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Changeset 11954 for NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/doc/latex/NEMO/subfiles/chap_DOM.tex – NEMO

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2019-11-22T17:15:18+01:00 (4 years ago)
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Branch 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles. Merge in trunk changes up to 11943 in preparation for end of year merge

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  • NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11598 r11954  
    66\label{chap:DOM} 
    77 
    8 % Missing things: 
    9 %  - istate: description of the initial state   ==> this has to be put elsewhere.. 
    10 %                  perhaps in MISC ?  By the way the initialisation of T S and dynamics 
    11 %                  should be put outside of DOM routine (better with TRC staff and off-line 
    12 %                  tracers) 
    13 %  -geo2ocean:  how to switch from geographic to mesh coordinate 
    14 %     - domclo:  closed sea and lakes.... management of closea sea area : specific to global configuration, both forced and coupled 
    15  
    16 %    {\em 4.0} & {\em Simon M\"{u}ller \& Andrew Coward} & 
    17 %    {\em 
    18 %      Compatibility changes Major simplification has moved many of the options to external domain configuration tools. 
    19 %      (see \autoref{apdx:DOMCFG}) 
    20 %    }                                                                                            \\ 
    21 %    {\em 3.x} & {\em Rachid Benshila, Gurvan Madec \& S\'{e}bastien Masson} & 
    22 %    {\em First version}                                                                          \\ 
     8% Missing things 
     9% -    istate: description of the initial state   ==> this has to be put elsewhere.. 
     10%              perhaps in MISC ?  By the way the initialisation of T S and dynamics 
     11%              should be put outside of DOM routine (better with TRC staff and off-line 
     12%              tracers) 
     13% - geo2ocean: how to switch from geographic to mesh coordinate 
     14% -    domclo: closed sea and lakes.... 
     15%              management of closea sea area: specific to global cfg, both forced and coupled 
    2316 
    2417\thispagestyle{plain} 
    … …  
    2922 
    3023{\footnotesize 
    31   \begin{tabularx}{\textwidth}{l||X|X} 
    32     Release & Author(s) & Modifications \\ 
    33     \hline 
    34     {\em   4.0} & {\em ...} & {\em ...} \\ 
    35     {\em   3.6} & {\em ...} & {\em ...} \\ 
    36     {\em   3.4} & {\em ...} & {\em ...} \\ 
    37     {\em <=3.4} & {\em ...} & {\em ...} 
     24  \begin{tabularx}{0.8\textwidth}{l||X|X} 
     25    Release                                                                                 & 
     26    Author(s)                                                                               & 
     27    Modifications                                                                           \\ 
     28    \hline 
     29    {\em 4.0                                                                              } & 
     30    {\em Simon M\"{u}ller \& Andrew Coward \newline \newline 
     31      Simona Flavoni and Tim Graham                                                       } & 
     32    {\em Compatibility changes: many options moved to external domain configuration tools 
     33      (see \autoref{apdx:DOMCFG}). \newline 
     34      Updates                                                                             } \\ 
     35    {\em 3.6                                                                              } & 
     36    {\em Rachid Benshila, Christian \'{E}th\'{e}, Pierre Mathiot and Gurvan Madec         } & 
     37    {\em Updates                                                                          } \\ 
     38    {\em $\leq$ 3.4                                                                       } & 
     39    {\em Gurvan Madec and S\'{e}bastien Masson                                            } & 
     40    {\em First version                                                                    } 
    3841  \end{tabularx} 
    3942} 
    … …  
    4144\clearpage 
    4245 
    43 Having defined the continuous equations in \autoref{chap:MB} and chosen a time discretisation \autoref{chap:TD}, 
     46Having defined the continuous equations in \autoref{chap:MB} and 
     47chosen a time discretisation \autoref{chap:TD}, 
    4448we need to choose a grid for spatial discretisation and related numerical algorithms. 
    4549In the present chapter, we provide a general description of the staggered grid used in \NEMO, 
    … …  
    5458\label{subsec:DOM_cell} 
    5559 
    56 \begin{figure}[!tb] 
     60\begin{figure} 
    5761  \centering 
    58   \includegraphics[width=0.66\textwidth]{Fig_cell} 
     62  \includegraphics[width=0.33\textwidth]{DOM_cell} 
    5963  \caption[Arrangement of variables in the unit cell of space domain]{ 
    6064    Arrangement of variables in the unit cell of space domain. 
    6165    $t$ indicates scalar points where 
    6266    temperature, salinity, density, pressure and horizontal divergence are defined. 
    63     $(u,v,w)$ indicates vector points, 
    64     and $f$ indicates vorticity points where 
     67    $(u,v,w)$ indicates vector points, and $f$ indicates vorticity points where 
    6568    both relative and planetary vorticities are defined.} 
    6669  \label{fig:DOM_cell} 
    6770\end{figure} 
    6871 
    69 The numerical techniques used to solve the Primitive Equations in this model are based on the traditional, 
    70 centred second-order finite difference approximation. 
     72The numerical techniques used to solve the Primitive Equations in this model are based on 
     73the traditional, centred second-order finite difference approximation. 
    7174Special attention has been given to the homogeneity of the solution in the three spatial directions. 
    7275The arrangement of variables is the same in all directions. 
    73 It consists of cells centred on scalar points ($t$, $S$, $p$, $\rho$) with vector points $(u, v, w)$ defined in 
    74 the centre of each face of the cells (\autoref{fig:DOM_cell}). 
    75 This is the generalisation to three dimensions of the well-known ``C'' grid in Arakawa's classification 
    76 \citep{mesinger.arakawa_bk76}. 
    77 The relative and planetary vorticity, $\zeta$ and $f$, are defined in the centre of each vertical edge and 
    78 the barotropic stream function $\psi$ is defined at horizontal points overlying the $\zeta$ and $f$-points. 
    79  
    80 The ocean mesh (\ie\ the position of all the scalar and vector points) is defined by the transformation that 
    81 gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 
    82 The grid-points are located at integer or integer and a half value of $(i,j,k)$ as indicated on \autoref{tab:DOM_cell}. 
    83 In all the following, subscripts $u$, $v$, $w$, $f$, $uw$, $vw$ or $fw$ indicate the position of 
    84 the grid-point where the scale factors are defined. 
     76It consists of cells centred on scalar points ($t$, $S$, $p$, $\rho$) with 
     77vector points $(u, v, w)$ defined in the centre of each face of the cells (\autoref{fig:DOM_cell}). 
     78This is the generalisation to three dimensions of the well-known ``C'' grid in 
     79Arakawa's classification \citep{mesinger.arakawa_bk76}. 
     80The relative and planetary vorticity, $\zeta$ and $f$, are defined in the centre of each 
     81vertical edge and the barotropic stream function $\psi$ is defined at horizontal points overlying 
     82the $\zeta$ and $f$-points. 
     83 
     84The ocean mesh (\ie\ the position of all the scalar and vector points) is defined by 
     85the transformation that gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 
     86The grid-points are located at integer or integer and a half value of $(i,j,k)$ as indicated on 
     87\autoref{tab:DOM_cell}. 
     88In all the following, 
     89subscripts $u$, $v$, $w$, $f$, $uw$, $vw$ or $fw$ indicate the position of the grid-point where 
     90the scale factors are defined. 
    8591Each scale factor is defined as the local analytical value provided by \autoref{eq:MB_scale_factors}. 
    8692As a result, the mesh on which partial derivatives $\pd[]{\lambda}$, $\pd[]{\varphi}$ and 
    8793$\pd[]{z}$ are evaluated is a uniform mesh with a grid size of unity. 
    88 Discrete partial derivatives are formulated by the traditional, centred second order finite difference approximation 
    89 while the scale factors are chosen equal to their local analytical value. 
     94Discrete partial derivatives are formulated by 
     95the traditional, centred second order finite difference approximation while 
     96the scale factors are chosen equal to their local analytical value. 
    9097An important point here is that the partial derivative of the scale factors must be evaluated by 
    9198centred finite difference approximation, not from their analytical expression. 
    92 This preserves the symmetry of the discrete set of equations and therefore satisfies many of 
    93 the continuous properties (see \autoref{apdx:INVARIANTS}). 
     99This preserves the symmetry of the discrete set of equations and 
     100therefore satisfies many of the continuous properties (see \autoref{apdx:INVARIANTS}). 
    94101A similar, related remark can be made about the domain size: 
    95 when needed, an area, volume, or the total ocean depth must be evaluated as the product or sum of the relevant scale factors 
    96 (see \autoref{eq:DOM_bar} in the next section). 
    97  
    98 \begin{table}[!tb] 
     102when needed, an area, volume, or the total ocean depth must be evaluated as 
     103the product or sum of the relevant scale factors (see \autoref{eq:DOM_bar} in the next section). 
     104 
     105\begin{table} 
    99106  \centering 
    100   \begin{tabular}{|p{46pt}|p{56pt}|p{56pt}|p{56pt}|} 
    101     \hline 
    102     t & $i      $ & $j      $ & $k      $ \\ 
    103     \hline 
    104     u & $i + 1/2$ & $j      $ & $k      $ \\ 
    105     \hline 
    106     v & $i      $ & $j + 1/2$ & $k      $ \\ 
    107     \hline 
    108     w & $i      $ & $j      $ & $k + 1/2$ \\ 
    109     \hline 
    110     f & $i + 1/2$ & $j + 1/2$ & $k      $ \\ 
    111     \hline 
    112     uw   & $i + 1/2$ & $j      $ & $k + 1/2$ \\ 
    113     \hline 
    114     vw   & $i      $ & $j + 1/2$ & $k + 1/2$ \\ 
    115     \hline 
    116     fw   & $i + 1/2$ & $j + 1/2$ & $k + 1/2$ \\ 
     107  \begin{tabular}{|l|l|l|l|} 
     108    \hline 
     109    t   & $i      $ & $j      $ & $k      $ \\ 
     110    \hline 
     111    u   & $i + 1/2$ & $j      $ & $k      $ \\ 
     112    \hline 
     113    v   & $i      $ & $j + 1/2$ & $k      $ \\ 
     114    \hline 
     115    w   & $i      $ & $j      $ & $k + 1/2$ \\ 
     116    \hline 
     117    f   & $i + 1/2$ & $j + 1/2$ & $k      $ \\ 
     118    \hline 
     119    uw  & $i + 1/2$ & $j      $ & $k + 1/2$ \\ 
     120    \hline 
     121    vw  & $i      $ & $j + 1/2$ & $k + 1/2$ \\ 
     122    \hline 
     123    fw  & $i + 1/2$ & $j + 1/2$ & $k + 1/2$ \\ 
    117124    \hline 
    118125  \end{tabular} 
    … …  
    120127    Location of grid-points as a function of integer or 
    121128    integer and a half value of the column, line or level. 
    122     This indexing is only used for the writing of the semi -discrete equations. 
     129    This indexing is only used for the writing of the semi-discrete equations. 
    123130    In the code, the indexing uses integer values only and 
    124131    is positive downwards in the vertical with $k=1$ at the surface. 
    … …  
    137144firstly, there is no ambiguity in the scale factors appearing in the discrete equations, 
    138145since they are first introduced in the continuous equations; 
    139 secondly, analytical transformations encourage good practice by the definition of smoothly varying grids 
    140 (rather than allowing the user to set arbitrary jumps in thickness between adjacent layers) \citep{treguier.dukowicz.ea_JGR96}. 
     146secondly, analytical transformations encourage good practice by 
     147the definition of smoothly varying grids 
     148(rather than allowing the user to set arbitrary jumps in thickness between adjacent layers) 
     149\citep{treguier.dukowicz.ea_JGR96}. 
    141150An example of the effect of such a choice is shown in \autoref{fig:DOM_zgr_e3}. 
    142 \begin{figure}[!t] 
     151\begin{figure} 
    143152  \centering 
    144   \includegraphics[width=0.66\textwidth]{Fig_zgr_e3} 
     153  \includegraphics[width=0.5\textwidth]{DOM_zgr_e3} 
    145154  \caption[Comparison of grid-point position, vertical grid-size and scale factors]{ 
    146155    Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical, 
    … …  
    159168\label{subsec:DOM_operators} 
    160169 
    161 Given the values of a variable $q$ at adjacent points, the differencing and averaging operators at 
    162 the midpoint between them are: 
     170Given the values of a variable $q$ at adjacent points, 
     171the differencing and averaging operators at the midpoint between them are: 
    163172\begin{alignat*}{2} 
    164173  % \label{eq:DOM_di_mi} 
    … …  
    168177 
    169178Similar operators are defined with respect to $i + 1/2$, $j$, $j + 1/2$, $k$, and $k + 1/2$. 
    170 Following \autoref{eq:MB_grad} and \autoref{eq:MB_lap}, the gradient of a variable $q$ defined at a $t$-point has 
    171 its three components defined at $u$-, $v$- and $w$-points while its Laplacian is defined at the $t$-point. 
     179Following \autoref{eq:MB_grad} and \autoref{eq:MB_lap}, 
     180the gradient of a variable $q$ defined at a $t$-point has 
     181its three components defined at $u$-, $v$- and $w$-points while 
     182its Laplacian is defined at the $t$-point. 
    172183These operators have the following discrete forms in the curvilinear $s$-coordinates system: 
    173 \[ 
     184\begin{gather*} 
    174185  % \label{eq:DOM_grad} 
    175186  \nabla q \equiv   \frac{1}{e_{1u}} \delta_{i + 1/2} [q] \; \, \vect i 
    176187                  + \frac{1}{e_{2v}} \delta_{j + 1/2} [q] \; \, \vect j 
    177                   + \frac{1}{e_{3w}} \delta_{k + 1/2} [q] \; \, \vect k 
    178 \] 
    179 \begin{multline*} 
     188                  + \frac{1}{e_{3w}} \delta_{k + 1/2} [q] \; \, \vect k \\ 
    180189  % \label{eq:DOM_lap} 
    181190  \Delta q \equiv   \frac{1}{e_{1t} \, e_{2t} \, e_{3t}} 
    182191                    \; \lt[   \delta_i \lt( \frac{e_{2u} \, e_{3u}}{e_{1u}} \; \delta_{i + 1/2} [q] \rt) 
    183                             + \delta_j \lt( \frac{e_{1v} \, e_{3v}}{e_{2v}} \; \delta_{j + 1/2} [q] \rt) \; \rt] \\ 
     192                            + \delta_j \lt( \frac{e_{1v} \, e_{3v}}{e_{2v}} \; \delta_{j + 1/2} [q] \rt) \; \rt] 
    184193                  + \frac{1}{e_{3t}} 
    185194                              \delta_k \lt[ \frac{1              }{e_{3w}} \; \delta_{k + 1/2} [q] \rt] 
    186 \end{multline*} 
    187  
    188 Following \autoref{eq:MB_curl} and \autoref{eq:MB_div}, a vector $\vect A = (a_1,a_2,a_3)$ defined at 
    189 vector points $(u,v,w)$ has its three curl components defined at $vw$-, $uw$, and $f$-points, and 
     195\end{gather*} 
     196 
     197Following \autoref{eq:MB_curl} and \autoref{eq:MB_div}, 
     198a vector $\vect A = (a_1,a_2,a_3)$ defined at vector points $(u,v,w)$ has 
     199its three curl components defined at $vw$-, $uw$, and $f$-points, and 
    190200its divergence defined at $t$-points: 
    191 \begin{multline} 
     201\begin{multline*} 
    192202% \label{eq:DOM_curl} 
    193203  \nabla \times \vect A \equiv   \frac{1}{e_{2v} \, e_{3vw}} 
    … …  
    200210                                 \Big[   \delta_{i + 1/2} (e_{2v} \, a_2) 
    201211                                       - \delta_{j + 1/2} (e_{1u} \, a_1) \Big] \vect k 
    202 \end{multline} 
    203 \begin{equation} 
     212\end{multline*} 
     213\[ 
    204214% \label{eq:DOM_div} 
    205215  \nabla \cdot \vect A \equiv   \frac{1}{e_{1t} \, e_{2t} \, e_{3t}} 
    206216                                \Big[ \delta_i (e_{2u} \, e_{3u} \, a_1) + \delta_j (e_{1v} \, e_{3v} \, a_2) \Big] 
    207217                              + \frac{1}{e_{3t}} \delta_k (a_3) 
    208 \end{equation} 
    209  
    210 The vertical average over the whole water column is denoted by an overbar and is for 
    211 a masked field $q$ (\ie\ a quantity that is equal to zero inside solid areas): 
     218\] 
     219 
     220The vertical average over the whole water column is denoted by an overbar and 
     221is for a masked field $q$ (\ie\ a quantity that is equal to zero inside solid areas): 
    212222\begin{equation} 
    213223  \label{eq:DOM_bar} 
    … …  
    215225\end{equation} 
    216226where $H_q$  is the ocean depth, which is the masked sum of the vertical scale factors at $q$ points, 
    217 $k^b$ and $k^o$ are the bottom and surface $k$-indices, and the symbol $\sum \limits_k$ refers to a summation over 
    218 all grid points of the same type in the direction indicated by the subscript (here $k$). 
     227$k^b$ and $k^o$ are the bottom and surface $k$-indices, 
     228and the symbol $\sum \limits_k$ refers to a summation over all grid points of the same type in 
     229the direction indicated by the subscript (here $k$). 
    219230 
    220231In continuous form, the following properties are satisfied: 
    … …  
    226237\end{gather} 
    227238 
    228 It is straightforward to demonstrate that these properties are verified locally in discrete form as soon as 
    229 the scalar $q$ is taken at $t$-points and the vector $\vect A$ has its components defined at 
     239It is straightforward to demonstrate that these properties are verified locally in discrete form as 
     240soon as the scalar $q$ is taken at $t$-points and the vector $\vect A$ has its components defined at 
    230241vector points $(u,v,w)$. 
    231242 
    232243Let $a$ and $b$ be two fields defined on the mesh, with a value of zero inside continental areas. 
    233 It can be shown that the differencing operators ($\delta_i$, $\delta_j$ and $\delta_k$) 
    234 are skew-symmetric linear operators, and further that the averaging operators $\overline{\cdots}^{\, i}$, 
    235 $\overline{\cdots}^{\, j}$ and $\overline{\cdots}^{\, k}$) are symmetric linear operators, \ie 
    236 \begin{alignat}{4} 
     244It can be shown that the differencing operators ($\delta_i$, $\delta_j$ and 
     245$\delta_k$) are skew-symmetric linear operators, 
     246and further that the averaging operators ($\overline{\cdots}^{\, i}$, $\overline{\cdots}^{\, j}$ and 
     247$\overline{\cdots}^{\, k}$) are symmetric linear operators, \ie 
     248\begin{alignat}{5} 
    237249  \label{eq:DOM_di_adj} 
    238250  &\sum \limits_i a_i \; \delta_i [b]      &\equiv &- &&\sum \limits_i \delta      _{   i + 1/2} [a] &b_{i + 1/2} \\ 
    … …  
    241253\end{alignat} 
    242254 
    243 In other words, the adjoint of the differencing and averaging operators are $\delta_i^* = \delta_{i + 1/2}$ and 
     255In other words, 
     256the adjoint of the differencing and averaging operators are $\delta_i^* = \delta_{i + 1/2}$ and 
    244257$(\overline{\cdots}^{\, i})^* = \overline{\cdots}^{\, i + 1/2}$, respectively. 
    245258These two properties will be used extensively in the \autoref{apdx:INVARIANTS} to 
    … …  
    250263\label{subsec:DOM_Num_Index} 
    251264 
    252 \begin{figure}[!tb] 
     265\begin{figure} 
    253266  \centering 
    254   \includegraphics[width=0.66\textwidth]{Fig_index_hor} 
     267  \includegraphics[width=0.33\textwidth]{DOM_index_hor} 
    255268  \caption[Horizontal integer indexing]{ 
    256269    Horizontal integer indexing used in the \fortran\ code. 
    … …  
    261274 
    262275The array representation used in the \fortran\ code requires an integer indexing. 
    263 However, the analytical definition of the mesh (see \autoref{subsec:DOM_cell}) is associated with the use of 
    264 integer values for $t$-points only while all the other points involve integer and a half values. 
     276However, the analytical definition of the mesh (see \autoref{subsec:DOM_cell}) is associated with 
     277the use of integer values for $t$-points only while 
     278all the other points involve integer and a half values. 
    265279Therefore, a specific integer indexing has been defined for points other than $t$-points 
    266280(\ie\ velocity and vorticity grid-points). 
    267 Furthermore, the direction of the vertical indexing has been reversed and the surface level set at $k = 1$. 
     281Furthermore, the direction of the vertical indexing has been reversed and 
     282the surface level set at $k = 1$. 
    268283 
    269284%% ================================================================================================= 
    … …  
    281296\label{subsec:DOM_Num_Index_vertical} 
    282297 
    283 In the vertical, the chosen indexing requires special attention since the direction of the $k$-axis in 
    284 the \fortran\ code is the reverse of that used in the semi -discrete equations and 
    285 given in \autoref{subsec:DOM_cell}. 
    286 The sea surface corresponds to the $w$-level $k = 1$, which is the same index as the $t$-level just below 
    287 (\autoref{fig:DOM_index_vert}). 
     298In the vertical, the chosen indexing requires special attention since 
     299the direction of the $k$-axis in the \fortran\ code is the reverse of 
     300that used in the semi-discrete equations and given in \autoref{subsec:DOM_cell}. 
     301The sea surface corresponds to the $w$-level $k = 1$, 
     302which is the same index as the $t$-level just below (\autoref{fig:DOM_index_vert}). 
    288303The last $w$-level ($k = jpk$) either corresponds to or is below the ocean floor while 
    289304the last $t$-level is always outside the ocean domain (\autoref{fig:DOM_index_vert}). 
    290305Note that a $w$-point and the directly underlaying $t$-point have a common $k$ index 
    291306(\ie\ $t$-points and their nearest $w$-point neighbour in negative index direction), 
    292 in contrast to the indexing on the horizontal plane where the $t$-point has the same index as 
    293 the nearest velocity points in the positive direction of the respective horizontal axis index 
     307in contrast to the indexing on the horizontal plane where 
     308the $t$-point has the same index as the nearest velocity points in 
     309the positive direction of the respective horizontal axis index 
    294310(compare the dashed area in \autoref{fig:DOM_index_hor} and \autoref{fig:DOM_index_vert}). 
    295311Since the scale factors are chosen to be strictly positive, 
    … …  
    298314accommodate the opposing vertical index directions in implementation and documentation. 
    299315 
    300 \begin{figure}[!pt] 
     316\begin{figure} 
    301317  \centering 
    302   \includegraphics[width=0.66\textwidth]{Fig_index_vert} 
     318  \includegraphics[width=0.33\textwidth]{DOM_index_vert} 
    303319  \caption[Vertical integer indexing]{ 
    304320    Vertical integer indexing used in the \fortran\ code. 
    … …  
    314330 
    315331Two typical methods are available to specify the spatial domain configuration; 
    316 they can be selected using parameter \np{ln_read_cfg}{ln\_read\_cfg} parameter in namelist \nam{cfg}{cfg}. 
     332they can be selected using parameter \np{ln_read_cfg}{ln\_read\_cfg} parameter in 
     333namelist \nam{cfg}{cfg}. 
    317334 
    318335If \np{ln_read_cfg}{ln\_read\_cfg} is set to \forcode{.true.}, 
    319 the domain-specific parameters and fields are read from a netCDF input file, 
    320 whose name (without its .nc suffix) can be specified as the value of the \np{cn_domcfg}{cn\_domcfg} parameter in namelist \nam{cfg}{cfg}. 
     336the domain-specific parameters and fields are read from a NetCDF input file, 
     337whose name (without its .nc suffix) can be specified as 
     338the value of the \np{cn_domcfg}{cn\_domcfg} parameter in namelist \nam{cfg}{cfg}. 
    321339 
    322340If \np{ln_read_cfg}{ln\_read\_cfg} is set to \forcode{.false.}, 
    … …  
    324342subroutines \mdl{usrdef\_hgr} and \mdl{usrdef\_zgr}. 
    325343These subroutines can be supplied in the \path{MY_SRC} directory of the configuration, 
    326 and default versions that configure the spatial domain for the GYRE reference configuration are present in 
    327 the \path{./src/OCE/USR} directory. 
     344and default versions that configure the spatial domain for the GYRE reference configuration are 
     345present in the \path{./src/OCE/USR} directory. 
    328346 
    329347In version 4.0 there are no longer any options for reading complex bathymetries and 
    … …  
    332350to run similar models with and without partial bottom boxes and/or sigma-coordinates, 
    333351supporting such choices leads to overly complex code. 
    334 Worse still is the difficulty of ensuring the model configurations intended to be identical are indeed so when 
    335 the model domain itself can be altered by runtime selections. 
    336 The code previously used to perform vertical discretisation has been incorporated into an external tool 
    337 (\path{./tools/DOMAINcfg}) which is briefly described in \autoref{apdx:DOMCFG}. 
    338  
    339 The next subsections summarise the parameter and fields related to the configuration of the whole model domain. 
    340 These represent the minimum information that must be provided either via the \np{cn_domcfg}{cn\_domcfg} file or set by code 
    341 inserted into user-supplied versions of the \texttt{usrdef\_*} subroutines. 
     352Worse still is the difficulty of ensuring the model configurations intended to be identical are 
     353indeed so when the model domain itself can be altered by runtime selections. 
     354The code previously used to perform vertical discretisation has been incorporated into 
     355an external tool (\path{./tools/DOMAINcfg}) which is briefly described in \autoref{apdx:DOMCFG}. 
     356 
     357The next subsections summarise the parameter and fields related to 
     358the configuration of the whole model domain. 
     359These represent the minimum information that must be provided either via 
     360the \np{cn_domcfg}{cn\_domcfg} file or 
     361set by code inserted into user-supplied versions of the \texttt{usrdef\_*} subroutines. 
    342362The requirements are presented in three sections: 
    343363the domain size (\autoref{subsec:DOM_size}), the horizontal mesh (\autoref{subsec:DOM_hgr}), 
    … …  
    348368\label{subsec:DOM_size} 
    349369 
    350 The total size of the computational domain is set by the parameters \jp{jpiglo}, \jp{jpjglo} and \jp{jpkglo} for 
    351 the $i$, $j$ and $k$ directions, respectively. 
    352 Note, that the variables \texttt{jpi} and \texttt{jpj} refer to the size of each processor subdomain when 
    353 the code is run in parallel using domain decomposition (\key{mpp\_mpi} defined, 
    354 see \autoref{sec:LBC_mpp}). 
     370The total size of the computational domain is set by the parameters \jp{jpiglo}, \jp{jpjglo} and 
     371\jp{jpkglo} for the $i$, $j$ and $k$ directions, respectively. 
     372Note, that the variables \texttt{jpi} and \texttt{jpj} refer to 
     373the size of each processor subdomain when the code is run in parallel using domain decomposition 
     374(\key{mpp\_mpi} defined, see \autoref{sec:LBC_mpp}). 
    355375 
    356376The name of the configuration is set through parameter \np{cn_cfg}{cn\_cfg}, 
    … …  
    360380 
    361381The global lateral boundary condition type is selected from 8 options using parameter \jp{jperio}. 
    362 See \autoref{sec:LBC_jperio} for details on the available options and the corresponding values for \jp{jperio}. 
     382See \autoref{sec:LBC_jperio} for details on the available options and 
     383the corresponding values for \jp{jperio}. 
    363384 
    364385%% ================================================================================================= 
    … …  
    370391\label{sec:DOM_hgr_fields} 
    371392 
    372 The explicit specification of a range of mesh-related fields are required for the definition of a configuration. 
     393The explicit specification of a range of mesh-related fields are required for 
     394the definition of a configuration. 
    373395These include: 
    374396 
    375397\begin{clines} 
    376 int    jpiglo, jpjglo, jpkglo            /* global domain sizes                                          */ 
    377 int    jperio                            /* lateral global domain b.c.                                   */ 
    378 double glamt, glamu, glamv, glamf        /* geographic longitude (t,u,v and f points respectively)      */ 
    379 double gphit, gphiu, gphiv, gphif        /* geographic latitude                                          */ 
    380 double e1t, e1u, e1v, e1f                /* horizontal scale factors                                     */ 
    381 double e2t, e2u, e2v, e2f                /* horizontal scale factors                                     */ 
     398int    jpiglo, jpjglo, jpkglo     /* global domain sizes                                    */ 
     399int    jperio                     /* lateral global domain b.c.                             */ 
     400double glamt, glamu, glamv, glamf /* geographic longitude (t,u,v and f points respectively) */ 
     401double gphit, gphiu, gphiv, gphif /* geographic latitude                                    */ 
     402double e1t, e1u, e1v, e1f         /* horizontal scale factors                               */ 
     403double e2t, e2u, e2v, e2f         /* horizontal scale factors                               */ 
    382404\end{clines} 
    383405 
    … …  
    393415 
    394416\begin{clines} 
    395                                          /* Optional:                                                    */ 
    396 int    ORCA, ORCA_index                  /* configuration name, configuration resolution                 */ 
    397 double e1e2u, e1e2v                      /* U and V surfaces (if grid size reduction in some straits)    */ 
    398 double ff_f, ff_t                        /* Coriolis parameter (if not on the sphere)                    */ 
     417                        /* Optional:                                                 */ 
     418int    ORCA, ORCA_index /* configuration name, configuration resolution              */ 
     419double e1e2u, e1e2v     /* U and V surfaces (if grid size reduction in some straits) */ 
     420double ff_f, ff_t       /* Coriolis parameter (if not on the sphere)                 */ 
    399421\end{clines} 
    400422 
    … …  
    403425This is particularly useful for locations such as Gibraltar or Indonesian Throughflow pinch-points 
    404426(see \autoref{sec:MISC_strait} for illustrated examples). 
    405 The key is to reduce the faces of $T$-cell (\ie\ change the value of the horizontal scale factors at $u$- or $v$-point) but 
     427The key is to reduce the faces of $T$-cell 
     428(\ie\ change the value of the horizontal scale factors at $u$- or $v$-point) but 
    406429not the volume of the cells. 
    407430Doing otherwise can lead to numerical instability issues. 
    408431In normal operation the surface areas are computed from $e1u * e2u$ and $e1v * e2v$ but 
    409432in cases where a gridsize reduction is required, 
    410 the unaltered surface areas at $u$ and $v$ grid points (\texttt{e1e2u} and \texttt{e1e2v}, respectively) must be read or 
    411 pre-computed in \mdl{usrdef\_hgr}. 
    412 If these arrays are present in the \np{cn_domcfg}{cn\_domcfg} file they are read and the internal computation is suppressed. 
    413 Versions of \mdl{usrdef\_hgr} which set their own values of \texttt{e1e2u} and \texttt{e1e2v} should set 
    414 the surface-area computation flag: 
     433the unaltered surface areas at $u$ and $v$ grid points 
     434(\texttt{e1e2u} and \texttt{e1e2v}, respectively) must be read or pre-computed in \mdl{usrdef\_hgr}. 
     435If these arrays are present in the \np{cn_domcfg}{cn\_domcfg} file they are read and 
     436the internal computation is suppressed. 
     437Versions of \mdl{usrdef\_hgr} which set their own values of \texttt{e1e2u} and \texttt{e1e2v} should 
     438set the surface-area computation flag: 
    415439\texttt{ie1e2u\_v} to a non-zero value to suppress their re-computation. 
    416440 
    417441\smallskip 
    418442Similar logic applies to the other optional fields: 
    419 \texttt{ff\_f} and \texttt{ff\_t} which can be used to provide the Coriolis parameter at F- and T-points respectively if 
    420 the mesh is not on a sphere. 
    421 If present these fields will be read and used and the normal calculation ($2 * \Omega * \sin(\varphi)$) suppressed. 
    422 Versions of \mdl{usrdef\_hgr} which set their own values of \texttt{ff\_f} and \texttt{ff\_t} should set 
    423 the Coriolis computation flag: 
     443\texttt{ff\_f} and \texttt{ff\_t} which can be used to 
     444provide the Coriolis parameter at F- and T-points respectively if the mesh is not on a sphere. 
     445If present these fields will be read and used and 
     446the normal calculation ($2 * \Omega * \sin(\varphi)$) suppressed. 
     447Versions of \mdl{usrdef\_hgr} which set their own values of \texttt{ff\_f} and \texttt{ff\_t} should 
     448set the Coriolis computation flag: 
    424449\texttt{iff} to a non-zero value to suppress their re-computation. 
    425450 
    426 Note that longitudes, latitudes, and scale factors at $w$ points are exactly equal to those of $t$ points, 
    427 thus no specific arrays are defined at $w$ points. 
     451Note that longitudes, latitudes, and scale factors at $w$ points are exactly equal to 
     452those of $t$ points, thus no specific arrays are defined at $w$ points. 
    428453 
    429454%% ================================================================================================= 
    430455\subsection[Vertical grid (\textit{domzgr.F90})]{Vertical grid (\protect\mdl{domzgr})} 
    431456\label{subsec:DOM_zgr} 
     457 
    432458\begin{listing} 
    433459  \nlst{namdom} 
    … …  
    438464In the vertical, the model mesh is determined by four things: 
    439465\begin{enumerate} 
    440   \item the bathymetry given in meters; 
    441   \item the number of levels of the model (\jp{jpk}); 
    442   \item the analytical transformation $z(i,j,k)$ and the vertical scale factors (derivatives of the transformation); and 
    443   \item the masking system, \ie\ the number of wet model levels at each 
    444 $(i,j)$ location of the horizontal grid. 
     466\item the bathymetry given in meters; 
     467\item the number of levels of the model (\jp{jpk}); 
     468\item the analytical transformation $z(i,j,k)$ and the vertical scale factors 
     469  (derivatives of the transformation); and 
     470\item the masking system, 
     471  \ie\ the number of wet model levels at each $(i,j)$ location of the horizontal grid. 
    445472\end{enumerate} 
    446473 
    447 \begin{figure}[!tb] 
     474\begin{figure} 
    448475  \centering 
    449   \includegraphics[width=0.66\textwidth]{Fig_z_zps_s_sps} 
     476  \includegraphics[width=0.5\textwidth]{DOM_z_zps_s_sps} 
    450477  \caption[Ocean bottom regarding coordinate systems ($z$, $s$ and hybrid $s-z$)]{ 
    451478    The ocean bottom as seen by the model: 
    452     (a) $z$-coordinate with full step, 
    453     (b) $z$-coordinate with partial step, 
    454     (c) $s$-coordinate: terrain following representation, 
    455     (d) hybrid $s-z$ coordinate, 
    456     (e) hybrid $s-z$ coordinate with partial step, and 
    457     (f) same as (e) but in the non-linear free surface (\protect\np[=.false.]{ln_linssh}{ln\_linssh}). 
    458     Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).} 
     479    \begin{enumerate*}[label=(\textit{\alph*})] 
     480    \item $z$-coordinate with full step, 
     481    \item $z$-coordinate with partial step, 
     482    \item $s$-coordinate: terrain following representation, 
     483    \item hybrid $s-z$ coordinate, 
     484    \item hybrid $s-z$ coordinate with partial step, and 
     485    \item same as (e) but in the non-linear free surface 
     486      (\protect\np[=.false.]{ln_linssh}{ln\_linssh}). 
     487  \end{enumerate*} 
     488  Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).} 
    459489  \label{fig:DOM_z_zps_s_sps} 
    460490\end{figure} 
    … …  
    463493it is not intended to be an option which can be changed in the middle of an experiment. 
    464494The one exception to this statement being the choice of linear or non-linear free surface. 
    465 In v4.0 the linear free surface option is implemented as a special case of the non-linear free surface. 
     495In v4.0 the linear free surface option is implemented as 
     496a special case of the non-linear free surface. 
    466497This is computationally wasteful since it uses the structures for time-varying 3D metrics 
    467498for fields that (in the linear free surface case) are fixed. 
    468 However, the linear free-surface is rarely used and implementing it this way means 
    469 a single configuration file can support both options. 
    470  
    471 By default a non-linear free surface is used (\np{ln_linssh}{ln\_linssh} set to \forcode{=.false.} in \nam{dom}{dom}): 
    472 the coordinate follow the time-variation of the free surface so that the transformation is time dependent: 
    473 $z(i,j,k,t)$ (\eg\ \autoref{fig:DOM_z_zps_s_sps}f). 
    474 When a linear free surface is assumed (\np{ln_linssh}{ln\_linssh} set to \forcode{=.true.} in \nam{dom}{dom}), 
    475 the vertical coordinates are fixed in time, but the seawater can move up and down across the $z_0$ surface 
     499However, the linear free-surface is rarely used and 
     500implementing it this way means a single configuration file can support both options. 
     501 
     502By default a non-linear free surface is used 
     503(\np{ln_linssh}{ln\_linssh} set to \forcode{=.false.} in \nam{dom}{dom}): 
     504the coordinate follow the time-variation of the free surface so that 
     505the transformation is time dependent: $z(i,j,k,t)$ (\eg\ \autoref{fig:DOM_z_zps_s_sps}f). 
     506When a linear free surface is assumed 
     507(\np{ln_linssh}{ln\_linssh} set to \forcode{=.true.} in \nam{dom}{dom}), 
     508the vertical coordinates are fixed in time, but 
     509the seawater can move up and down across the $z_0$ surface 
    476510(in other words, the top of the ocean in not a rigid lid). 
    477511 
    478512Note that settings: 
    479 \np{ln_zco}{ln\_zco}, \np{ln_zps}{ln\_zps}, \np{ln_sco}{ln\_sco} and \np{ln_isfcav}{ln\_isfcav} mentioned in the following sections 
    480 appear to be namelist options but they are no longer truly namelist options for \NEMO. 
     513\np{ln_zco}{ln\_zco}, \np{ln_zps}{ln\_zps}, \np{ln_sco}{ln\_sco} and \np{ln_isfcav}{ln\_isfcav} 
     514mentioned in the following sections appear to be namelist options but 
     515they are no longer truly namelist options for \NEMO. 
    481516Their value is written to and read from the domain configuration file and 
    482517they should be treated as fixed parameters for a particular configuration. 
    483 They are namelist options for the \texttt{DOMAINcfg} tool that can be used to build the configuration file and 
    484 serve both to provide a record of the choices made whilst building the configuration and 
    485 to trigger appropriate code blocks within \NEMO. 
     518They are namelist options for the \texttt{DOMAINcfg} tool that can be used to 
     519build the configuration file and serve both to provide a record of the choices made whilst 
     520building the configuration and to trigger appropriate code blocks within \NEMO. 
    486521These values should not be altered in the \np{cn_domcfg}{cn\_domcfg} file. 
    487522 
    … …  
    501536A further choice related to vertical coordinate concerns 
    502537the presence (or not) of ocean cavities beneath ice shelves within the model domain. 
    503 A setting of \np{ln_isfcav}{ln\_isfcav} as \forcode{.true.} indicates that the domain contains ocean cavities, 
     538A setting of \np{ln_isfcav}{ln\_isfcav} as \forcode{.true.} indicates that 
     539the domain contains ocean cavities, 
    504540otherwise the top, wet layer of the ocean will always be at the ocean surface. 
    505541This option is currently only available for $z$- or $zps$-coordinates. 
    506542In the latter case, partial steps are also applied at the ocean/ice shelf interface. 
    507543 
    508 Within the model, the arrays describing the grid point depths and vertical scale factors are three set of 
    509 three dimensional arrays $(i,j,k)$ defined at \textit{before}, \textit{now} and \textit{after} time step. 
     544Within the model, 
     545the arrays describing the grid point depths and vertical scale factors are 
     546three set of three dimensional arrays $(i,j,k)$ defined at 
     547\textit{before}, \textit{now} and \textit{after} time step. 
    510548The time at which they are defined is indicated by a suffix: $\_b$, $\_n$, or $\_a$, respectively. 
    511549They are updated at each model time step. 
    … …  
    534572\end{clines} 
    535573 
    536 This set of vertical metrics is sufficient to describe the initial depth and thickness of every gridcell in 
    537 the model regardless of the choice of vertical coordinate. 
     574This set of vertical metrics is sufficient to describe the initial depth and thickness of 
     575every gridcell in the model regardless of the choice of vertical coordinate. 
    538576With constant z-levels, e3 metrics will be uniform across each horizontal level. 
    539577In the partial step case each e3 at the \jp{bottom\_level} 
    … …  
    541579may vary from its horizontal neighbours. 
    542580And, in s-coordinates, variations can occur throughout the water column. 
    543 With the non-linear free-surface, all the coordinates behave more like the s-coordinate in 
    544 that variations occur throughout the water column with displacements related to the sea surface height. 
     581With the non-linear free-surface, all the coordinates behave more like the s-coordinate in that 
     582variations occur throughout the water column with displacements related to the sea surface height. 
    545583These variations are typically much smaller than those arising from bottom fitted coordinates. 
    546584The values for vertical metrics supplied in the domain configuration file can be considered as 
    547585those arising from a flat sea surface with zero elevation. 
    548586 
    549 The \jp{bottom\_level} and \jp{top\_level} 2D arrays define the \jp{bottom\_level} and top wet levels in each grid column. 
     587The \jp{bottom\_level} and \jp{top\_level} 2D arrays define 
     588the \jp{bottom\_level} and top wet levels in each grid column. 
    550589Without ice cavities, \jp{top\_level} is essentially a land mask (0 on land; 1 everywhere else). 
    551590With ice cavities, \jp{top\_level} determines the first wet point below the overlying ice shelf. 
    … …  
    556595 
    557596From \jp{top\_level} and \jp{bottom\_level} fields, the mask fields are defined as follows: 
    558 \begin{alignat*}{2} 
    559   tmask(i,j,k) &= &  & 
    560     \begin{cases} 
    561                   0 &\text{if $                  k  <    top\_level(i,j)$} \\ 
    562                   1 &\text{if $bottom\_level(i,j) \leq k \leq   top\_level(i,j)$} \\ 
    563                   0 &\text{if $                  k  >     bottom\_level(i,j)$} 
    564     \end{cases} 
    565   \\ 
    566   umask(i,j,k) &= &  &tmask(i,j,k) * tmask(i + 1,j,    k) \\ 
    567   vmask(i,j,k) &= &  &tmask(i,j,k) * tmask(i    ,j + 1,k) \\ 
    568   fmask(i,j,k) &= &  &tmask(i,j,k) * tmask(i + 1,j,    k) \\ 
    569                &  &* &tmask(i,j,k) * tmask(i + 1,j,    k) \\ 
    570   wmask(i,j,k) &= &  &tmask(i,j,k) * tmask(i    ,j,k - 1) \\ 
    571   \text{with~} wmask(i,j,1) &= & &tmask(i,j,1) 
    572 \end{alignat*} 
     597\begin{align*} 
     598  tmask(i,j,k) &= 
     599  \begin{cases} 
     600    0 &\text{if $                             k <    top\_level(i,j)$} \\ 
     601    1 &\text{if $     bottom\_level(i,j) \leq k \leq top\_level(i,j)$} \\ 
     602    0 &\text{if $k >  bottom\_level(i,j)                            $} 
     603  \end{cases} \\ 
     604  umask(i,j,k) &= tmask(i,j,k) * tmask(i + 1,j,    k) \\ 
     605  vmask(i,j,k) &= tmask(i,j,k) * tmask(i    ,j + 1,k) \\ 
     606  fmask(i,j,k) &= tmask(i,j,k) * tmask(i + 1,j,    k) * tmask(i,j,k) * tmask(i + 1,j,    k) \\ 
     607  wmask(i,j,k) &= tmask(i,j,k) * tmask(i    ,j,k - 1) \\ 
     608  \text{with~} wmask(i,j,1) &= tmask(i,j,1) 
     609\end{align*} 
    573610 
    574611Note that, without ice shelves cavities, 
    575 masks at $t-$ and $w-$points are identical with the numerical indexing used (\autoref{subsec:DOM_Num_Index}). 
    576 Nevertheless, $wmask$ are required with ocean cavities to deal with the top boundary (ice shelf/ocean interface) 
     612masks at $t-$ and $w-$points are identical with the numerical indexing used 
     613(\autoref{subsec:DOM_Num_Index}). 
     614Nevertheless, 
     615$wmask$ are required with ocean cavities to deal with the top boundary (ice shelf/ocean interface) 
    577616exactly in the same way as for the bottom boundary. 
    578617 
    … …  
    588627\label{subsec:DOM_closea} 
    589628 
    590 When a global ocean is coupled to an atmospheric model it is better to represent all large water bodies 
    591 (\eg\ Great Lakes, Caspian sea \dots) even if the model resolution does not allow their communication with 
    592 the rest of the ocean. 
     629When a global ocean is coupled to an atmospheric model it is better to 
     630represent all large water bodies (\eg\ Great Lakes, Caspian sea, \dots) even if 
     631the model resolution does not allow their communication with the rest of the ocean. 
    593632This is unnecessary when the ocean is forced by fixed atmospheric conditions, 
    594633so these seas can be removed from the ocean domain. 
    595 The user has the option to set the bathymetry in closed seas to zero (see \autoref{sec:MISC_closea}) and 
    596 to optionally decide on the fate of any freshwater imbalance over the area. 
    597 The options are explained in \autoref{sec:MISC_closea} but it should be noted here that 
    598 a successful use of these options requires appropriate mask fields to be present in the domain configuration file. 
     634The user has the option to 
     635set the bathymetry in closed seas to zero (see \autoref{sec:MISC_closea}) and to 
     636optionally decide on the fate of any freshwater imbalance over the area. 
     637The options are explained in \autoref{sec:MISC_closea} but 
     638it should be noted here that a successful use of these options requires 
     639appropriate mask fields to be present in the domain configuration file. 
    599640Among the possibilities are: 
    600641 
    601642\begin{clines} 
    602 int    closea_mask          /* non-zero values in closed sea areas for optional masking                  */ 
    603 int    closea_mask_rnf      /* non-zero values in closed sea areas with runoff locations (precip only)  */ 
    604 int    closea_mask_emp      /* non-zero values in closed sea areas with runoff locations (total emp)     */ 
     643int closea_mask     /* non-zero values in closed sea areas for optional masking                */ 
     644int closea_mask_rnf /* non-zero values in closed sea areas with runoff locations (precip only) */ 
     645int closea_mask_emp /* non-zero values in closed sea areas with runoff locations (total emp)   */ 
    605646\end{clines} 
    606647 
    … …  
    610651 
    611652Most of the arrays relating to a particular ocean model configuration discussed in this chapter 
    612 (grid-point position, scale factors) 
    613 can be saved in a file if 
    614 namelist parameter \np{ln_write_cfg}{ln\_write\_cfg} (namelist \nam{cfg}{cfg}) is set to \forcode{.true.}; 
     653(grid-point position, scale factors) can be saved in a file if 
     654namelist parameter \np{ln_write_cfg}{ln\_write\_cfg} (namelist \nam{cfg}{cfg}) is set to 
     655\forcode{.true.}; 
    615656the output filename is set through parameter \np{cn_domcfg_out}{cn\_domcfg\_out}. 
    616657This is only really useful if 
    … …  
    619660 
    620661Alternatively, all the arrays relating to a particular ocean model configuration 
    621 (grid-point position, scale factors, depths and masks) 
    622 can be saved in a file called \texttt{mesh\_mask} if 
    623 namelist parameter \np{ln_meshmask}{ln\_meshmask} (namelist \nam{dom}{dom}) is set to \forcode{.true.}. 
     662(grid-point position, scale factors, depths and masks) can be saved in 
     663a file called \texttt{mesh\_mask} if 
     664namelist parameter \np{ln_meshmask}{ln\_meshmask} (namelist \nam{dom}{dom}) is set to 
     665\forcode{.true.}. 
    624666This file contains additional fields that can be useful for post-processing applications. 
    625667 
    … …  
    627669\section[Initial state (\textit{istate.F90} and \textit{dtatsd.F90})]{Initial state (\protect\mdl{istate} and \protect\mdl{dtatsd})} 
    628670\label{sec:DOM_DTA_tsd} 
     671 
    629672\begin{listing} 
    630673  \nlst{namtsd} 
    … …  
    638681 
    639682\begin{description} 
    640 \item [{\np[=.true.]{ln_tsd_init}{ln\_tsd\_init}}] Use T and S input files that can be given on the model grid itself or on their native input data grids. 
    641   In the latter case, the data will be interpolated on-the-fly both in the horizontal and the vertical to the model grid 
     683\item [{\np[=.true.]{ln_tsd_init}{ln\_tsd\_init}}] Use T and S input files that can be given on 
     684  the model grid itself or on their native input data grids. 
     685  In the latter case, 
     686  the data will be interpolated on-the-fly both in the horizontal and the vertical to the model grid 
    642687  (see \autoref{subsec:SBC_iof}). 
    643   The information relating to the input files are specified in the \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures. 
     688  The information relating to the input files are specified in 
     689  the \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures. 
    644690  The computation is done in the \mdl{dtatsd} module. 
    645 \item [{\np[=.false.]{ln_tsd_init}{ln\_tsd\_init}}] Initial values for T and S are set via a user supplied \rou{usr\_def\_istate} routine contained in \mdl{userdef\_istate}. 
     691\item [{\np[=.false.]{ln_tsd_init}{ln\_tsd\_init}}] Initial values for T and S are set via 
     692  a user supplied \rou{usr\_def\_istate} routine contained in \mdl{userdef\_istate}. 
    646693  The default version sets horizontally uniform T and profiles as used in the GYRE configuration 
    647694  (see \autoref{sec:CFGS_gyre}). 
    648695\end{description} 
    649696 
    650 \onlyinsubfile{\input{../../global/epilogue}} 
     697\subinc{\input{../../global/epilogue}} 
    651698 
    652699\end{document} 
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