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branches/2017/dev_merge_2017/DOC/TexFiles/Chapters/Chap_DOM.tex
r9019 r9363 43 43 \begin{figure}[!tb] \begin{center} 44 44 \includegraphics[width=0.90\textwidth]{Fig_cell} 45 \caption{ \ label{Fig_cell}45 \caption{ \protect\label{Fig_cell} 46 46 Arrangement of variables. $t$ indicates scalar points where temperature, 47 47 salinity, density, pressure and horizontal divergence are defined. ($u$,$v$,$w$) … … 95 95 fw & $i+1/2$ & $j+1/2$ & $k+1/2$ \\ \hline 96 96 \end{tabular} 97 \caption{ \ label{Tab_cell}97 \caption{ \protect\label{Tab_cell} 98 98 Location of grid-points as a function of integer or integer and a half value of the column, 99 99 line or level. This indexing is only used for the writing of the semi-discrete equation. … … 204 204 \begin{figure}[!tb] \begin{center} 205 205 \includegraphics[width=0.90\textwidth]{Fig_index_hor} 206 \caption{ \ label{Fig_index_hor}206 \caption{ \protect\label{Fig_index_hor} 207 207 Horizontal integer indexing used in the \textsc{Fortran} code. The dashed area indicates 208 208 the cell in which variables contained in arrays have the same $i$- and $j$-indices} … … 254 254 \begin{figure}[!pt] \begin{center} 255 255 \includegraphics[width=.90\textwidth]{Fig_index_vert} 256 \caption{ \ label{Fig_index_vert}256 \caption{ \protect\label{Fig_index_vert} 257 257 Vertical integer indexing used in the \textsc{Fortran } code. Note that 258 258 the $k$-axis is orientated downward. The dashed area indicates the cell in … … 324 324 % ================================================================ 325 325 \section [Domain: Horizontal Grid (mesh) (\textit{domhgr})] 326 {Domain: Horizontal Grid (mesh) \small{(\ mdl{domhgr} module)} }326 {Domain: Horizontal Grid (mesh) \small{(\protect\mdl{domhgr} module)} } 327 327 \label{DOM_hgr} 328 328 … … 388 388 \begin{figure}[!t] \begin{center} 389 389 \includegraphics[width=0.90\textwidth]{Fig_zgr_e3} 390 \caption{ \ label{Fig_zgr_e3}390 \caption{ \protect\label{Fig_zgr_e3} 391 391 Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical, 392 392 and (b) analytically derived grid-point position and scale factors. … … 428 428 % ================================================================ 429 429 \section [Domain: Vertical Grid (\textit{domzgr})] 430 {Domain: Vertical Grid \small{(\ mdl{domzgr} module)} }430 {Domain: Vertical Grid \small{(\protect\mdl{domzgr} module)} } 431 431 \label{DOM_zgr} 432 432 %-----------------------------------------nam_zgr & namdom------------------------------------------- … … 447 447 \begin{figure}[!tb] \begin{center} 448 448 \includegraphics[width=1.0\textwidth]{Fig_z_zps_s_sps} 449 \caption{ \ label{Fig_z_zps_s_sps}449 \caption{ \protect\label{Fig_z_zps_s_sps} 450 450 The ocean bottom as seen by the model: 451 451 (a) $z$-coordinate with full step, … … 454 454 (d) hybrid $s-z$ coordinate, 455 455 (e) hybrid $s-z$ coordinate with partial step, and 456 (f) same as (e) but in the non-linear free surface (\ np{ln\_linssh}=false).456 (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}=false). 457 457 Note that the non-linear free surface can be used with any of the 458 458 5 coordinates (a) to (e).} … … 550 550 % z-coordinate and reference coordinate transformation 551 551 % ------------------------------------------------------------------------------------------------------------- 552 \subsection[$z$-coordinate (\ np{ln\_zco}]553 {$z$-coordinate (\ np{ln\_zco}=true) and reference coordinate}552 \subsection[$z$-coordinate (\protect\np{ln\_zco}] 553 {$z$-coordinate (\protect\np{ln\_zco}=true) and reference coordinate} 554 554 \label{DOM_zco} 555 555 … … 557 557 \begin{figure}[!tb] \begin{center} 558 558 \includegraphics[width=0.90\textwidth]{Fig_zgr} 559 \caption{ \ label{Fig_zgr}559 \caption{ \protect\label{Fig_zgr} 560 560 Default vertical mesh for ORCA2: 30 ocean levels (L30). Vertical level functions for 561 561 (a) T-point depth and (b) the associated scale factor as computed … … 679 679 31 & \textbf{5250.23}& 5000.00 & \textbf{500.56} & 500.33 \\ \hline 680 680 \end{tabular} \end{center} 681 \caption{ \ label{Tab_orca_zgr}681 \caption{ \protect\label{Tab_orca_zgr} 682 682 Default vertical mesh in $z$-coordinate for 30 layers ORCA2 configuration as computed 683 683 from \eqref{DOM_zgr_ana} using the coefficients given in \eqref{DOM_zgr_coef}} … … 688 688 % z-coordinate with partial step 689 689 % ------------------------------------------------------------------------------------------------------------- 690 \subsection [$z$-coordinate with partial step (\ np{ln\_zps})]691 {$z$-coordinate with partial step (\ np{ln\_zps}=.true.)}690 \subsection [$z$-coordinate with partial step (\protect\np{ln\_zps})] 691 {$z$-coordinate with partial step (\protect\np{ln\_zps}=.true.)} 692 692 \label{DOM_zps} 693 693 %--------------------------------------------namdom------------------------------------------------------- … … 721 721 % s-coordinate 722 722 % ------------------------------------------------------------------------------------------------------------- 723 \subsection [$s$-coordinate (\ np{ln\_sco})]724 {$s$-coordinate (\ np{ln\_sco}=true)}723 \subsection [$s$-coordinate (\protect\np{ln\_sco})] 724 {$s$-coordinate (\protect\np{ln\_sco}=true)} 725 725 \label{DOM_sco} 726 726 %------------------------------------------nam_zgr_sco--------------------------------------------------- … … 790 790 \begin{figure}[!ht] \begin{center} 791 791 \includegraphics[width=1.0\textwidth]{Fig_sco_function} 792 \caption{ \ label{Fig_sco_function}792 \caption{ \protect\label{Fig_sco_function} 793 793 Examples of the stretching function applied to a seamount; from left to right: 794 794 surface, surface and bottom, and bottom intensified resolutions} … … 850 850 % z*- or s*-coordinate 851 851 % ------------------------------------------------------------------------------------------------------------- 852 \subsection{$z^*$- or $s^*$-coordinate (\ np{ln\_linssh}=false) }852 \subsection{$z^*$- or $s^*$-coordinate (\protect\np{ln\_linssh}=false) } 853 853 \label{DOM_zgr_star} 854 854 … … 913 913 % ================================================================ 914 914 \section [Domain: Initial State (\textit{istate and dtatsd})] 915 {Domain: Initial State \small{(\ mdl{istate} and\mdl{dtatsd} modules)} }915 {Domain: Initial State \small{(\protect\mdl{istate} and \protect\mdl{dtatsd} modules)} } 916 916 \label{DTA_tsd} 917 917 %-----------------------------------------namtsd-------------------------------------------
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