{namtra_qsr} 
     768  \caption{\texttt{namtra\_qsr}} 
     769  \label{lst:namtra_qsr} 
     770\end{listing} 
    762771%-------------------------------------------------------------------------------------------------------------- 
    763772 
     
    857866%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    858867\begin{figure}[!t] 
    859   \begin{center} 
    860     \includegraphics[width=\textwidth]{Fig_TRA_Irradiance} 
    861     \caption{ 
    862       \protect\label{fig:TRA_qsr_irradiance} 
    863       Penetration profile of the downward solar irradiance calculated by four models. 
    864       Two waveband chlorophyll-independent formulation (blue), 
    865       a chlorophyll-dependent monochromatic formulation (green), 
    866       4 waveband RGB formulation (red), 
    867       61 waveband Morel (1988) formulation (black) for a chlorophyll concentration of 
    868       (a) Chl=0.05 mg/m$^3$ and (b) Chl=0.5 mg/m$^3$. 
    869       From \citet{lengaigne.menkes.ea_CD07}. 
    870     } 
    871   \end{center} 
     868  \centering 
     869  \includegraphics[width=\textwidth]{Fig_TRA_Irradiance} 
     870  \caption[Penetration profile of the downward solar irradiance calculated by four models]{ 
     871    Penetration profile of the downward solar irradiance calculated by four models. 
     872    Two waveband chlorophyll-independent formulation (blue), 
     873    a chlorophyll-dependent monochromatic formulation (green), 
     874    4 waveband RGB formulation (red), 
     875    61 waveband Morel (1988) formulation (black) for a chlorophyll concentration of 
     876    (a) Chl=0.05 mg/m$^3$ and (b) Chl=0.5 mg/m$^3$. 
     877    From \citet{lengaigne.menkes.ea_CD07}.} 
     878  \label{fig:TRA_qsr_irradiance} 
    872879\end{figure} 
    873880%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    881888%--------------------------------------------nambbc-------------------------------------------------------- 
    882889 
    883 \nlst{nambbc} 
     890\begin{listing} 
     891  \nlst{nambbc} 
     892  \caption{\texttt{nambbc}} 
     893  \label{lst:nambbc} 
     894\end{listing} 
    884895%-------------------------------------------------------------------------------------------------------------- 
    885896%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    886897\begin{figure}[!t] 
    887   \begin{center} 
    888     \includegraphics[width=\textwidth]{Fig_TRA_geoth} 
    889     \caption{ 
    890       \protect\label{fig:TRA_geothermal} 
    891       Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{emile-geay.madec_OS09}. 
    892       It is inferred from the age of the sea floor and the formulae of \citet{stein.stein_N92}. 
    893     } 
    894   \end{center} 
     898  \centering 
     899  \includegraphics[width=\textwidth]{Fig_TRA_geoth} 
     900  \caption[Geothermal heat flux]{ 
     901    Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{emile-geay.madec_OS09}. 
     902    It is inferred from the age of the sea floor and the formulae of \citet{stein.stein_N92}.} 
     903  \label{fig:TRA_geothermal} 
    895904\end{figure} 
    896905%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    920929%--------------------------------------------nambbl--------------------------------------------------------- 
    921930 
    922 \nlst{nambbl} 
     931\begin{listing} 
     932  \nlst{nambbl} 
     933  \caption{\texttt{nambbl}} 
     934  \label{lst:nambbl} 
     935\end{listing} 
    923936%-------------------------------------------------------------------------------------------------------------- 
    924937 
     
    9991012%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    10001013\begin{figure}[!t] 
    1001   \begin{center} 
    1002     \includegraphics[width=\textwidth]{Fig_BBL_adv} 
    1003     \caption{ 
    1004       \protect\label{fig:TRA_bbl} 
    1005       Advective/diffusive Bottom Boundary Layer. 
    1006       The BBL parameterisation is activated when $\rho^i_{kup}$ is larger than $\rho^{i + 1}_{kdnw}$. 
    1007       Red arrows indicate the additional overturning circulation due to the advective BBL. 
    1008       The transport of the downslope flow is defined either as the transport of the bottom ocean cell (black arrow), 
    1009       or as a function of the along slope density gradient. 
    1010       The green arrow indicates the diffusive BBL flux directly connecting $kup$ and $kdwn$ ocean bottom cells. 
    1011     } 
    1012   \end{center} 
     1014  \centering 
     1015  \includegraphics[width=\textwidth]{Fig_BBL_adv} 
     1016  \caption[Advective/diffusive bottom boundary layer]{ 
     1017    Advective/diffusive Bottom Boundary Layer. 
     1018    The BBL parameterisation is activated when $\rho^i_{kup}$ is larger than $\rho^{i + 1}_{kdnw}$. 
     1019    Red arrows indicate the additional overturning circulation due to the advective BBL. 
     1020    The transport of the downslope flow is defined either 
     1021    as the transport of the bottom ocean cell (black arrow), 
     1022    or as a function of the along slope density gradient. 
     1023    The green arrow indicates the diffusive BBL flux directly connecting 
     1024    $kup$ and $kdwn$ ocean bottom cells.} 
     1025  \label{fig:TRA_bbl} 
    10131026\end{figure} 
    10141027%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    10851098%--------------------------------------------namtra_dmp------------------------------------------------- 
    10861099 
    1087 \nlst{namtra_dmp} 
     1100\begin{listing} 
     1101  \nlst{namtra_dmp} 
     1102  \caption{\texttt{namtra\_dmp}} 
     1103  \label{lst:namtra_dmp} 
     1104\end{listing} 
    10881105%-------------------------------------------------------------------------------------------------------------- 
    10891106 
     
    11401157\label{sec:TRA_nxt} 
    11411158%--------------------------------------------namdom----------------------------------------------------- 
    1142  
    1143 \nlst{namdom} 
    11441159%-------------------------------------------------------------------------------------------------------------- 
    11451160 
     
    11791194%--------------------------------------------nameos----------------------------------------------------- 
    11801195 
    1181 \nlst{nameos} 
     1196\begin{listing} 
     1197  \nlst{nameos} 
     1198  \caption{\texttt{nameos}} 
     1199  \label{lst:nameos} 
     1200\end{listing} 
    11821201%-------------------------------------------------------------------------------------------------------------- 
    11831202 
     
    12831302%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    12841303\begin{table}[!tb] 
    1285   \begin{center} 
    1286     \begin{tabular}{|l|l|l|l|} 
    1287       \hline 
    1288       coeff.      & computer name   & S-EOS           & description                      \\ 
    1289       \hline 
    1290       $a_0$       & \np{rn\_a0}     & $1.6550~10^{-1}$ & linear thermal expansion coeff. \\ 
    1291       \hline 
    1292       $b_0$       & \np{rn\_b0}     & $7.6554~10^{-1}$ & linear haline  expansion coeff. \\ 
    1293       \hline 
    1294       $\lambda_1$ & \np{rn\_lambda1}& $5.9520~10^{-2}$ & cabbeling coeff. in $T^2$       \\ 
    1295       \hline 
    1296       $\lambda_2$ & \np{rn\_lambda2}& $5.4914~10^{-4}$ & cabbeling coeff. in $S^2$       \\ 
    1297       \hline 
    1298       $\nu$       & \np{rn\_nu}     & $2.4341~10^{-3}$ & cabbeling coeff. in $T \, S$    \\ 
    1299       \hline 
    1300       $\mu_1$     & \np{rn\_mu1}    & $1.4970~10^{-4}$ & thermobaric coeff. in T         \\ 
    1301       \hline 
    1302       $\mu_2$     & \np{rn\_mu2}    & $1.1090~10^{-5}$ & thermobaric coeff. in S         \\ 
    1303       \hline 
    1304     \end{tabular} 
    1305     \caption{ 
    1306       \protect\label{tab:TRA_SEOS} 
    1307       Standard value of S-EOS coefficients. 
    1308     } 
    1309 \end{center} 
     1304  \centering 
     1305  \begin{tabular}{|l|l|l|l|} 
     1306    \hline 
     1307    coeff.     & computer name   & S-EOS           & description                      \\ 
     1308    \hline 
     1309    $a_0$       & \np{rn\_a0}     & $1.6550~10^{-1}$ & linear thermal expansion coeff. \\ 
     1310    \hline 
     1311    $b_0$         & \np{rn\_b0}     & $7.6554~10^{-1}$ & linear haline  expansion coeff. \\ 
     1312    \hline 
     1313    $\lambda_1$   & \np{rn\_lambda1}& $5.9520~10^{-2}$ & cabbeling coeff. in $T^2$       \\ 
     1314    \hline 
     1315    $\lambda_2$   & \np{rn\_lambda2}& $5.4914~10^{-4}$ & cabbeling coeff. in $S^2$       \\ 
     1316    \hline 
     1317    $\nu$       & \np{rn\_nu}     & $2.4341~10^{-3}$ & cabbeling coeff. in $T \, S$      \\ 
     1318    \hline 
     1319    $\mu_1$     & \np{rn\_mu1}   & $1.4970~10^{-4}$ & thermobaric coeff. in T         \\ 
     1320    \hline 
     1321    $\mu_2$     & \np{rn\_mu2}   & $1.1090~10^{-5}$ & thermobaric coeff. in S         \\ 
     1322    \hline 
     1323  \end{tabular} 
     1324  \caption{Standard value of S-EOS coefficients} 
     1325  \label{tab:TRA_SEOS} 
    13101326\end{table} 
    13111327%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    13911407%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    13921408\begin{figure}[!p] 
    1393   \begin{center} 
    1394     \includegraphics[width=\textwidth]{Fig_partial_step_scheme} 
    1395     \caption{ 
    1396       \protect\label{fig:TRA_Partial_step_scheme} 
    1397       Discretisation of the horizontal difference and average of tracers in the $z$-partial step coordinate 
    1398       (\protect\np{ln\_zps}\forcode{=.true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$. 
    1399       A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$, 
    1400       the tracer value at the depth of the shallower tracer point of the two adjacent bottom $T$-points. 
    1401       The horizontal difference is then given by: $\delta_{i + 1/2} T_k = \widetilde T_k^{\, i + 1} -T_k^{\, i}$ and 
    1402       the average by: $\overline T_k^{\, i + 1/2} = (\widetilde T_k^{\, i + 1/2} - T_k^{\, i}) / 2$. 
    1403     } 
    1404   \end{center} 
     1409  \centering 
     1410  \includegraphics[width=\textwidth]{Fig_partial_step_scheme} 
     1411  \caption[Discretisation of the horizontal difference and average of tracers in 
     1412  the $z$-partial step coordinate]{ 
     1413    Discretisation of the horizontal difference and average of tracers in 
     1414    the $z$-partial step coordinate (\protect\np{ln\_zps}\forcode{=.true.}) in 
     1415    the case $(e3w_k^{i + 1} - e3w_k^i) > 0$. 
     1416    A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$, 
     1417    the tracer value at the depth of the shallower tracer point of 
     1418    the two adjacent bottom $T$-points. 
     1419    The horizontal difference is then given by: 
     1420    $\delta_{i + 1/2} T_k = \widetilde T_k^{\, i + 1} -T_k^{\, i}$ and 
     1421    the average by: 
     1422    $\overline T_k^{\, i + 1/2} = (\widetilde T_k^{\, i + 1/2} - T_k^{\, i}) / 2$.} 
     1423  \label{fig:TRA_Partial_step_scheme} 
    14051424\end{figure} 
    14061425%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r11543 r11558  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3%% Custom aliases 
     4\newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 
    25 
    36\begin{document} 
     
    4548%--------------------------------------------namzdf-------------------------------------------------------- 
    4649 
    47 \nlst{namzdf} 
     50\begin{listing} 
     51  \nlst{namzdf} 
     52  \caption{\texttt{namzdf}} 
     53  \label{lst:namzdf} 
     54\end{listing} 
    4855%-------------------------------------------------------------------------------------------------------------- 
    4956 
     
    8087%--------------------------------------------namric--------------------------------------------------------- 
    8188 
    82 \nlst{namzdf_ric} 
     89\begin{listing} 
     90  \nlst{namzdf_ric} 
     91  \caption{\texttt{namzdf\_ric}} 
     92  \label{lst:namzdf_ric} 
     93\end{listing} 
    8394%-------------------------------------------------------------------------------------------------------------- 
    8495 
     
    137148%--------------------------------------------namzdf_tke-------------------------------------------------- 
    138149 
    139 \nlst{namzdf_tke} 
     150\begin{listing} 
     151  \nlst{namzdf_tke} 
     152  \caption{\texttt{namzdf\_tke}} 
     153  \label{lst:namzdf_tke} 
     154\end{listing} 
    140155%-------------------------------------------------------------------------------------------------------------- 
    141156 
     
    238253%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    239254\begin{figure}[!t] 
    240   \begin{center} 
    241     \includegraphics[width=\textwidth]{Fig_mixing_length} 
    242     \caption{ 
    243       \protect\label{fig:ZDF_mixing_length} 
    244       Illustration of the mixing length computation. 
    245     } 
    246   \end{center} 
     255  \centering 
     256  \includegraphics[width=\textwidth]{Fig_mixing_length} 
     257  \caption[Mixing length computation]{Illustration of the mixing length computation} 
     258  \label{fig:ZDF_mixing_length} 
    247259\end{figure} 
    248260%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    421433%--------------------------------------------namzdf_gls--------------------------------------------------------- 
    422434 
    423 \nlst{namzdf_gls} 
     435\begin{listing} 
     436  \nlst{namzdf_gls} 
     437  \caption{\texttt{namzdf\_gls}} 
     438  \label{lst:namzdf_gls} 
     439\end{listing} 
    424440%-------------------------------------------------------------------------------------------------------------- 
    425441 
     
    475491%--------------------------------------------------TABLE-------------------------------------------------- 
    476492\begin{table}[htbp] 
    477   \begin{center} 
    478     % \begin{tabular}{cp{70pt}cp{70pt}cp{70pt}cp{70pt}cp{70pt}cp{70pt}c} 
    479     \begin{tabular}{ccccc} 
    480       &   $k-kl$   & $k-\epsilon$ & $k-\omega$ &   generic   \\ 
    481       % & \citep{mellor.yamada_RG82} &  \citep{rodi_JGR87}       & \citep{wilcox_AJ88} &                 \\ 
    482       \hline 
    483       \hline 
    484       \np{nn\_clo}     & \textbf{0} &   \textbf{1}  &   \textbf{2}   &    \textbf{3}   \\ 
    485       \hline 
    486       $( p , n , m )$          &   ( 0 , 1 , 1 )   & ( 3 , 1.5 , -1 )   & ( -1 , 0.5 , -1 )    &  ( 2 , 1 , -0.67 )  \\ 
    487       $\sigma_k$      &    2.44         &     1.              &      2.                &      0.8          \\ 
    488       $\sigma_\psi$  &    2.44         &     1.3            &      2.                 &       1.07       \\ 
    489       $C_1$              &      0.9         &     1.44          &      0.555          &       1.           \\ 
    490       $C_2$              &      0.5         &     1.92          &      0.833          &       1.22       \\ 
    491       $C_3$              &      1.           &     1.              &      1.                &       1.           \\ 
    492       $F_{wall}$        &      Yes        &       --             &     --                  &      --          \\ 
    493       \hline 
    494       \hline 
    495     \end{tabular} 
    496     \caption{ 
    497       \protect\label{tab:ZDF_GLS} 
    498       Set of predefined GLS parameters, or equivalently predefined turbulence models available with 
    499       \protect\np{ln\_zdfgls}\forcode{=.true.} and controlled by the \protect\np{nn\_clos} namelist variable in \protect\nam{zdf\_gls}. 
    500     } 
    501   \end{center} 
     493  \centering 
     494  % \begin{tabular}{cp{70pt}cp{70pt}cp{70pt}cp{70pt}cp{70pt}cp{70pt}c} 
     495  \begin{tabular}{ccccc} 
     496    &   $k-kl$   & $k-\epsilon$ & $k-\omega$ &   generic   \\ 
     497    % & \citep{mellor.yamada_RG82} &  \citep{rodi_JGR87}       & \citep{wilcox_AJ88} &                 \\ 
     498    \hline 
     499    \hline 
     500    \np{nn\_clo}     & \textbf{0} &   \textbf{1}  &   \textbf{2}   &    \textbf{3}   \\ 
     501    \hline 
     502    $( p , n , m )$         &   ( 0 , 1 , 1 )   & ( 3 , 1.5 , -1 )   & ( -1 , 0.5 , -1 )    &  ( 2 , 1 , -0.67 )  \\ 
     503    $\sigma_k$      &    2.44         &     1.              &      2.                &      0.8          \\ 
     504    $\sigma_\psi$  &    2.44         &     1.3            &      2.                 &       1.07       \\ 
     505    $C_1$              &      0.9         &     1.44          &      0.555          &       1.           \\ 
     506    $C_2$              &      0.5         &     1.92          &      0.833          &       1.22       \\ 
     507    $C_3$              &      1.           &     1.              &      1.                &       1.           \\ 
     508    $F_{wall}$        &      Yes        &       --             &     --                  &      --          \\ 
     509    \hline 
     510    \hline 
     511  \end{tabular} 
     512  \caption[Set of predefined GLS parameters or equivalently predefined turbulence models available]{ 
     513    Set of predefined GLS parameters, or equivalently predefined turbulence models available with 
     514    \protect\np{ln\_zdfgls}\forcode{=.true.} and controlled by 
     515    the \protect\np{nn\_clos} namelist variable in \protect\nam{zdf\_gls}.} 
     516  \label{tab:ZDF_GLS} 
    502517\end{table} 
    503518%-------------------------------------------------------------------------------------------------------------- 
     
    542557%--------------------------------------------namzdf_osm--------------------------------------------------------- 
    543558 
    544 \nlst{namzdf_osm} 
     559\begin{listing} 
     560  \nlst{namzdf_osm} 
     561  \caption{\texttt{namzdf\_osm}} 
     562  \label{lst:namzdf_osm} 
     563\end{listing} 
    545564%-------------------------------------------------------------------------------------------------------------- 
    546565 
     
    556575%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    557576\begin{figure}[!t] 
    558   \begin{center} 
    559     \includegraphics[width=\textwidth]{Fig_ZDF_TKE_time_scheme} 
    560     \caption{ 
    561       \protect\label{fig:ZDF_TKE_time_scheme} 
    562       Illustration of the subgrid kinetic energy integration in GLS and TKE schemes and its links to the momentum and tracer time integration. 
    563     } 
    564   \end{center} 
     577  \centering 
     578  \includegraphics[width=\textwidth]{Fig_ZDF_TKE_time_scheme} 
     579  \caption[Subgrid kinetic energy integration in GLS and TKE schemes]{ 
     580    Illustration of the subgrid kinetic energy integration in GLS and TKE schemes and 
     581    its links to the momentum and tracer time integration.} 
     582  \label{fig:ZDF_TKE_time_scheme} 
    565583\end{figure} 
    566584%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    676694%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    677695\begin{figure}[!htb] 
    678   \begin{center} 
    679     \includegraphics[width=\textwidth]{Fig_npc} 
    680     \caption{ 
    681       \protect\label{fig:ZDF_npc} 
    682       Example of an unstable density profile treated by the non penetrative convective adjustment algorithm. 
    683       $1^{st}$ step: the initial profile is checked from the surface to the bottom. 
    684       It is found to be unstable between levels 3 and 4. 
    685       They are mixed. 
    686       The resulting $\rho$ is still larger than $\rho$(5): levels 3 to 5 are mixed. 
    687       The resulting $\rho$ is still larger than $\rho$(6): levels 3 to 6 are mixed. 
    688       The $1^{st}$ step ends since the density profile is then stable below the level 3. 
    689       $2^{nd}$ step: the new $\rho$ profile is checked following the same procedure as in $1^{st}$ step: 
    690       levels 2 to 5 are mixed. 
    691       The new density profile is checked. 
    692       It is found stable: end of algorithm. 
    693     } 
    694   \end{center} 
     696  \centering 
     697  \includegraphics[width=\textwidth]{Fig_npc} 
     698  \caption[Unstable density profile treated by the non penetrative convective adjustment algorithm]{ 
     699    Example of an unstable density profile treated by 
     700    the non penetrative convective adjustment algorithm. 
     701    $1^{st}$ step: the initial profile is checked from the surface to the bottom. 
     702    It is found to be unstable between levels 3 and 4. 
     703    They are mixed. 
     704    The resulting $\rho$ is still larger than $\rho$(5): levels 3 to 5 are mixed. 
     705    The resulting $\rho$ is still larger than $\rho$(6): levels 3 to 6 are mixed. 
     706    The $1^{st}$ step ends since the density profile is then stable below the level 3. 
     707    $2^{nd}$ step: the new $\rho$ profile is checked following the same procedure as in $1^{st}$ step: 
     708    levels 2 to 5 are mixed. 
     709    The new density profile is checked. 
     710    It is found stable: end of algorithm.} 
     711  \label{fig:ZDF_npc} 
    695712\end{figure} 
    696713%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    838855%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    839856\begin{figure}[!t] 
    840   \begin{center} 
    841     \includegraphics[width=\textwidth]{Fig_zdfddm} 
    842     \caption{ 
    843       \protect\label{fig:ZDF_ddm} 
    844       From \citet{merryfield.holloway.ea_JPO99} : 
    845       (a) Diapycnal diffusivities $A_f^{vT}$ and $A_f^{vS}$ for temperature and salt in regions of salt fingering. 
    846       Heavy curves denote $A^{\ast v} = 10^{-3}~m^2.s^{-1}$ and thin curves $A^{\ast v} = 10^{-4}~m^2.s^{-1}$; 
    847       (b) diapycnal diffusivities $A_d^{vT}$ and $A_d^{vS}$ for temperature and salt in regions of 
    848       diffusive convection. 
    849       Heavy curves denote the Federov parameterisation and thin curves the Kelley parameterisation. 
    850       The latter is not implemented in \NEMO. 
    851     } 
    852   \end{center} 
     857  \centering 
     858  \includegraphics[width=\textwidth]{Fig_zdfddm} 
     859  \caption[Diapycnal diffusivities for temperature and salt in regions of salt fingering and 
     860  diffusive convection]{ 
     861    From \citet{merryfield.holloway.ea_JPO99}: 
     862    (a) Diapycnal diffusivities $A_f^{vT}$ and $A_f^{vS}$ for temperature and salt in 
     863    regions of salt fingering. 
     864    Heavy curves denote $A^{\ast v} = 10^{-3}~m^2.s^{-1}$ and 
     865    thin curves $A^{\ast v} = 10^{-4}~m^2.s^{-1}$; 
     866    (b) diapycnal diffusivities $A_d^{vT}$ and $A_d^{vS}$ for temperature and salt in 
     867    regions of diffusive convection. 
     868    Heavy curves denote the Federov parameterisation and thin curves the Kelley parameterisation. 
     869    The latter is not implemented in \NEMO.} 
     870  \label{fig:ZDF_ddm} 
    853871\end{figure} 
    854872%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    893911%--------------------------------------------namdrg-------------------------------------------------------- 
    894912% 
    895 \nlst{namdrg} 
    896 \nlst{namdrg_top} 
    897 \nlst{namdrg_bot} 
     913\begin{listing} 
     914  \nlst{namdrg} 
     915  \caption{\texttt{namdrg}} 
     916  \label{lst:namdrg} 
     917\end{listing} 
     918\begin{listing} 
     919  \nlst{namdrg_top} 
     920  \caption{\texttt{namdrg\_top}} 
     921  \label{lst:namdrg_top} 
     922\end{listing} 
     923\begin{listing} 
     924  \nlst{namdrg_bot} 
     925  \caption{\texttt{namdrg\_bot}} 
     926  \label{lst:namdrg_bot} 
     927\end{listing} 
    898928 
    899929%-------------------------------------------------------------------------------------------------------------- 
     
    11751205%--------------------------------------------namzdf_iwm------------------------------------------ 
    11761206% 
    1177 \nlst{namzdf_iwm} 
     1207\begin{listing} 
     1208  \nlst{namzdf_iwm} 
     1209  \caption{\texttt{namzdf\_iwm}} 
     1210  \label{lst:namzdf_iwm} 
     1211\end{listing} 
    11781212%-------------------------------------------------------------------------------------------------------------- 
    11791213 
     
    12871321 
    12881322\begin{table}[htbp] 
    1289   \begin{center} 
    1290     % \begin{tabular}{cp{70pt}cp{70pt}cp{70pt}cp{70pt}} 
    1291     \begin{tabular}{r|ccc} 
    1292       \hline 
    1293       spatial discretization &   2nd order centered   & 3rd order upwind & 4th order compact  \\ 
    1294       advective CFL criterion     & 0.904 &   0.472  &   0.522    \\ 
    1295       \hline 
    1296     \end{tabular} 
    1297     \caption{ 
    1298       \protect\label{tab:ZDF_zad_Aimp_CFLcrit} 
    1299       The advective CFL criteria for a range of spatial discretizations for the Leap-Frog with Robert Asselin filter time-stepping 
    1300       ($\nu=0.1$) as given in \citep{lemarie.debreu.ea_OM15}. 
    1301     } 
    1302   \end{center} 
     1323  \centering 
     1324  % \begin{tabular}{cp{70pt}cp{70pt}cp{70pt}cp{70pt}} 
     1325  \begin{tabular}{r|ccc} 
     1326    \hline 
     1327    spatial discretization  & 2$^nd$ order centered & 3$^rd$ order upwind & 4$^th$ order compact \\ 
     1328    advective CFL criterion &                 0.904 &              0.472  &                0.522 \\ 
     1329    \hline 
     1330  \end{tabular} 
     1331  \caption[Advective CFL criteria for the leapfrog with Robert Asselin filter time-stepping]{ 
     1332    The advective CFL criteria for a range of spatial discretizations for 
     1333    the leapfrog with Robert Asselin filter time-stepping 
     1334    ($\nu=0.1$) as given in \citep{lemarie.debreu.ea_OM15}.} 
     1335  \label{tab:ZDF_zad_Aimp_CFLcrit} 
    13031336\end{table} 
    13041337 
     
    13311364Cu_{cut} &= 2Cu_{max} - Cu_{min} \nonumber \\ 
    13321365Fcu    &= 4Cu_{max}*(Cu_{max}-Cu_{min}) \nonumber \\ 
    1333 C\kern-0.14em f &= 
     1366\cf &= 
    13341367     \begin{cases} 
    13351368        0.0                                                        &\text{if $Cu \leq Cu_{min}$} \\ 
     
    13401373 
    13411374\begin{figure}[!t] 
    1342   \begin{center} 
    1343     \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_coeff} 
    1344     \caption{ 
    1345       \protect\label{fig:ZDF_zad_Aimp_coeff} 
    1346       The value of the partitioning coefficient ($C\kern-0.14em f$) used to partition vertical velocities into parts to 
    1347       be treated implicitly and explicitly for a range of typical Courant numbers (\forcode{ln_zad_Aimp=.true.}) 
    1348     } 
    1349   \end{center} 
     1375  \centering 
     1376  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_coeff} 
     1377  \caption[Partitioning coefficient used to partition vertical velocities into parts]{ 
     1378    The value of the partitioning coefficient (\cf) used to partition vertical velocities into 
     1379    parts to be treated implicitly and explicitly for a range of typical Courant numbers 
     1380    (\forcode{ln_zad_Aimp=.true.}).} 
     1381  \label{fig:ZDF_zad_Aimp_coeff} 
    13501382\end{figure} 
    13511383 
     
    13561388\begin{align} 
    13571389  \label{eq:ZDF_Eqn_zad_Aimp_partition2} 
    1358     w_{i_{ijk}} &= C\kern-0.14em f_{ijk} w_{n_{ijk}}     \nonumber \\ 
    1359     w_{n_{ijk}} &= (1-C\kern-0.14em f_{ijk}) w_{n_{ijk}} 
     1390    w_{i_{ijk}} &= \cf_{ijk} w_{n_{ijk}}     \nonumber \\ 
     1391    w_{n_{ijk}} &= (1-\cf_{ijk}) w_{n_{ijk}} 
    13601392\end{align} 
    13611393 
     
    13631395the three cases from \autoref{eq:ZDF_Eqn_zad_Aimp_partition} can be considered as: 
    13641396fully-explicit; mixed explicit/implicit and mostly-implicit.  With the settings shown the 
    1365 coefficient ($C\kern-0.14em f$) varies as shown in \autoref{fig:ZDF_zad_Aimp_coeff}. Note with these values 
     1397coefficient (\cf) varies as shown in \autoref{fig:ZDF_zad_Aimp_coeff}. Note with these values 
    13661398the $Cu_{cut}$ boundary between the mixed implicit-explicit treatment and 'mostly 
    13671399implicit' is 0.45 which is just below the stability limited given in 
     
    13811413 
    13821414\begin{figure}[!t] 
    1383   \begin{center} 
    1384     \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_overflow_frames} 
    1385     \caption{ 
    1386       \protect\label{fig:ZDF_zad_Aimp_overflow_frames} 
    1387       A time-series of temperature vertical cross-sections for the OVERFLOW test case. These results are for the default 
    1388       settings with \forcode{nn_rdt=10.0} and without adaptive implicit vertical advection (\forcode{ln_zad_Aimp=.false.}). 
    1389     } 
    1390   \end{center} 
     1415  \centering 
     1416  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_overflow_frames} 
     1417  \caption[OVERFLOW: time-series of temperature vertical cross-sections]{ 
     1418    A time-series of temperature vertical cross-sections for the OVERFLOW test case. 
     1419    These results are for the default settings with \forcode{nn_rdt=10.0} and 
     1420    without adaptive implicit vertical advection (\forcode{ln_zad_Aimp=.false.}).} 
     1421  \label{fig:ZDF_zad_Aimp_overflow_frames} 
    13911422\end{figure} 
    13921423 
    13931424\subsection{Adaptive-implicit vertical advection in the OVERFLOW test-case} 
     1425 
    13941426The \href{https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/guide/html/test\_cases.html\#overflow}{OVERFLOW test case} 
    13951427provides a simple illustration of the adaptive-implicit advection in action. The example here differs from the basic test case 
     
    14281460implicit and explicit components of the vertical velocity are available via XIOS as 
    14291461\texttt{wimp} and \texttt{wexp} respectively.  Likewise, the partitioning coefficient 
    1430 ($C\kern-0.14em f$) is also available as \texttt{wi\_cff}. For a quick oversight of 
     1462(\cf) is also available as \texttt{wi\_cff}. For a quick oversight of 
    14311463the schemes activity the global maximum values of the absolute implicit component 
    14321464of the vertical velocity and the partitioning coefficient are written to the netCDF 
     
    14601492 
    14611493\begin{figure}[!t] 
    1462   \begin{center} 
    1463     \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_overflow_all_rdt} 
    1464     \caption{ 
    1465       \protect\label{fig:ZDF_zad_Aimp_overflow_all_rdt} 
    1466       Sample temperature vertical cross-sections from mid- and end-run using different values for \forcode{nn_rdt} 
    1467       and with or without adaptive implicit vertical advection. Without the adaptive implicit vertical advection only 
    1468       the run with the shortest timestep is able to run to completion. Note also that the colour-scale has been 
    1469       chosen to confirm that temperatures remain within the original range of 10$^o$ to 20$^o$. 
    1470     } 
    1471   \end{center} 
     1494  \centering 
     1495  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_overflow_all_rdt} 
     1496  \caption[OVERFLOW: sample temperature vertical cross-sections from mid- and end-run]{ 
     1497    Sample temperature vertical cross-sections from mid- and end-run using 
     1498    different values for \forcode{nn_rdt} and with or without adaptive implicit vertical advection. 
     1499    Without the adaptive implicit vertical advection 
     1500    only the run with the shortest timestep is able to run to completion. 
     1501    Note also that the colour-scale has been chosen to confirm that 
     1502    temperatures remain within the original range of 10$^o$ to 20$^o$.} 
     1503  \label{fig:ZDF_zad_Aimp_overflow_all_rdt} 
    14721504\end{figure} 
    14731505 
    14741506\begin{figure}[!t] 
    1475   \begin{center} 
    1476     \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_maxCf} 
    1477     \caption{ 
    1478       \protect\label{fig:ZDF_zad_Aimp_maxCf} 
    1479       The maximum partitioning coefficient during a series of test runs with increasing model timestep length. 
    1480       At the larger timesteps, the vertical velocity is treated mostly implicitly at some location throughout 
    1481       the run. 
    1482     } 
    1483   \end{center} 
     1507  \centering 
     1508  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_maxCf} 
     1509  \caption[OVERFLOW: maximum partitioning coefficient during a series of test runs]{ 
     1510    The maximum partitioning coefficient during a series of test runs with 
     1511    increasing model timestep length. 
     1512    At the larger timesteps, 
     1513    the vertical velocity is treated mostly implicitly at some location throughout the run.} 
     1514  \label{fig:ZDF_zad_Aimp_maxCf} 
    14841515\end{figure} 
    14851516 
    14861517\begin{figure}[!t] 
    1487   \begin{center} 
    1488     \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_maxCf_loc} 
    1489     \caption{ 
    1490       \protect\label{fig:ZDF_zad_Aimp_maxCf_loc} 
    1491       The maximum partitioning coefficient for the  \forcode{nn_rdt=10.0s} case overlaid with  information on the gridcell i- and k- 
    1492       locations of the maximum value. 
    1493     } 
    1494   \end{center} 
     1518  \centering 
     1519  \includegraphics[width=\textwidth]{Fig_ZDF_zad_Aimp_maxCf_loc} 
     1520  \caption[OVERFLOW: maximum partitioning coefficient for the case overlaid]{ 
     1521    The maximum partitioning coefficient for the \forcode{nn_rdt=10.0} case overlaid with 
     1522    information on the gridcell i- and k-locations of the maximum value.} 
     1523  \label{fig:ZDF_zad_Aimp_maxCf_loc} 
    14951524\end{figure} 
    14961525 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r11543 r11558  
    2828%------------------------------------------namcfg---------------------------------------------------- 
    2929 
    30 \nlst{namcfg} 
     30\begin{listing} 
     31  \nlst{namcfg} 
     32  \caption{\texttt{namcfg}} 
     33  \label{lst:namcfg} 
     34\end{listing} 
    3135%------------------------------------------------------------------------------------------------------------- 
    3236 
     
    8993%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    9094\begin{figure}[!t] 
    91   \begin{center} 
    92     \includegraphics[width=\textwidth]{Fig_ORCA_NH_mesh} 
    93     \caption{ 
    94       \protect\label{fig:CFGS_ORCA_msh} 
    95       ORCA mesh conception. 
    96       The departure from an isotropic Mercator grid start poleward of 20\deg{N}. 
    97       The two "north pole" are the foci of a series of embedded ellipses (blue curves) which 
    98       are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). 
    99       Then, following \citet{madec.imbard_CD96}, the normal to the series of ellipses (red curves) is computed which 
    100       provides the j-lines of the mesh (pseudo longitudes). 
    101     } 
    102   \end{center} 
     95  \centering 
     96  \includegraphics[width=\textwidth]{Fig_ORCA_NH_mesh} 
     97  \caption[ORCA mesh conception]{ 
     98    ORCA mesh conception. 
     99    The departure from an isotropic Mercator grid start poleward of 20\deg{N}. 
     100    The two "north pole" are the foci of a series of embedded ellipses (blue curves) which 
     101    are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). 
     102    Then, following \citet{madec.imbard_CD96}, 
     103    the normal to the series of ellipses (red curves) is computed which 
     104    provides the j-lines of the mesh (pseudo longitudes).} 
     105  \label{fig:CFGS_ORCA_msh} 
    103106\end{figure} 
    104107%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    121124%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    122125\begin{figure}[!tbp] 
    123   \begin{center} 
    124     \includegraphics[width=\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
    125     \includegraphics[width=\textwidth]{Fig_ORCA_aniso} 
    126     \caption { 
    127       \protect\label{fig:CFGS_ORCA_e1e2} 
    128       \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and 
    129       \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) 
    130       for ORCA 0.5\deg ~mesh. 
    131       South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1. 
    132       Poleward of 20\deg{N}, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in 
    133       vicinity of Victoria Island (Canadian Arctic Archipelago). 
    134     } 
    135   \end{center} 
     126  \centering 
     127  \includegraphics[width=\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
     128  \includegraphics[width=\textwidth]{Fig_ORCA_aniso} 
     129  \caption[Horizontal scale factors and ratio of anisotropy for ORCA 0.5\deg\ mesh]{ 
     130    \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and 
     131    \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) 
     132    for ORCA 0.5\deg\ mesh. 
     133    South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1. 
     134    Poleward of 20\deg{N}, 
     135    the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in 
     136    vicinity of Victoria Island (Canadian Arctic Archipelago).} 
     137  \label{fig:CFGS_ORCA_e1e2} 
    136138\end{figure} 
    137139%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    163165%--------------------------------------------------TABLE-------------------------------------------------- 
    164166\begin{table}[!t] 
    165   \begin{center} 
    166     \begin{tabular}{p{4cm} c c c c} 
    167       Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\ 
    168       \hline \hline 
    169 %             4   \deg &              4   &          92 &          76 \\ 
    170              2   \deg &              2   &         182 &         149 \\ 
    171              1   \deg &              1   &         362 &         292 \\ 
    172              0.5 \deg &              05  &         722 &         511 \\ 
    173              0.25\deg &              025 &        1442 &        1021 \\ 
    174       \hline \hline 
    175     \end{tabular} 
    176     \caption{ 
    177       \protect\label{tab:CFGS_ORCA} 
    178       Domain size of ORCA family configurations. 
    179       The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file. 
    180     } 
    181   \end{center} 
     167  \centering 
     168  \begin{tabular}{p{4cm} c c c c} 
     169    Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\ 
     170    \hline \hline 
     171    % 4   \deg\ &              4   &          92 &          76 \\ 
     172    2   \deg\ &              2   &         182 &         149 \\ 
     173    1   \deg\ &              1   &         362 &         292 \\ 
     174    0.5 \deg\ &              05  &         722 &         511 \\ 
     175    0.25\deg\ &              025 &        1442 &        1021 \\ 
     176    \hline \hline 
     177  \end{tabular} 
     178  \caption[Domain size of ORCA family configurations]{ 
     179    Domain size of ORCA family configurations. 
     180    The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.} 
     181  \label{tab:CFGS_ORCA} 
    182182\end{table} 
    183183%-------------------------------------------------------------------------------------------------------------- 
     
    277277%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    278278\begin{figure}[!t] 
    279   \begin{center} 
    280     \includegraphics[width=\textwidth]{Fig_GYRE} 
    281     \caption{ 
    282       \protect\label{fig:CFGS_GYRE} 
    283       Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54. 
    284       From \citet{levy.klein.ea_OM10}. 
    285     } 
    286   \end{center} 
     279  \centering 
     280  \includegraphics[width=\textwidth]{Fig_GYRE} 
     281  \caption[Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54]{ 
     282    Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54. 
     283    From \citet{levy.klein.ea_OM10}.} 
     284  \label{fig:CFGS_GYRE} 
    287285\end{figure} 
    288286%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r11552 r11558  
    2727balance the net evaporation occurring over the Mediterranean region. 
    2828This problem occurs even in eddy permitting simulations. 
    29 For example, in ORCA 1/4\deg several straits of the Indonesian archipelago (Ombai, Lombok...) 
     29For example, in ORCA 1/4\deg\ several straits of the Indonesian archipelago (Ombai, Lombok...) 
    3030are much narrow than even a single ocean grid-point. 
    3131 
     
    7272\end{itemize} 
    7373 
    74  
    7574The second method is to increase the viscous boundary layer thickness by a local increase 
    7675of the fmask value at the coast. This method can also be effective in wider passages.  The 
     
    8685%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    8786\begin{figure}[!tbp] 
    88   \begin{center} 
    89     \includegraphics[width=\textwidth]{Fig_Gibraltar} 
    90     \includegraphics[width=\textwidth]{Fig_Gibraltar2} 
    91     \caption{ 
    92       \protect\label{fig:MISC_strait_hand} 
    93       Example of the Gibraltar strait defined in a $1^{\circ} \times 1^{\circ}$ mesh. 
    94       \textit{Top}: using partially open cells. 
    95       The meridional scale factor at $v$-point is reduced on both sides of the strait to account for 
    96       the real width of the strait (about 20 km). 
    97       Note that the scale factors of the strait $T$-point remains unchanged. 
    98       \textit{Bottom}: using viscous boundary layers. 
    99       The four fmask parameters along the strait coastlines are set to a value larger than 4, 
    100       \ie\ "strong" no-slip case (see \autoref{fig:LBC_shlat}) creating a large viscous boundary layer that 
    101       allows a reduced transport through the strait. 
    102     } 
    103   \end{center} 
     87  \centering 
     88  \includegraphics[width=\textwidth]{Fig_Gibraltar} 
     89  \includegraphics[width=\textwidth]{Fig_Gibraltar2} 
     90  \caption[Two methods to defined the Gibraltar strait]{ 
     91    Example of the Gibraltar strait defined in a 1\deg\ $\times$ 1\deg\ mesh. 
     92    \textit{Top}: using partially open cells. 
     93    The meridional scale factor at $v$-point is reduced on both sides of the strait to 
     94    account for the real width of the strait (about 20 km). 
     95    Note that the scale factors of the strait $T$-point remains unchanged. 
     96    \textit{Bottom}: using viscous boundary layers. 
     97    The four fmask parameters along the strait coastlines are set to a value larger than 4, 
     98    \ie\ "strong" no-slip case (see \autoref{fig:LBC_shlat}) creating a large viscous boundary layer 
     99    that allows a reduced transport through the strait.} 
     100  \label{fig:MISC_strait_hand} 
    104101\end{figure} 
    105102%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    107104%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    108105\begin{figure}[!tbp] 
    109   \begin{center} 
    110     \includegraphics[width=\textwidth]{Fig_closea_mask_example} 
    111     \caption{ 
    112       \protect\label{fig:MISC_closea_mask_example} 
    113       Example of mask fields for the closea module. \textit{Left}: a 
    114       closea\_mask field; \textit{Right}: a closea\_mask\_rnf 
    115       field. In this example, if ln\_closea is set to .true., the mean 
    116       freshwater flux over each of the American Great Lakes will be 
    117       set to zero, and the total residual for all the lakes, if 
    118       negative, will be put into the St Laurence Seaway in the area 
    119       shown. 
    120     } 
    121   \end{center} 
     106  \centering 
     107  \includegraphics[width=\textwidth]{Fig_closea_mask_example} 
     108  \caption[Mask fields for the \protect\mdl{closea} module]{ 
     109    Example of mask fields for the \protect\mdl{closea} module. 
     110    \textit{Left}: a closea\_mask field; 
     111    \textit{Right}: a closea\_mask\_rnf field. 
     112    In this example, if \protect\np{ln\_closea} is set to \forcode{.true.}, 
     113    the mean freshwater flux over each of the American Great Lakes will be set to zero, 
     114    and the total residual for all the lakes, if negative, will be put into 
     115    the St Laurence Seaway in the area shown.} 
     116  \label{fig:MISC_closea_mask_example} 
    122117\end{figure} 
    123118%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    351346%--------------------------------------------namctl------------------------------------------------------- 
    352347 
    353 \nlst{namctl} 
     348\begin{listing} 
     349  \nlst{namctl} 
     350  \caption{\texttt{namctl}} 
     351  \label{lst:namctl} 
     352\end{listing} 
    354353%-------------------------------------------------------------------------------------------------------------- 
    355354 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r11543 r11558  
    130130%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    131131\begin{figure}[!ht] 
    132   \begin{center} 
    133     \includegraphics[width=\textwidth]{Fig_I_ocean_bc} 
    134     \caption{ 
    135       \protect\label{fig:MB_ocean_bc} 
    136       The ocean is bounded by two surfaces, $z = - H(i,j)$ and $z = \eta(i,j,t)$, 
    137       where $H$ is the depth of the sea floor and $\eta$ the height of the sea surface. 
    138       Both $H$ and $\eta$ are referenced to $z = 0$. 
    139     } 
    140   \end{center} 
     132  \centering 
     133  \includegraphics[width=\textwidth]{Fig_I_ocean_bc} 
     134  \caption[Ocean boundary conditions]{ 
     135    The ocean is bounded by two surfaces, $z = - H(i,j)$ and $z = \eta(i,j,t)$, 
     136    where $H$ is the depth of the sea floor and $\eta$ the height of the sea surface. 
     137    Both $H$ and $\eta$ are referenced to $z = 0$.} 
     138  \label{fig:MB_ocean_bc} 
    141139\end{figure} 
    142140%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    333331% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    334332\begin{figure}[!tb] 
    335   \begin{center} 
    336     \includegraphics[width=\textwidth]{Fig_I_earth_referential} 
    337     \caption{ 
    338       \protect\label{fig:MB_referential} 
    339       the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear 
    340       coordinate system $(i,j,k)$. 
    341     } 
    342   \end{center} 
     333  \centering 
     334  \includegraphics[width=\textwidth]{Fig_I_earth_referential} 
     335  \caption[Geographical and curvilinear coordinate systems]{ 
     336    the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear 
     337    coordinate system $(i,j,k)$.} 
     338  \label{fig:MB_referential} 
    343339\end{figure} 
    344340%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    749745%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    750746\begin{figure}[!b] 
    751   \begin{center} 
    752     \includegraphics[width=\textwidth]{Fig_z_zstar} 
    753     \caption{ 
    754       \protect\label{fig:MB_z_zstar} 
    755       (a) $z$-coordinate in linear free-surface case ; 
    756       (b) $z$-coordinate in non-linear free surface case ; 
    757       (c) re-scaled height coordinate 
    758       (become popular as the \zstar-coordinate \citep{adcroft.campin_OM04}). 
    759     } 
    760   \end{center} 
     747  \centering 
     748  \includegraphics[width=\textwidth]{Fig_z_zstar} 
     749  \caption[Curvilinear z-coordinate systems (\{non-\}linear free-surface cases and re-scaled \zstar)]{ 
     750    (a) $z$-coordinate in linear free-surface case ; 
     751    (b) $z$-coordinate in non-linear free surface case ; 
     752    (c) re-scaled height coordinate 
     753    (become popular as the \zstar-coordinate \citep{adcroft.campin_OM04}).} 
     754  \label{fig:MB_z_zstar} 
    761755\end{figure} 
    762756%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11544 r11558  
    140140%--------------------------------------------namdom---------------------------------------------------- 
    141141 
    142 \nlst{namdom} 
    143142%-------------------------------------------------------------------------------------------------------------- 
    144143The split-explicit free surface formulation used in OPA follows the one proposed by \citet{Griffies2004?}. 
     
    149148%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    150149\begin{figure}[!t] 
    151   \begin{center} 
    152     \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts} 
    153     \caption{ 
    154       \protect\label{fig:MBZ_dyn_dynspg_ts} 
    155       Schematic of the split-explicit time stepping scheme for the barotropic and baroclinic modes, 
    156       after \citet{Griffies2004?}. 
    157       Time increases to the right. 
    158       Baroclinic time steps are denoted by $t-\Delta t$, $t, t+\Delta t$, and $t+2\Delta t$. 
    159       The curved line represents a leap-frog time step, 
    160       and the smaller barotropic time steps $N \Delta t=2\Delta t$ are denoted by the zig-zag line. 
    161       The vertically integrated forcing \textbf{M}(t) computed at 
    162       baroclinic time step t represents the interaction between the barotropic and baroclinic motions. 
    163       While keeping the total depth, tracer, and freshwater forcing fields fixed, 
    164       a leap-frog integration carries the surface height and vertically integrated velocity from 
    165       t to $t+2 \Delta t$ using N barotropic time steps of length $\Delta t$. 
    166       Time averaging the barotropic fields over the N+1 time steps (endpoints included) 
    167       centers the vertically integrated velocity at the baroclinic timestep $t+\Delta t$. 
    168       A baroclinic leap-frog time step carries the surface height to $t+\Delta t$ using the convergence of 
    169       the time averaged vertically integrated velocity taken from baroclinic time step t. 
    170     } 
    171   \end{center} 
     150  \centering 
     151  \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts} 
     152  \caption[Schematic of the split-explicit time stepping scheme for 
     153  the barotropic and baroclinic modes, after \citet{Griffies2004?}]{ 
     154    Schematic of the split-explicit time stepping scheme for the barotropic and baroclinic modes, 
     155    after \citet{Griffies2004?}. 
     156    Time increases to the right. 
     157    Baroclinic time steps are denoted by $t-\Delta t$, $t, t+\Delta t$, and $t+2\Delta t$. 
     158    The curved line represents a leap-frog time step, 
     159    and the smaller barotropic time steps $N \Delta t=2\Delta t$ are denoted by the zig-zag line. 
     160    The vertically integrated forcing \textbf{M}(t) computed at 
     161    baroclinic time step t represents the interaction between the barotropic and baroclinic motions. 
     162    While keeping the total depth, tracer, and freshwater forcing fields fixed, 
     163    a leap-frog integration carries the surface height and vertically integrated velocity from 
     164    t to $t+2 \Delta t$ using N barotropic time steps of length $\Delta t$. 
     165    Time averaging the barotropic fields over the N+1 time steps (endpoints included) 
     166    centers the vertically integrated velocity at the baroclinic timestep $t+\Delta t$. 
     167    A baroclinic leap-frog time step carries the surface height to $t+\Delta t$ using 
     168    the convergence of the time averaged vertically integrated velocity taken from 
     169    baroclinic time step t.} 
     170  \label{fig:MBZ_dyn_dynspg_ts} 
    172171\end{figure} 
    173172%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11543 r11558  
    186186%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    187187\begin{figure}[!t] 
    188   \begin{center} 
    189     \includegraphics[width=\textwidth]{Fig_TimeStepping_flowchart_v4} 
    190     \caption{ 
    191       \protect\label{fig:TD_TimeStep_flowchart} 
    192       Sketch of the leapfrog time stepping sequence in \NEMO\ with split-explicit free surface. The latter combined 
    193        with non-linear free surface requires the dynamical tendency being updated prior tracers tendency to ensure 
    194        conservation. Note the use of time integrated fluxes issued from the barotropic loop  in subsequent calculations 
    195        of tracer advection and in the continuity equation. Details about the time-splitting scheme can be found 
    196        in \autoref{subsec:DYN_spg_ts}. 
    197     } 
    198   \end{center} 
     188  \centering 
     189  \includegraphics[width=\textwidth]{Fig_TimeStepping_flowchart_v4} 
     190  \caption[Leapfrog time stepping sequence with split-explicit free surface]{ 
     191    Sketch of the leapfrog time stepping sequence in \NEMO\ with split-explicit free surface. 
     192    The latter combined with non-linear free surface requires the dynamical tendency being 
     193    updated prior tracers tendency to ensure conservation. 
     194    Note the use of time integrated fluxes issued from the barotropic loop in 
     195    subsequent calculations of tracer advection and in the continuity equation. 
     196    Details about the time-splitting scheme can be found in \autoref{subsec:DYN_spg_ts}.} 
     197  \label{fig:TD_TimeStep_flowchart} 
    199198\end{figure} 
    200199%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    248247%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    249248\begin{figure}[!t] 
    250   \begin{center} 
    251     \includegraphics[width=\textwidth]{Fig_MLF_forcing} 
    252     \caption{ 
    253       \protect\label{fig:TD_MLF_forcing} 
    254       Illustration of forcing integration methods. 
    255       (top) ''Traditional'' formulation: 
    256       the forcing is defined at the same time as the variable to which it is applied 
    257       (integer value of the time step index) and it is applied over a $2 \rdt$ period. 
    258       (bottom)  modified formulation: 
    259       the forcing is defined in the middle of the time (integer and a half value of the time step index) and 
    260       the mean of two successive forcing values ($n - 1 / 2$, $n + 1 / 2$) is applied over a $2 \rdt$ period. 
    261     } 
    262   \end{center} 
     249  \centering 
     250  \includegraphics[width=\textwidth]{Fig_MLF_forcing} 
     251  \caption[Forcing integration methods for modified leapfrog (top and bottom)]{ 
     252    Illustration of forcing integration methods. 
     253    (top) ''Traditional'' formulation: 
     254    the forcing is defined at the same time as the variable to which it is applied 
     255    (integer value of the time step index) and it is applied over a $2 \rdt$ period. 
     256    (bottom)  modified formulation: 
     257    the forcing is defined in the middle of the time 
     258    (integer and a half value of the time step index) and 
     259    the mean of two successive forcing values ($n - 1 / 2$, $n + 1 / 2$) is applied over 
     260    a $2 \rdt$ period.} 
     261  \label{fig:TD_MLF_forcing} 
    263262\end{figure} 
    264263%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    271270 
    272271%--------------------------------------------namrun------------------------------------------- 
    273 \nlst{namrun} 
     272\begin{listing} 
     273  \nlst{namrun} 
     274  \caption{\texttt{namrun}} 
     275  \label{lst:namrun} 
     276\end{listing} 
    274277%-------------------------------------------------------------------------------------------------------------- 
    275278 
     
    317320%--------------------------------------------namrun------------------------------------------- 
    318321 
    319 \nlst{namdom} 
    320322%-------------------------------------------------------------------------------------------------------------- 
    321323 
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