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Changeset 14257 for NEMO/trunk/doc/latex/NEMO/subfiles – NEMO

Ignore:
Timestamp:
2021-01-04T16:13:36+01:00 (3 years ago)
Author:
nicolasmartin
Message:

Overall review of LaTeX sources (not tested completely as of now):

  • Reworking global files: main document.tex, add glossary.tex, cosmetic changes...
  • Ignore missing namelists (namsbc_isf, namsbc_iscpl and namptr)
  • Removal of references for unused indices (\hfile, \ifile and \jp)
  • Update of .svnignore and svn:ignore properties accordingly
  • Split of manual abstract into a common NEMO abs for all and a specific one for each engine
  • Shrinking variables names used in the frontmatter
Location:
NEMO/trunk/doc/latex/NEMO/subfiles
Files:
24 edited

Legend:

Unmodified
Added
Removed

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

    r14178 r14257  
    77 
    88%    {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains }  \\ 
    9  
    10 \thispagestyle{plain} 
    119 
    1210\chaptertoc 
    … …  
    9189 \item [{\np{jphgr_mesh}{jphgr\_mesh}=0}]  The most general curvilinear orthogonal grids. 
    9290  The coordinates and their first derivatives with respect to $i$ and $j$ are provided 
    93   in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module. 
     91  in a input file (\textit{coordinates.nc}), read in \rou{hgr\_read} subroutine of the domhgr module. 
    9492  This is now the only option available within \NEMO\ itself from v4.0 onwards. 
    9593\item [{\np{jphgr_mesh}{jphgr\_mesh}=1 to 5}] A few simple analytical grids are provided (see below). 
    … …  
    156154The reference coordinate transformation $z_0(k)$ defines the arrays $gdept_0$ and 
    157155$gdepw_0$ for $t$- and $w$-points, respectively. See \autoref{sec:DOMCFG_sco} for the 
    158 S-coordinate options.  As indicated on \autoref{fig:DOM_index_vert} \jp{jpk} is the number of 
    159 $w$-levels.  $gdepw_0(1)$ is the ocean surface.  There are at most \jp{jpk}-1 $t$-points 
     156S-coordinate options.  As indicated on \autoref{fig:DOM_index_vert} \texttt{jpk} is the number of 
     157$w$-levels.  $gdepw_0(1)$ is the ocean surface.  There are at most \texttt{jpk}-1 $t$-points 
    160158inside the ocean, the additional $t$-point at $jk = jpk$ is below the sea floor and is not 
    161159used.  The vertical location of $w$- and $t$-levels is defined from the analytic 
    … …  
    167165 
    168166It is possible to define a simple regular vertical grid by giving zero stretching 
    169 (\np[=0]{ppacr}{ppacr}).  In that case, the parameters \jp{jpk} (number of $w$-levels) 
     167(\np[=0]{ppacr}{ppacr}).  In that case, the parameters \texttt{jpk} (number of $w$-levels) 
    170168and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid. 
    171169 
    … …  
    179177\end{gather} 
    180178 
    181 where $k = 1$ to \jp{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels.  Such an 
     179where $k = 1$ to \texttt{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels.  Such an 
    182180expression allows us to define a nearly uniform vertical location of levels at the ocean 
    183181top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}). 
    … …  
    227225\end{equation} 
    228226 
    229 With the choice of the stretching $h_{cr} = 3$ and the number of levels \jp{jpk}~$= 31$, 
     227With the choice of the stretching $h_{cr} = 3$ and the number of levels \texttt{jpk}~$= 31$, 
    230228the four coefficients $h_{sur}$, $h_0$, $h_1$, and $h_{th}$ in 
    231229\autoref{eq:DOMCFG_zgr_ana_2} have been determined such that \autoref{eq:DOMCFG_zgr_coef} 
    … …  
    245243  Values from $3$ to $10$ are usual. 
    246244\item \np{ppkth}{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs 
    247   (nondimensional, usually of order 1/2 or 2/3 of \jp{jpk}) 
     245  (nondimensional, usually of order 1/2 or 2/3 of \texttt{jpk}) 
    248246\item \np{ppdzmin}{ppdzmin}: minimum thickness for the top layer (in meters). 
    249247\item \np{pphmax}{pphmax}: total depth of the ocean (meters). 
    … …  
    251249 
    252250As an example, for the $45$ layers used in the DRAKKAR configuration those parameters are: 
    253 \jp{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$, 
     251\texttt{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$, 
    254252\np{pphmax}{pphmax}~$= 5750~m$. 
    255253 
    … …  
    346344  This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 
    347345\item [{\np[=1]{nn_bathy}{nn\_bathy}}]: read a bathymetry and ice shelf draft (if needed). 
    348   The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at 
     346  The \textit{bathy\_meter.nc} file (Netcdf format) provides the ocean depth (positive, in meters) at 
    349347  each grid point of the model grid. 
    350348  The bathymetry is usually built by interpolating a standard bathymetry product (\eg\ ETOPO2) onto 
    … …  
    353351  no wet levels are defined (all levels are masked). 
    354352 
    355   The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 
     353  The \textit{isfdraft\_meter.nc} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 
    356354  each grid point of the model grid. 
    357355  This file is only needed if \np[=.true.]{ln_isfcav}{ln\_isfcav}. 
    … …  
    396394bathymetry varies by less than one level thickness from one grid point to the next).  The 
    397395reference layer thicknesses $e_{3t}^0$ have been defined in the absence of bathymetry. 
    398 With partial steps, layers from 1 to \jp{jpk}-2 can have a thickness smaller than 
     396With partial steps, layers from 1 to \texttt{jpk-2} can have a thickness smaller than 
    399397$e_{3t}(jk)$. 
    400398 
    401 The model deepest layer (\jp{jpk}-1) is allowed to have either a smaller or larger 
     399The model deepest layer (\texttt{jpk-1}) is allowed to have either a smaller or larger 
    402400thickness than $e_{3t}(jpk)$: the maximum thickness allowed is $2*e_{3t}(jpk - 1)$. 
    403401 

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

    r11693 r14257  
    55\chapter{Note on some algorithms} 
    66\label{apdx:ALGOS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r11693 r14257  
    55\chapter{Diffusive Operators} 
    66\label{apdx:DIFFOPERS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r11693 r14257  
    55\chapter{Discrete Invariants of the Equations} 
    66\label{apdx:INVARIANTS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r11693 r14257  
    88%    {\em 4.0} & {\em Mike Bell} & {\em review}  \\ 
    99%    {\em 3.x} & {\em Gurvan Madec} & {\em original}  \\ 
    10  
    11 \thispagestyle{plain} 
    1210 
    1311\chaptertoc 

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

    r14113 r14257  
    1515\chapter{Iso-Neutral Diffusion and Eddy Advection using Triads} 
    1616\label{apdx:TRIADS} 
    17  
    18 \thispagestyle{plain} 
    1917 
    2018\chaptertoc 

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

    r11693 r14257  
    88%    {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\ 
    99%    {\em 3.4} & {\em D. J. Lea, M. Martin, K. Mogensen, A. Weaver} & {\em Initial version}  \\ 
    10  
    11 \thispagestyle{plain} 
    1210 
    1311\chaptertoc 

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

    r13970 r14257  
    1111%    {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em }  \\ 
    1212%    {\em }      & {\em Christian Ethe, Sebastien Masson } & {\em }  \\ 
    13  
    14 \thispagestyle{plain} 
    1513 
    1614\chaptertoc 
    … …  
    666664\end{forlines} 
    667665 
    668 \noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d} 
     666\noindent will give the following file name radical: \textit{myfile\_ORCA2\_19891231\_freq1d} 
    669667 
    670668%% ================================================================================================= 
    … …  
    19421940When \np[=.true.]{ln_subbas}{ln\_subbas}, transports and stream function are computed for the Atlantic, Indian, 
    19431941Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean. 
    1944 The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays, 
     1942The sub-basin decomposition requires an input file (\textit{subbasins}) which contains three 2D mask arrays, 
    19451943the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:DIA_mask_subasins}). 
    19461944 
    19471945\begin{listing} 
    1948   \nlst{namptr} 
     1946%  \nlst{namptr} 
    19491947  \caption{\forcode{&namptr}} 
    19501948  \label{lst:namptr} 

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

    r11693 r14257  
    55\chapter{Diurnal SST Models (DIU)} 
    66\label{chap:DIU} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r11693 r14257  
    1414% -    domclo: closed sea and lakes.... 
    1515%              management of closea sea area: specific to global cfg, both forced and coupled 
    16  
    17 \thispagestyle{plain} 
    1816 
    1917\chaptertoc 
    … …  
    368366\label{subsec:DOM_size} 
    369367 
    370 The 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. 
     368The total size of the computational domain is set by the parameters \texttt{jpiglo}, \texttt{jpjglo} and 
     369\texttt{jpkglo} for the $i$, $j$ and $k$ directions, respectively. 
    372370Note, that the variables \texttt{jpi} and \texttt{jpj} refer to 
    373371the size of each processor subdomain when the code is run in parallel using domain decomposition 
    … …  
    379377in which case \np{cn_cfg}{cn\_cfg} and \np{nn_cfg}{nn\_cfg} are set from these values accordingly). 
    380378 
    381 The global lateral boundary condition type is selected from 8 options using parameter \jp{jperio}. 
     379The global lateral boundary condition type is selected from 8 options using parameter \texttt{jperio}. 
    382380See \autoref{sec:LBC_jperio} for details on the available options and 
    383 the corresponding values for \jp{jperio}. 
     381the corresponding values for \texttt{jperio}. 
    384382 
    385383%% ================================================================================================= 
    … …  
    465463\begin{enumerate} 
    466464\item the bathymetry given in meters; 
    467 \item the number of levels of the model (\jp{jpk}); 
     465\item the number of levels of the model (\texttt{jpk}); 
    468466\item the analytical transformation $z(i,j,k)$ and the vertical scale factors 
    469467  (derivatives of the transformation); and 
    … …  
    575573every gridcell in the model regardless of the choice of vertical coordinate. 
    576574With constant z-levels, e3 metrics will be uniform across each horizontal level. 
    577 In the partial step case each e3 at the \jp{bottom\_level} 
    578 (and, possibly, \jp{top\_level} if ice cavities are present) 
     575In the partial step case each e3 at the \texttt{bottom\_level} 
     576(and, possibly, \texttt{top\_level} if ice cavities are present) 
    579577may vary from its horizontal neighbours. 
    580578And, in s-coordinates, variations can occur throughout the water column. 
    … …  
    585583those arising from a flat sea surface with zero elevation. 
    586584 
    587 The \jp{bottom\_level} and \jp{top\_level} 2D arrays define 
    588 the \jp{bottom\_level} and top wet levels in each grid column. 
    589 Without ice cavities, \jp{top\_level} is essentially a land mask (0 on land; 1 everywhere else). 
    590 With ice cavities, \jp{top\_level} determines the first wet point below the overlying ice shelf. 
     585The \texttt{bottom\_level} and \texttt{top\_level} 2D arrays define 
     586the \texttt{bottom\_level} and top wet levels in each grid column. 
     587Without ice cavities, \texttt{top\_level} is essentially a land mask (0 on land; 1 everywhere else). 
     588With ice cavities, \texttt{top\_level} determines the first wet point below the overlying ice shelf. 
    591589 
    592590%% ================================================================================================= 
    … …  
    594592\label{subsec:DOM_msk} 
    595593 
    596 From \jp{top\_level} and \jp{bottom\_level} fields, the mask fields are defined as follows: 
     594From \texttt{top\_level} and \texttt{bottom\_level} fields, the mask fields are defined as follows: 
    597595\begin{align*} 
    598596  tmask(i,j,k) &= 

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

    r14177 r14257  
    55\chapter{Ocean Dynamics (DYN)} 
    66\label{chap:DYN} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r14178 r14257  
    55\chapter{Lateral Boundary Condition (LBC)} 
    66\label{chap:LBC} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    161159 
    162160%% ================================================================================================= 
    163 \section[Model domain boundary condition (\forcode{jperio})]{Model domain boundary condition (\protect\jp{jperio})} 
     161\section{Model domain boundary condition (\forcode{jperio})} 
    164162\label{sec:LBC_jperio} 
    165163 
    … …  
    170168 
    171169%% ================================================================================================= 
    172 \subsection[Closed, cyclic (\forcode{=0,1,2,7})]{Closed, cyclic (\protect\jp{jperio}\forcode{=0,1,2,7})} 
     170\subsection{Closed, cyclic (\forcode{jperio={0,1,2,7}})} 
    173171\label{subsec:LBC_jperio012} 
    174172 
    175173The choice of closed or cyclic model domain boundary condition is made by 
    176 setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}. 
     174setting \forcode{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}. 
    177175Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}. 
    178176The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$, 
    … …  
    183181\begin{description} 
    184182 
    185 \item [For closed boundary (\jp{jperio}\forcode{=0})], solid walls are imposed at all model boundaries: 
     183\item [For closed boundary (\forcode{jperio=0})], solid walls are imposed at all model boundaries: 
    186184  first and last rows and columns are set to zero. 
    187185 
    188 \item [For cyclic east-west boundary (\jp{jperio}\forcode{=1})], first and last rows are set to zero (closed) whilst the first column is set to 
     186\item [For cyclic east-west boundary (\forcode{jperio=1})], first and last rows are set to zero (closed) whilst the first column is set to 
    189187  the value of the last-but-one column and the last column to the value of the second one 
    190188  (\autoref{fig:LBC_jperio}-a). 
    191189  Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end. 
    192190 
    193 \item [For cyclic north-south boundary (\jp{jperio}\forcode{=2})], first and last columns are set to zero (closed) whilst the first row is set to 
     191\item [For cyclic north-south boundary (\forcode{jperio=2})], first and last columns are set to zero (closed) whilst the first row is set to 
    194192  the value of the last-but-one row and the last row to the value of the second one 
    195193  (\autoref{fig:LBC_jperio}-a). 
    196194  Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end. 
    197195 
    198 \item [Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{=7})] combines cases 1 and 2. 
     196\item [Bi-cyclic east-west and north-south boundary (\forcode{jperio=7})] combines cases 1 and 2. 
    199197 
    200198\end{description} 
    … …  
    209207 
    210208%% ================================================================================================= 
    211 \subsection[North-fold (\forcode{=3,6})]{North-fold (\protect\jp{jperio}\forcode{=3,6})} 
     209\subsection{North-fold (\forcode{jperio={3,6}})} 
    212210\label{subsec:LBC_north_fold} 
    213211 
    … …  
    288286Each processor is independent and without message passing or synchronous process, programs run alone and access just its own local memory. 
    289287For this reason, 
    290 the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \jp{jpi}, \jp{jpj}, \jp{jpk}. 
     288the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \texttt{jpi}, \texttt{jpj}, \texttt{jpk}. 
    291289These dimensions include the internal domain and the overlapping rows. 
    292 The number of rows to exchange (known as the halo) is usually set to one (nn\_hls=1, in \mdl{par\_oce}, 
     290The number of rows to exchange (known as the halo) is usually set to one (\forcode{nn_hls=1}, in \mdl{par\_oce}, 
    293291and must be kept to one until further notice). 
    294 The whole domain dimensions are named \jp{jpiglo}, \jp{jpjglo} and \jp{jpk}. 
     292The whole domain dimensions are named \texttt{jpiglo}, \texttt{jpjglo} and \texttt{jpk}. 
    295293The relationship between the whole domain and a sub-domain is: 
    296294\begin{gather*} 
    … …  
    299297\end{gather*} 
    300298 
    301 One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \jp{jpi} is now always equal to nlci and \jp{jpj} equal to nlcj. 
     299One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \texttt{jpi} is now always equal to nlci and \texttt{jpj} equal to nlcj. 
    302300 
    303301An element of $T_{l}$, a local array (subdomain) corresponds to an element of $T_{g}$, 
    … …  
    309307with $1 \leq i \leq jpi$, $1  \leq j \leq jpj $ , and  $1  \leq k \leq jpk$. 
    310308 
    311 The 1-d arrays $mig(1:\jp{jpi})$ and $mjg(1:\jp{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\jp{jpiglo})$, $mi1(1:\jp{jpiglo})$ and $mj0(1:\jp{jpjglo})$, $mj1(1:\jp{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\ 
     309The 1-d arrays $mig(1:\texttt{jpi})$ and $mjg(1:\texttt{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\texttt{jpiglo})$, $mi1(1:\texttt{jpiglo})$ and $mj0(1:\texttt{jpjglo})$, $mj1(1:\texttt{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\ 
    312310 
    313311The \NEMO\ model computes equation terms with the help of mask arrays (0 on land points and 1 on sea points). It is therefore possible that an MPI subdomain contains only land points. To save ressources, we try to supress from the computational domain as much land subdomains as possible. For example if $N_{mpi}$ processes are allocated to NEMO, the domain decomposition will be given by the following equation: 
    … …  
    372370The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}. 
    373371Each boundary set can be either defined as a series of straight line segments directly in the namelist 
    374 (\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided). 
    375 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file. 
     372(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\textit{coordinates.bdy.nc}'' file must be provided). 
     373The coordinates.bdy file is analagous to the usual \NEMO\ ``\textit{coordinates.nc}'' file. 
    376374In the example above, there are two boundary sets, the first of which is defined via a file and 
    377375the second is defined in the namelist. 
    … …  
    570568 
    571569The boundary geometry for each set may be defined in a namelist \forcode{&nambdy_index} or 
    572 by reading in a ``\ifile{coordinates.bdy}'' file. 
    573 The \texttt{nambdy\_index} namelist defines a series of straight-line segments for north, east, south and west boundaries. 
    574 One \texttt{nambdy\_index} namelist block is needed for each boundary condition defined by indexes. 
     570by reading in a ``\textit{coordinates.bdy.nc}'' file. 
     571The \forcode{&nambdy_index} namelist defines a series of straight-line segments for north, east, south and west boundaries. 
     572One \forcode{&nambdy_index} namelist block is needed for each boundary condition defined by indexes. 
    575573For the northern boundary, \texttt{nbdysegn} gives the number of segments, 
    576 \jp{jpjnob} gives the $j$ index for each segment and \jp{jpindt} and 
    577 \jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. 
     574\texttt{jpjnob} gives the $j$ index for each segment and \texttt{jpindt} and 
     575\texttt{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. 
    578576These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$). 
    579577The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np[>1]{nn_rimwidth}{nn\_rimwidth}. 
    580578 
    581 The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file. 
     579The boundary geometry may also be defined from a ``\textit{coordinates.bdy.nc}'' file. 
    582580\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. 
    583581The file should contain the index arrays for each of the $T$, $U$ and $V$ grids. 
    … …  
    633631  \centering 
    634632  \includegraphics[width=0.66\textwidth]{LBC_nc_header} 
    635   \caption[Header for a \protect\ifile{coordinates.bdy} file]{ 
    636     Example of the header for a \protect\ifile{coordinates.bdy} file} 
     633  \caption[Header for a \textit{coordinates.bdy.nc} file]{ 
     634    Example of the header for a \textit{coordinates.bdy.nc} file} 
    637635  \label{fig:LBC_nc_header} 
    638636\end{figure} 
    … …  
    684682\texttt{<constituent>\_z1} and \texttt{<constituent>\_z2} for the real and imaginary parts of 
    685683SSH, respectively, are expected to be available in file 
    686 \ifile{<input>\_grid\_T}, variables \texttt{<constituent>\_u1} and 
     684\textit{<input>\_grid\_T.nc}, variables \texttt{<constituent>\_u1} and 
    687685\texttt{<constituent>\_u2} for the real and imaginary parts of u, respectively, in file 
    688 \ifile{<input>\_grid\_U}, and \texttt{<constituent>\_v1} and 
     686\textit{<input>\_grid\_U.nc}, and \texttt{<constituent>\_v1} and 
    689687\texttt{<constituent>\_v2} for the real and imaginary parts of v, respectively, in file 
    690 \ifile{<input>\_grid\_V}; when data along open boundary segments is used, 
     688\textit{<input>\_grid\_V.nc}; when data along open boundary segments is used, 
    691689variables \texttt{z1} and \texttt{z2} (real and imaginary part of SSH) are 
    692 expected to be available in file \ifile{<input><constituent>\_grid\_T}, 
     690expected to be available in file \textit{<input><constituent>\_grid\_T.nc}, 
    693691variables \texttt{u1} and \texttt{u2} (real and imaginary part of u) in file 
    694 \ifile{<input><constituent>\_grid\_U}, and variables \texttt{v1} and \texttt{v2} 
     692\textit{<input><constituent>\_grid\_U.nc}, and variables \texttt{v1} and \texttt{v2} 
    695693(real and imaginary part of v) in file 
    696 \ifile{<input><constituent>\_grid\_V}.\par 
     694\textit{<input><constituent>\_grid\_V.nc}.\par 
    697695 
    698696Note that the barotropic velocity components are assumed to be defined 

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

    r14113 r14257  
    55\chapter{Lateral Ocean Physics (LDF)} 
    66\label{chap:LDF} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r14177 r14257  
    1414%    {\em --\texttt{"}--} & {\em ... K. Mogensen, A. Vidard, A. Weaver} & {\em ---\texttt{"}---}  \\ 
    1515%\end{tabular} 
    16  
    17 \thispagestyle{plain} 
    1816 
    1917\chaptertoc 
    … …  
    420418 
    421419To use Sea Level Anomaly (SLA) data the mean dynamic topography (MDT) must be provided in a separate file defined on 
    422 the model grid called \ifile{slaReferenceLevel}. 
     420the model grid called \textit{slaReferenceLevel.nc}. 
    423421The MDT is required in order to produce the model equivalent sea level anomaly from the model sea surface height. 
    424422Below is an example header for this file (on the ORCA025 grid). 

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

    r14177 r14257  
    55\chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB, TDE)} 
    66\label{chap:SBC} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    646644parameters. It is therefore recommended to chose version 3.6 over 3. 
    647645 
    648 \subsection{Cool-skin and warm-layer parametrizations} 
    649 %\subsection[Cool-skin and warm-layer parameterizations (\forcode{ln_skin_cs} \& \forcode{ln_skin_wl})]{Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \& \np{ln_skin_wl}{ln\_skin\_wl})} 
     646\subsection[Cool-skin and warm-layer parameterizations (   \forcode{ln_skin_cs}               \& \forcode{ln_skin_wl}              )] 
     647           {Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \&      \np{ln_skin_wl}{ln\_skin\_wl})} 
    650648\label{subsec:SBC_skin} 
    651649 
    … …  
    979977  ocean tide model}: Mf, Mm, Ssa, Mtm, Msf, Msqm, Sa, K1, O1, P1, Q1, J1, S1, 
    980978M2, S2, N2, K2, nu2, mu2, 2N2, L2, T2, eps2, lam2, R2, M3, MKS2, MN4, MS4, M4, 
    981 N4, S4, M6, and M8; see file \hf{tide} and \mdl{tide\_mod} for further 
     979N4, S4, M6, and M8; see file \textit{tide.h90} and \mdl{tide\_mod} for further 
    982980information and references\footnote{As a legacy option \np{ln_tide_var} can be 
    983981  set to \forcode{0}, in which case the 19 tidal constituents (M2, N2, 2N2, S2, 
    984982  K2, K1, O1, Q1, P1, M4, Mf, Mm, Msqm, Mtm, S1, MU2, NU2, L2, and T2; see file 
    985   \hf{tide}) and associated parameters that have been available in NEMO version 
     983  \textit{tide.h90}) and associated parameters that have been available in NEMO version 
    986984  4.0 and earlier are available}. Constituents to be included in the tidal forcing 
    987985(surface and lateral boundaries) are selected by enumerating their respective 
    … …  
    10131011potential). The tidal tilt factor $\gamma = 1 + k - h$ includes the 
    10141012Love numbers $k$ and $h$ \citep{love_PRSL09}; this factor is 
    1015 configurable using \np{rn_tide_gamma} (default value 0.7). Optionally, 
     1013configurable using \np{rn_tide_gamma}{rn\_tide\_gamma} (default value 0.7). Optionally, 
    10161014when \np[=.true.]{ln_tide_ramp}{ln\_tide\_ramp}, the equilibrium tidal 
    10171015forcing can be ramped up linearly from zero during the initial 
    … …  
    11871185 
    11881186\begin{listing} 
    1189   \nlst{namsbc_isf} 
     1187%  \nlst{namsbc_isf} 
    11901188  \caption{\forcode{&namsbc_isf}} 
    11911189  \label{lst:namsbc_isf} 
    … …  
    12921290 
    12931291\begin{listing} 
    1294   \nlst{namsbc_iscpl} 
     1292%  \nlst{namsbc_iscpl} 
    12951293  \caption{\forcode{&namsbc_iscpl}} 
    12961294  \label{lst:namsbc_iscpl} 

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

    r11693 r14257  
    55\chapter{Stochastic Parametrization of EOS (STO)} 
    66\label{chap:STO} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r13476 r14257  
    55\chapter{Ocean Tracers (TRA)} 
    66\label{chap:TRA} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    930928When \np{nn_geoflx}{nn\_geoflx} is set to 2, 
    931929a spatially varying geothermal heat flux is introduced which is provided in 
    932 the \ifile{geothermal\_heating} NetCDF file 
     930the \textit{geothermal\_heating.nc} NetCDF file 
    933931(\autoref{fig:TRA_geothermal}) \citep{emile-geay.madec_OS09}. 
    934932 
    … …  
    11511149\citep{madec.delecluse.ea_JPO96}. 
    11521150 
    1153 For generating \ifile{resto}, 
     1151For generating \textit{resto.nc}, 
    11541152see the documentation for the DMP tools provided with the source code under \path{./tools/DMP_TOOLS}. 
    11551153 
    … …  
    11751173$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp}, its default value is \forcode{10.e-3}. 
    11761174Note that the forcing correction term in the filter is not applied in linear free surface 
    1177 (\jp{ln\_linssh}\forcode{=.true.}) (see \autoref{subsec:TRA_sbc}). 
     1175(\np[=.true.]{ln_linssh}{ln\_linssh}) (see \autoref{subsec:TRA_sbc}). 
    11781176Not also that in constant volume case, the time stepping is performed on $T$, 
    11791177not on its content, $e_{3t}T$. 

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

    r14177 r14257  
    88\chapter{Vertical Ocean Physics (ZDF)} 
    99\label{chap:ZDF} 
    10  
    11 \thispagestyle{plain} 
    1210 
    1311\chaptertoc 
    … …  
    11811179These values are assigned in \mdl{zdfdrg}. 
    11821180Note that there is support for local enhancement of these values via an externally defined 2D mask array 
    1183 (\np[=.true.]{ln_boost}{ln\_boost}) given in the \ifile{bfr\_coef} input NetCDF file. 
     1181(\np[=.true.]{ln_boost}{ln\_boost}) given in the \textit{bfr\_coef.nc} input NetCDF file. 
    11841182The mask values should vary from 0 to 1. 
    11851183Locations with a non-zero mask value will have the friction coefficient increased by 

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

    r14196 r14257  
    55\chapter{Configurations} 
    66\label{chap:CFGS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    8583the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES). 
    8684An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2. 
    87 The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file, 
     85The domain of ORCA2 configuration is defined in \textit{ORCA\_R2\_zps\_domcfg.nc} file, 
    8886this file is available in tar file on the \NEMO\ community zenodo platform: \\ 
    8987https://doi.org/10.5281/zenodo.2640723 
    … …  
    152150Each of configuration is set through the \textit{domain\_cfg} domain configuration file, 
    153151which sets the grid size and configuration name parameters. 
    154 The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file 
     152The \NEMO\ System Team provides only ORCA2 domain input file "\textit{ORCA\_R2\_zps\_domcfg.nc}" file 
    155153(\autoref{tab:CFGS_ORCA}). 
    156154 
    … …  
    158156  \centering 
    159157  \begin{tabular}{p{4cm} c c c c} 
    160     Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\ 
     158    Horizontal Grid & \texttt{ORCA\_index} & \texttt{jpiglo} & \texttt{jpjglo} \\ 
    161159    \hline \hline 
    162160    % 4   \deg\ &              4   &          92 &          76 \\ 
    … …  
    246244Its horizontal resolution (and thus the size of the domain) is determined by 
    247245setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: 
     246 
    248247\begin{align*} 
    249   \jp{jpiglo} = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\ 
    250   \jp{jpjglo} = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} 
     248   jpiglo = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\ 
     249   jpjglo = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} 
    251250\end{align*} 
    252251 
    253252Obviously, the namelist parameters have to be adjusted to the chosen resolution, 
    254253see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations). 
    255 In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}). 
     254In the vertical, GYRE uses the default 30 ocean levels (\forcode{jpk = 31}, \autoref{fig:DOM_zgr_e3}). 
    256255 
    257256\begin{listing} 

  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex

    r11693 r14257  
    55\chapter{Invariants of the Primitive Equations} 
    66\label{chap:CONS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r14113 r14257  
    55\chapter{Miscellaneous Topics} 
    66\label{chap:MISC} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    205203 
    206204\noindent Consider an ORCA1 
    207 configuration using the extended grid domain configuration file: \ifile{eORCA1\_domcfg.nc} 
     205configuration using the extended grid domain configuration file: \textit{eORCA1\_domcfg.nc} 
    208206This file define a horizontal domain of 362x332.  The first row with 
    209207open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran\ indexing) 
    … …  
    226224\noindent Note that with this option, the j-size of the global domain is (extended 
    227225j-size minus \np{open_ocean_jstart}{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value 
    228 for the configuration. This means an alternative version of \ifile{eORCA1\_domcfg.nc} must 
     226for the configuration. This means an alternative version of \textit{eORCA1\_domcfg.nc} must 
    229227be created for when \np{ln_use_jattr}{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a 
    230228convenient way of achieving this: 
    … …  
    234232\end{cmds} 
    235233 
    236 The domain configuration file is unique in this respect since it also contains the value of \jp{jpjglo} 
     234The domain configuration file is unique in this respect since it also contains the value of \texttt{jpjglo} 
    237235that is read and used by the model. 
    238236Any other global, 2D and 3D, netcdf, input field can be prepared for use in a reduced domain by adding the 
    … …  
    374372 
    375373When more information is required for monitoring or debugging purposes, the various 
    376 forms of output can be selected via the \np{sn\_cfctl} structure. As well as simple 
     374forms of output can be selected via the \np{sn_cfctl}{sn\_cfctl} structure. As well as simple 
    377375on-off switches this structure also allows selection of a range of processors for 
    378376individual reporting (where appropriate) and a time-increment option to restrict 
    … …  
    449447systems so bug-hunting efforts using this facility should also utilise the \fortran: 
    450448 
    451 \begin{forlines}  
    452    CALL FLUSH(numout) 
    453 \end{forlines} 
     449\forline|CALL FLUSH(numout)| 
    454450 
    455451statement after any additional write statements to ensure that file contents reflect 
    … …  
    482478 
    483479\begin{forlines} 
    484    sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only 
    485    sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
    486      sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
    487        sn_cfctl%l_runstat = .FALSE. ! switches and which areas produce reports with the proc integer settings. 
    488        sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure 
    489        sn_cfctl%l_oceout  = .FALSE. ! that  all areas report. 
    490        sn_cfctl%l_layout  = .FALSE. ! 
    491        sn_cfctl%l_prtctl  = .FALSE. ! 
    492        sn_cfctl%l_prttrc  = .FALSE. ! 
    493        sn_cfctl%l_oasout  = .FALSE. ! 
    494        sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0] 
    495        sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000] 
    496        sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
    497        sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
     480   sn_cfctl%l_glochk  = .false. ! Range sanity checks are local (F) or global (T). Set T for debugging only 
     481   sn_cfctl%l_allon   = .false. ! IF T activate all options. If F deactivate all unless l_config is T 
     482   sn_cfctl%l_config  = .true.  ! IF .true. then control which reports are written with the following 
     483   sn_cfctl%l_runstat = .false. ! switches and which areas produce reports with the proc integer settings. 
     484   sn_cfctl%l_trcstat = .false. ! The default settings for the proc integers should ensure 
     485   sn_cfctl%l_oceout  = .false. ! that  all areas report. 
     486   sn_cfctl%l_layout  = .false. ! 
     487   sn_cfctl%l_prtctl  = .false. ! 
     488   sn_cfctl%l_prttrc  = .false. ! 
     489   sn_cfctl%l_oasout  = .false. ! 
     490   sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0] 
     491   sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000] 
     492   sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
     493   sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
    498494\end{forlines} 
    499495 

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

    r14113 r14257  
    55\chapter{Model Basics} 
    66\label{chap:MB} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r14178 r14257  
    44 
    55\chapter{ essai \zstar \sstar} 
    6  
    7 \thispagestyle{plain} 
    86 
    97\chaptertoc 

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

    r11693 r14257  
    55\chapter{Time Domain} 
    66\label{chap:TD} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
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