Changeset 11578


Ignore:
Timestamp:
2019-09-19T19:44:36+02:00 (12 months ago)
Author:
nicolasmartin
Message:

New LaTeX commands \nam and \np to mention namelist content (step 2)
So far so good, the manual compiles successfully 4 times and everything seems in its right place

Location:
NEMO/trunk/doc/latex/NEMO/subfiles
Files:
17 edited

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

    r11577 r11578  
    5151 
    5252The user has three options available in defining a horizontal grid, which involve the 
    53 namelist variable \np{jphgr_mesh}{jphgr\_mesh} of the \nam{dom} (\texttt{DOMAINcfg} variant only) 
     53namelist variable \np{jphgr_mesh}{jphgr\_mesh} of the \nam{dom}{dom} (\texttt{DOMAINcfg} variant only) 
    5454namelist. 
    5555 
     
    8181In these two cases (\np{jphgr_mesh}{jphgr\_mesh}=1 or 4), the grid position is defined by the 
    8282longitude and latitude of the south-westernmost point (\np{ppglamt0} 
    83 and \np{ppgphi0}). Note that for the Mercator grid the user need only provide 
     83and \np{ppgphi0}{ppgphi0}). Note that for the Mercator grid the user need only provide 
    8484an approximate starting latitude: the real latitude will be recalculated analytically, 
    8585in order to ensure that the equator corresponds to line passing through $t$- 
     
    8787 
    8888Rectangular grids ignoring the spherical geometry are defined with 
    89 \np{jphgr_mesh}{jphgr\_mesh} = 2, 3, 5. The domain is either an $f$-plane (\np{jphgr\_mesh} = 2, 
     89\np{jphgr_mesh}{jphgr\_mesh} = 2, 3, 5. The domain is either an $f$-plane (\np{jphgr_mesh}{jphgr\_mesh} = 2, 
    9090Coriolis factor is constant) or a beta-plane (\np{jphgr_mesh}{jphgr\_mesh} = 3, the Coriolis factor 
    9191is linear in the $j$-direction). The grid size is uniform in meter in each direction, 
     
    9494with the first $t$-point. The meridional coordinate (gphi. arrays) is in kilometers, 
    9595and the second $t$-point corresponds to coordinate $gphit=0$. The input 
    96 variable \np{ppglam0} is ignored. \np{ppgphi0} is used to set the reference 
     96variable \np{ppglam0}{ppglam0} is ignored. \np{ppgphi0}{ppgphi0} is used to set the reference 
    9797latitude for computation of the Coriolis parameter. In the case of the beta plane, 
    98 \np{ppgphi0} corresponds to the center of the domain. Finally, the special case 
     98\np{ppgphi0}{ppgphi0} corresponds to the center of the domain. Finally, the special case 
    9999\np{jphgr_mesh}{jphgr\_mesh}=5 corresponds to a beta plane in a rotated domain for the 
    100100GYRE configuration, representing a classical mid-latitude double gyre system. 
     
    132132the vertical scale factors.  The user must provide the analytical expression of both $z_0$ 
    133133and its first derivative with respect to $k$.  This is done in routine \mdl{domzgr} 
    134 through statement functions, using parameters provided in the \nam{dom} namelist 
     134through statement functions, using parameters provided in the \nam{dom}{dom} namelist 
    135135(\texttt{DOMAINcfg} variant). 
    136136 
    137137It is possible to define a simple regular vertical grid by giving zero stretching 
    138 (\np{ppacr}\forcode{ = 0}).  In that case, the parameters \jp{jpk} (number of $w$-levels) 
    139 and \np{pphmax} (total ocean depth in meters) fully define the grid. 
     138(\np{ppacr}{ppacr}\forcode{ = 0}).  In that case, the parameters \jp{jpk} (number of $w$-levels) 
     139and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid. 
    140140 
    141141For climate-related studies it is often desirable to concentrate the vertical resolution 
     
    152152top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}). 
    153153 
    154 A double hyperbolic tangent version (\np{ldbletanh}\forcode{ = .true.}) is also available 
     154A double hyperbolic tangent version (\np{ldbletanh}{ldbletanh}\forcode{ = .true.}) is also available 
    155155which permits finer control and is used, typically, to obtain a well resolved upper ocean 
    156156without compromising on resolution at depth using a moderate number of levels. 
     
    204204The resulting depths and scale factors as a function of the model levels are shown in 
    205205\autoref{fig:DOMCFG_zgr} and given in \autoref{tab:DOMCFG_orca_zgr}. 
    206 Those values correspond to the parameters \np{ppsur}, \np{ppa0}, \np{ppa1}, \np{ppkth} in \nam{cfg} namelist. 
     206Those values correspond to the parameters \np{ppsur}{ppsur}, \np{ppa0}{ppa0}, \np{ppa1}{ppa1}, \np{ppkth}{ppkth} in \nam{cfg}{cfg} namelist. 
    207207 
    208208Rather than entering parameters $h_{sur}$, $h_0$, and $h_1$ directly, it is possible to 
    209 recalculate them.  In that case the user sets \np{ppsur}~$=$~\np{ppa0}~$=$~\np{ppa1}~$= 
    210 999999$., in \nam{cfg} namelist, and specifies instead the four following parameters: 
     209recalculate them.  In that case the user sets \np{ppsur}{ppsur}~$=$~\np{ppa0}{ppa0}~$=$~\np{ppa1}{ppa1}~$= 
     210999999$., in \nam{cfg}{cfg} namelist, and specifies instead the four following parameters: 
    211211\begin{itemize} 
    212212\item 
    213   \np{ppacr}~$= h_{cr}$: stretching factor (nondimensional). 
    214   The larger \np{ppacr}, the smaller the stretching. 
     213  \np{ppacr}{ppacr}~$= h_{cr}$: stretching factor (nondimensional). 
     214  The larger \np{ppacr}{ppacr}, the smaller the stretching. 
    215215  Values from $3$ to $10$ are usual. 
    216216\item 
    217   \np{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs 
     217  \np{ppkth}{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs 
    218218  (nondimensional, usually of order 1/2 or 2/3 of \jp{jpk}) 
    219219\item 
    220   \np{ppdzmin}: minimum thickness for the top layer (in meters). 
     220  \np{ppdzmin}{ppdzmin}: minimum thickness for the top layer (in meters). 
    221221\item 
    222   \np{pphmax}: total depth of the ocean (meters). 
     222  \np{pphmax}{pphmax}: total depth of the ocean (meters). 
    223223\end{itemize} 
    224224 
    225225As an example, for the $45$ layers used in the DRAKKAR configuration those parameters are: 
    226 \jp{jpk}~$= 46$, \np{ppacr}~$= 9$, \np{ppkth}~$= 23.563$, \np{ppdzmin}~$= 6~m$, 
    227 \np{pphmax}~$= 5750~m$. 
     226\jp{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$, 
     227\np{pphmax}{pphmax}~$= 5750~m$. 
    228228 
    229229%% %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    312312 
    313313Three options are possible for defining the bathymetry, according to the namelist variable 
    314 \np{nn_bathy}{nn\_bathy} (found in \nam{dom} namelist (\texttt{DOMAINCFG} variant) ): 
     314\np{nn_bathy}{nn\_bathy} (found in \nam{dom}{dom} namelist (\texttt{DOMAINCFG} variant) ): 
    315315\begin{description} 
    316316\item[\np{nn_bathy}{nn\_bathy}\forcode{ = 0}]: 
    317317  a flat-bottom domain is defined. 
    318318  The total depth $z_w (jpk)$ is given by the coordinate transformation. 
    319   The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}. 
     319  The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}{jperio}. 
    320320\item[\np{nn_bathy}{nn\_bathy}\forcode{ = -1}]: 
    321321  a domain with a bump of topography one third of the domain width at the central latitude. 
     
    387387thickness than $e_{3t}(jpk)$: the maximum thickness allowed is $2*e_{3t}(jpk - 1)$. 
    388388 
    389 This has to be kept in mind when specifying values in \nam{dom} namelist 
    390 (\texttt{DOMAINCFG} variant), such as the maximum depth \np{pphmax} in partial steps. 
    391  
    392 For example, with \np{pphmax}~$= 5750~m$ for the DRAKKAR 45 layer grid, the maximum ocean 
     389This has to be kept in mind when specifying values in \nam{dom}{dom} namelist 
     390(\texttt{DOMAINCFG} variant), such as the maximum depth \np{pphmax}{pphmax} in partial steps. 
     391 
     392For example, with \np{pphmax}{pphmax}~$= 5750~m$ for the DRAKKAR 45 layer grid, the maximum ocean 
    393393depth allowed is actually $6000~m$ (the default thickness $e_{3t}(jpk - 1)$ being 
    394394$250~m$).  Two variables in the namdom namelist are used to define the partial step 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

    r11577 r11578  
    6464Typically the increments are spread evenly over the full window. 
    6565In addition, two different weighting functions have been implemented. 
    66 The first function (namelist option \np{niaufn}=0) employs constant weights, 
     66The first function (namelist option \np{niaufn}{niaufn}=0) employs constant weights, 
    6767\begin{align} 
    6868  \label{eq:ASM_F1_i} 
     
    7777\end{align} 
    7878where $M = m-n$. 
    79 The second function (namelist option \np{niaufn}=1) employs peaked hat-like weights in order to give maximum weight in the centre of the sub-window, 
     79The second function (namelist option \np{niaufn}{niaufn}=1) employs peaked hat-like weights in order to give maximum weight in the centre of the sub-window, 
    8080with the weighting reduced linearly to a small value at the window end-points: 
    8181\begin{align} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

    r11577 r11578  
    13231323 
    13241324Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by 
    1325 the namelist parameter \np{ln_cfmeta}{ln\_cfmeta} in the \nam{run} namelist. 
     1325the namelist parameter \np{ln_cfmeta}{ln\_cfmeta} in the \nam{run}{run} namelist. 
    13261326This must be set to true if these metadata are to be included in the output files. 
    13271327 
     
    13451345most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files. 
    13461346\NEMO\ executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by 
    1347 setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4} namelist: 
     1347setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4}{nc4} namelist: 
    13481348 
    13491349%------------------------------------------namnc4---------------------------------------------------- 
     
    14381438 
    14391439When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via 
    1440 \rou{iom\_put} calls are set via an equivalent and identically named namelist to \nam{nc4} in 
     1440\rou{iom\_put} calls are set via an equivalent and identically named namelist to \nam{nc4}{nc4} in 
    14411441\textit{xmlio\_server.def}. 
    1442 Typically this namelist serves the mean files whilst the \nam{nc4} in the main namelist file continues to 
     1442Typically this namelist serves the mean files whilst the \nam{nc4}{nc4} in the main namelist file continues to 
    14431443serve the restart files. 
    14441444This duplication is unfortunate but appropriate since, if using io\_servers, the domain sizes of 
     
    14491449%       Tracer/Dynamics Trends 
    14501450% ------------------------------------------------------------------------------------------------------------- 
    1451 \section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd})} 
     1451\section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd}{trd})} 
    14521452\label{sec:DIA_trd} 
    14531453 
     
    14641464\mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation 
    14651465(\ie\ at the end of each \textit{dyn....F90} and/or \textit{tra....F90} routines). 
    1466 This capability is controlled by options offered in \nam{trd} namelist. 
     1466This capability is controlled by options offered in \nam{trd}{trd} namelist. 
    14671467Note that the output are done with XIOS, and therefore the \key{iomput} is required. 
    14681468 
    1469 What is done depends on the \nam{trd} logical set to \forcode{.true.}: 
     1469What is done depends on the \nam{trd}{trd} logical set to \forcode{.true.}: 
    14701470 
    14711471\begin{description} 
     
    15131513The on-line computation of floats advected either by the three dimensional velocity field or constraint to 
    15141514remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project. 
    1515 Options are defined by \nam{flo} namelist variables. 
     1515Options are defined by \nam{flo}{flo} namelist variables. 
    15161516The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option), 
    15171517or on a $4^th$ Runge-Hutta algorithm (\np{ln_flork4}{ln\_flork4}\forcode{=.true.}). 
     
    15721572} \\ 
    15731573 
    1574 \np{jpnfl} is the total number of floats during the run. 
     1574\np{jpnfl}{jpnfl} is the total number of floats during the run. 
    15751575When initial positions are read in a restart file (\np{ln_rstflo}{ln\_rstflo}\forcode{=.true.} ), 
    1576 \np{jpnflnewflo} can be added in the initialization file. 
     1576\np{jpnflnewflo}{jpnflnewflo} can be added in the initialization file. 
    15771577 
    15781578\subsubsection{Output data} 
     
    16311631% - \np{nb_ana}{nb\_ana}     is the number of harmonics to analyse 
    16321632 
    1633  - \np{tname}       is an array with names of tidal constituents to analyse 
    1634  
    1635  \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation. 
     1633 - \np{tname}{tname}       is an array with names of tidal constituents to analyse 
     1634 
     1635 \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000}{nit000} and \np{nitend}{nitend} of the simulation. 
    16361636 The restart capability is not implemented. 
    16371637 
     
    20352035 
    20362036In \mdl{diaptr} when \np{ln_diaptr}{ln\_diaptr}\forcode{=.true.} 
    2037 (see the \nam{ptr} namelist below) can be computed on-line the poleward heat and salt transports, 
     2037(see the \nam{ptr}{ptr} namelist below) can be computed on-line the poleward heat and salt transports, 
    20382038their advective and diffusive component, and the meriodional stream function . 
    20392039When \np{ln_subbas}{ln\_subbas}\forcode{=.true.}, transports and stream function are computed for the Atlantic, Indian, 
     
    21092109Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step. 
    21102110 
    2111 The variables can be activated by setting the \np{nn_diacfl}{nn\_diacfl} namelist parameter to 1 in the \nam{ctl} namelist. 
     2111The variables can be activated by setting the \np{nn_diacfl}{nn\_diacfl} namelist parameter to 1 in the \nam{ctl}{ctl} namelist. 
    21122112The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. 
    21132113In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

    r11577 r11578  
    3636both must be added to a foundation SST to obtain the true skin temperature. 
    3737 
    38 Both the cool skin and warm layer models are controlled through the namelist \nam{diu}: 
     38Both the cool skin and warm layer models are controlled through the namelist \nam{diu}{diu}: 
    3939 
    4040\begin{listing} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11577 r11578  
    335335 
    336336Two typical methods are available to specify the spatial domain configuration; 
    337 they can be selected using parameter \np{ln_read_cfg}{ln\_read\_cfg} parameter in namelist \nam{cfg}. 
     337they can be selected using parameter \np{ln_read_cfg}{ln\_read\_cfg} parameter in namelist \nam{cfg}{cfg}. 
    338338 
    339339If \np{ln_read_cfg}{ln\_read\_cfg} is set to \forcode{.true.}, 
    340340the domain-specific parameters and fields are read from a netCDF input file, 
    341 whose name (without its .nc suffix) can be specified as the value of the \np{cn_domcfg}{cn\_domcfg} parameter in namelist \nam{cfg}. 
     341whose name (without its .nc suffix) can be specified as the value of the \np{cn_domcfg}{cn\_domcfg} parameter in namelist \nam{cfg}{cfg}. 
    342342 
    343343If \np{ln_read_cfg}{ln\_read\_cfg} is set to \forcode{.false.}, 
     
    502502a single configuration file can support both options. 
    503503 
    504 By default a non-linear free surface is used (\np{ln_linssh}{ln\_linssh} set to \forcode{=.false.} in \nam{dom}): 
     504By default a non-linear free surface is used (\np{ln_linssh}{ln\_linssh} set to \forcode{=.false.} in \nam{dom}{dom}): 
    505505the coordinate follow the time-variation of the free surface so that the transformation is time dependent: 
    506506$z(i,j,k,t)$ (\eg\ \autoref{fig:DOM_z_zps_s_sps}f). 
    507 When a linear free surface is assumed (\np{ln_linssh}{ln\_linssh} set to \forcode{=.true.} in \nam{dom}), 
     507When a linear free surface is assumed (\np{ln_linssh}{ln\_linssh} set to \forcode{=.true.} in \nam{dom}{dom}), 
    508508the vertical coordinates are fixed in time, but the seawater can move up and down across the $z_0$ surface 
    509509(in other words, the top of the ocean in not a rigid lid). 
     
    652652(grid-point position, scale factors) 
    653653can be saved in a file if 
    654 namelist parameter \np{ln_write_cfg}{ln\_write\_cfg} (namelist \nam{cfg}) is set to \forcode{.true.}; 
     654namelist parameter \np{ln_write_cfg}{ln\_write\_cfg} (namelist \nam{cfg}{cfg}) is set to \forcode{.true.}; 
    655655the output filename is set through parameter \np{cn_domcfg_out}{cn\_domcfg\_out}. 
    656656This is only really useful if 
     
    661661(grid-point position, scale factors, depths and masks) 
    662662can be saved in a file called \texttt{mesh\_mask} if 
    663 namelist parameter \np{ln_meshmask}{ln\_meshmask} (namelist \nam{dom}) is set to \forcode{.true.}. 
     663namelist parameter \np{ln_meshmask}{ln\_meshmask} (namelist \nam{dom}{dom}) is set to \forcode{.true.}. 
    664664This file contains additional fields that can be useful for post-processing applications. 
    665665 
     
    677677%------------------------------------------------------------------------------------------ 
    678678 
    679 Basic initial state options are defined in \nam{tsd}. 
     679Basic initial state options are defined in \nam{tsd}{tsd}. 
    680680By default, the ocean starts from rest (the velocity field is set to zero) and 
    681681the initialization of temperature and salinity fields is controlled through the \np{ln_tsd_init}{ln\_tsd\_init} namelist parameter. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11577 r11578  
    327327A key point in \autoref{eq:DYN_een_e3f} is how the averaging in the \textbf{i}- and \textbf{j}- directions is made. 
    328328It uses the sum of masked t-point vertical scale factor divided either by the sum of the four t-point masks 
    329 (\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=1}), or just by $4$ (\np{nn\_een\_e3f}\forcode{=.true.}). 
     329(\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=1}), or just by $4$ (\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=.true.}). 
    330330The latter case preserves the continuity of $e_{3f}$ when one or more of the neighbouring $e_{3t}$ tends to zero and 
    331331extends by continuity the value of $e_{3f}$ into the land areas. 
     
    904904    In this particular exemple, 
    905905    a boxcar averaging window over \np{nn_baro}{nn\_baro} barotropic time steps is used 
    906     (\np{nn\_bt\_flt}\forcode{=1}) and \np{nn_baro}{nn\_baro}\forcode{=5}. 
     906    (\np{nn_bt_flt}{nn\_bt\_flt}\forcode{=1}) and \np{nn_baro}{nn\_baro}\forcode{=5}. 
    907907    Internal mode time steps (which are also the model time steps) are denoted by 
    908908    $t-\rdt$, $t$ and $t+\rdt$. 
     
    12651265%------------------------------------------------------------------------------------------------------------- 
    12661266 
    1267 Options are defined through the \nam{zdf} namelist variables. 
     1267Options are defined through the \nam{zdf}{zdf} namelist variables. 
    12681268The large vertical diffusion coefficient found in the surface mixed layer together with high vertical resolution implies that in the case of explicit time stepping there would be too restrictive a constraint on the time step. 
    12691269Two time stepping schemes can be used for the vertical diffusion term: 
     
    14091409flux is from a cell with water depth greater than \np{rn_wdmin1}{rn\_wdmin1} and 0 otherwise. If the user sets 
    14101410\np{ln_wd_dl_ramp}{ln\_wd\_dl\_ramp}\forcode{=.true.} the flux across the face is ramped down as the water depth decreases 
    1411 from 2 * \np{rn_wdmin1}{rn\_wdmin1} to \np{rn\_wdmin1}. The use of this ramp reduced grid-scale noise in idealised test cases. 
     1411from 2 * \np{rn_wdmin1}{rn\_wdmin1} to \np{rn_wdmin1}{rn\_wdmin1}. The use of this ramp reduced grid-scale noise in idealised test cases. 
    14121412 
    14131413At the point where the flux across a $u$-face is multiplied by zuwdmask , we have chosen 
     
    16491649%------------------------------------------------------------------------------------------------------------- 
    16501650 
    1651 Options are defined through the \nam{dom} namelist variables. 
     1651Options are defined through the \nam{dom}{dom} namelist variables. 
    16521652The general framework for dynamics time stepping is a leap-frog scheme, 
    16531653\ie\ a three level centred time scheme associated with an Asselin time filter (cf. \autoref{chap:TD}). 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11577 r11578  
    4343%The process of defining which areas are to be masked is described in \autoref{subsec:DOM_msk}. 
    4444 
    45 Options are defined through the \nam{lbc} namelist variables. 
     45Options are defined through the \nam{lbc}{lbc} namelist variables. 
    4646The discrete representation of a domain with complex boundaries (coastlines and bottom topography) leads to 
    4747arrays that include large portions where a computation is not required as the model variables remain at zero. 
     
    173173 
    174174The choice of closed or cyclic model domain boundary condition is made by 
    175 setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}. 
     175setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}. 
    176176Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}. 
    177177The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$, 
     
    296296The total number of subdomains corresponds to the number of MPI processes allocated to \NEMO\ when the model is launched 
    297297(\ie\ mpirun -np x ./nemo will automatically give x subdomains). 
    298 The i-axis is divided by \np{jpni} and the j-axis by \np{jpnj}. 
    299 These parameters are defined in \nam{mpp} namelist. 
    300 If \np{jpni} and \np{jpnj} are < 1, they will be automatically redefined in the code to give the best domain decomposition 
     298The i-axis is divided by \np{jpni}{jpni} and the j-axis by \np{jpnj}{jpnj}. 
     299These parameters are defined in \nam{mpp}{mpp} namelist. 
     300If \np{jpni}{jpni} and \np{jpnj}{jpnj} are < 1, they will be automatically redefined in the code to give the best domain decomposition 
    301301(see bellow). 
    302302 
     
    330330  N_{mpi} = jpni \times jpnj - N_{land} + N_{useless} 
    331331\] 
    332 $N_{land}$ is the total number of land subdomains in the domain decomposition defined by \np{jpni} and \np{jpnj}. $N_{useless}$ is the number of land subdomains that are kept in the compuational domain in order to make sure that $N_{mpi}$ MPI processes are indeed allocated to a given subdomain. The values of $N_{mpi}$, \np{jpni}, \np{jpnj},  $N_{land}$ and $N_{useless}$ are printed in the output file \texttt{ocean.output}. $N_{useless}$ must, of course, be as small as possible to limit the waste of ressources. A warning is issued in  \texttt{ocean.output} if $N_{useless}$ is not zero. Note that non-zero value of $N_{useless}$ is uselly required when using AGRIF as, up to now, the parent grid and each of the child grids must use all the $N_{mpi}$ processes. 
    333  
    334 If the domain decomposition is automatically defined (when \np{jpni} and \np{jpnj} are < 1), the decomposition chosen by the model will minimise the sub-domain size (defined as $max_{all domains}(jpi \times jpj)$) and maximize the number of eliminated land subdomains. This means that no other domain decomposition (a set of \np{jpni} and \np{jpnj} values) will use less processes than $(jpni  \times  jpnj - N_{land})$ and get a smaller subdomain size. 
    335 In order to specify $N_{mpi}$ properly (minimize $N_{useless}$), you must run the model once with \np{ln_list}{ln\_list} activated. In this case, the model will start the initialisation phase, print the list of optimum decompositions ($N_{mpi}$, \np{jpni} and \np{jpnj}) in \texttt{ocean.output} and directly abort. The maximum value of $N_{mpi}$ tested in this list is given by $max(N_{MPI\_tasks}, jpni \times jpnj)$. For example, run the model on 40 nodes with ln\_list activated and $jpni = 10000$ and $jpnj = 1$, will print the list of optimum domains decomposition from 1 to about 10000. 
    336  
    337 Processors are numbered from 0 to $N_{mpi} - 1$. Subdomains containning some ocean points are numbered first from 0 to $jpni * jpnj - N_{land} -1$. The remaining $N_{useless}$ land subdomains are numbered next, which means that, for a given (\np{jpni}, \np{jpnj}), the numbers attributed to he ocean subdomains do not vary with $N_{useless}$. 
     332$N_{land}$ is the total number of land subdomains in the domain decomposition defined by \np{jpni}{jpni} and \np{jpnj}{jpnj}. $N_{useless}$ is the number of land subdomains that are kept in the compuational domain in order to make sure that $N_{mpi}$ MPI processes are indeed allocated to a given subdomain. The values of $N_{mpi}$, \np{jpni}{jpni}, \np{jpnj}{jpnj},  $N_{land}$ and $N_{useless}$ are printed in the output file \texttt{ocean.output}. $N_{useless}$ must, of course, be as small as possible to limit the waste of ressources. A warning is issued in  \texttt{ocean.output} if $N_{useless}$ is not zero. Note that non-zero value of $N_{useless}$ is uselly required when using AGRIF as, up to now, the parent grid and each of the child grids must use all the $N_{mpi}$ processes. 
     333 
     334If the domain decomposition is automatically defined (when \np{jpni}{jpni} and \np{jpnj}{jpnj} are < 1), the decomposition chosen by the model will minimise the sub-domain size (defined as $max_{all domains}(jpi \times jpj)$) and maximize the number of eliminated land subdomains. This means that no other domain decomposition (a set of \np{jpni}{jpni} and \np{jpnj}{jpnj} values) will use less processes than $(jpni  \times  jpnj - N_{land})$ and get a smaller subdomain size. 
     335In order to specify $N_{mpi}$ properly (minimize $N_{useless}$), you must run the model once with \np{ln_list}{ln\_list} activated. In this case, the model will start the initialisation phase, print the list of optimum decompositions ($N_{mpi}$, \np{jpni}{jpni} and \np{jpnj}{jpnj}) in \texttt{ocean.output} and directly abort. The maximum value of $N_{mpi}$ tested in this list is given by $max(N_{MPI\_tasks}, jpni \times jpnj)$. For example, run the model on 40 nodes with ln\_list activated and $jpni = 10000$ and $jpnj = 1$, will print the list of optimum domains decomposition from 1 to about 10000. 
     336 
     337Processors are numbered from 0 to $N_{mpi} - 1$. Subdomains containning some ocean points are numbered first from 0 to $jpni * jpnj - N_{land} -1$. The remaining $N_{useless}$ land subdomains are numbered next, which means that, for a given (\np{jpni}{jpni}, \np{jpnj}{jpnj}), the numbers attributed to he ocean subdomains do not vary with $N_{useless}$. 
    338338 
    339339When land processors are eliminated, the value corresponding to these locations in the model output files is undefined. \np{ln_mskland}{ln\_mskland} must be activated in order avoid Not a Number values in output files. Note that it is better to not eliminate land processors when creating a meshmask file (\ie\ when setting a non-zero value to \np{nn_msh}{nn\_msh}). 
     
    378378%----------------------------------------------------------------------------------------------- 
    379379 
    380 Options are defined through the \nam{bdy} and \nam{bdy_dta}{bdy\_dta} namelist variables. 
     380Options are defined through the \nam{bdy}{bdy} and \nam{bdy_dta}{bdy\_dta} namelist variables. 
    381381The BDY module is the core implementation of open boundary conditions for regional configurations on 
    382382ocean temperature, salinity, barotropic-baroclinic velocities, ice-snow concentration, thicknesses, temperatures, salinity and melt ponds concentration and thickness. 
     
    397397The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}. 
    398398Each boundary set can be either defined as a series of straight line segments directly in the namelist 
    399 (\np{ln_coords_file}{ln\_coords\_file}\forcode{=.false.}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np{ln\_coords\_file}\forcode{=.true.}, and a ``\ifile{coordinates.bdy}'' file must be provided). 
     399(\np{ln_coords_file}{ln\_coords\_file}\forcode{=.false.}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np{ln_coords_file}{ln\_coords\_file}\forcode{=.true.}, and a ``\ifile{coordinates.bdy}'' file must be provided). 
    400400The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file. 
    401401In the example above, there are two boundary sets, the first of which is defined via a file and 
     
    422422 
    423423The boundary data is either set to initial conditions 
    424 (\np{nn_tra_dta}{nn\_tra\_dta}\forcode{=0}) or forced with external data from a file (\np{nn\_tra\_dta}\forcode{=1}). 
     424(\np{nn_tra_dta}{nn\_tra\_dta}\forcode{=0}) or forced with external data from a file (\np{nn_tra_dta}{nn\_tra\_dta}\forcode{=1}). 
    425425In case the 3d velocity data contain the total velocity (ie, baroclinic and barotropic velocity), 
    426426the bdy code can derived baroclinic and barotropic velocities by setting \np{ln_full_vel}{ln\_full\_vel}\forcode{=.true.} 
    427427For the barotropic solution there is also the option to use tidal harmonic forcing either by 
    428 itself (\np{nn_dyn2d_dta}{nn\_dyn2d\_dta}\forcode{=2}) or in addition to other external data (\np{nn\_dyn2d\_dta}\forcode{=3}).\\ 
     428itself (\np{nn_dyn2d_dta}{nn\_dyn2d\_dta}\forcode{=2}) or in addition to other external data (\np{nn_dyn2d_dta}{nn\_dyn2d\_dta}\forcode{=3}).\\ 
    429429If not set to initial conditions, sea-ice salinity, temperatures and melt ponds data at the boundary can either be read in a file or defined as constant (by \np{rn_ice_sal}{rn\_ice\_sal}, \np{rn_ice_tem}{rn\_ice\_tem}, \np{rn_ice_apnd}{rn\_ice\_apnd}, \np{rn_ice_hpnd}{rn\_ice\_hpnd}). Ice age is constant and defined by \np{rn_ice_age}{rn\_ice\_age}. 
    430430 
     
    700700tides (i.e., in \nam{_tide}{\_tide}, \np{ln_tide}{ln\_tide} needs to be set to 
    701701\forcode{.true.} and the required constituents need to be activated by 
    702 including their names in the \np{clname} array; see 
     702including their names in the \np{clname}{clname} array; see 
    703703\autoref{sec:SBC_tide}). Specific options related to the reading in of 
    704704the complex harmonic amplitudes of elevation (SSH) and barotropic 
     
    715715separately: when two-dimensional data is used, variables 
    716716\textit{tcname\_z1} and \textit{tcname\_z2} for real and imaginary SSH, 
    717 respectively, are expected in input file \np{filtide} with suffix 
     717respectively, are expected in input file \np{filtide}{filtide} with suffix 
    718718\ifile{\_grid\_T}, variables \textit{tcname\_u1} and 
    719719\textit{tcname\_u2} for real and imaginary u, respectively, are 
    720 expected in input file \np{filtide} with suffix \ifile{\_grid\_U}, and 
     720expected in input file \np{filtide}{filtide} with suffix \ifile{\_grid\_U}, and 
    721721\textit{tcname\_v1} and \textit{tcname\_v2} for real and imaginary v, 
    722 respectively, are expected in input file \np{filtide} with suffix 
     722respectively, are expected in input file \np{filtide}{filtide} with suffix 
    723723\ifile{\_grid\_V}; when data along open boundary segments is used, 
    724724variables \textit{z1} and \textit{z2} (real and imaginary part of SSH) 
    725 are expected to be available from file \np{filtide} with suffix 
     725are expected to be available from file \np{filtide}{filtide} with suffix 
    726726\ifile{tcname\_grid\_T}, variables \textit{u1} and \textit{u2} (real 
    727727and imaginary part of u) are expected to be available from file 
    728 \np{filtide} with suffix \ifile{tcname\_grid\_U}, and variables 
     728\np{filtide}{filtide} with suffix \ifile{tcname\_grid\_U}, and variables 
    729729\textit{v1} and \textit{v2} (real and imaginary part of v) are 
    730 expected to be available from file \np{filtide} with suffix 
     730expected to be available from file \np{filtide}{filtide} with suffix 
    731731\ifile{tcname\_grid\_V}. If \np{ln_bdytide_conj}{ln\_bdytide\_conj} is set to 
    732732\forcode{.true.}, the data is expected to be in complex conjugate 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

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    332332decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}. 
    333333Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05. 
    334 The provided fields can either be 2d (\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn\_aht\_ijk\_t}\forcode{=-30},  \np{nn\_ahm\_ijk\_t}\forcode{=-30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}). 
     334The provided fields can either be 2d (\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-30},  \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}). 
    335335 
    336336%-------------------------------------------------TABLE--------------------------------------------------- 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11577 r11578  
    3232The OBS code is called from \mdl{nemogcm} for model initialisation and to calculate the model equivalent values for observations on the 0th time step. 
    3333The code is then called again after each time step from \mdl{step}. 
    34 The code is only activated if the \nam{obs} namelist logical \np{ln_diaobs}{ln\_diaobs} is set to true. 
     34The code is only activated if the \nam{obs}{obs} namelist logical \np{ln_diaobs}{ln\_diaobs} is set to true. 
    3535 
    3636For all data types a 2D horizontal interpolator or averager is needed to 
     
    4848Otherwise (by default) the model value from the nearest time step to the observation time is used. 
    4949 
    50 The code is controlled by the namelist \nam{obs}. 
     50The code is controlled by the namelist \nam{obs}{obs}. 
    5151See the following sections for more details on setting up the namelist. 
    5252 
     
    9292\end{enumerate} 
    9393 
    94 Options are defined through the \nam{obs} namelist variables. 
     94Options are defined through the \nam{obs}{obs} namelist variables. 
    9595The options \np{ln_t3d}{ln\_t3d} and \np{ln_s3d}{ln\_s3d} switch on the temperature and salinity profile observation operator code. 
    9696The filename or array of filenames are specified using the \np{cn_profbfiles}{cn\_profbfiles} variable. 
     
    114114\label{sec:OBS_details} 
    115115 
    116 Here we show a more complete example namelist \nam{obs} and also show the NetCDF headers of 
     116Here we show a more complete example namelist \nam{obs}{obs} and also show the NetCDF headers of 
    117117the observation files that may be used with the observation operator. 
    118118 
     
    896896%-------------------------------------------------------------------------------------------------------- 
    897897\subsection{Configuring the standalone observation operator} 
    898 The observation files and settings understood by \nam{obs} have been outlined in the online observation operator section. 
    899 In addition is a further namelist \nam{sao} which used to set the input model fields for the SAO 
     898The observation files and settings understood by \nam{obs}{obs} have been outlined in the online observation operator section. 
     899In addition is a further namelist \nam{sao}{sao} which used to set the input model fields for the SAO 
    900900 
    901901\subsubsection{Single field} 
     
    907907\textbf{votemper}, \textbf{vosaline} and optionally \textbf{sshn} present. 
    908908 
    909 For each field read there must be an entry in the \nam{sao} namelist specifying 
     909For each field read there must be an entry in the \nam{sao}{sao} namelist specifying 
    910910the name of the file to read and the index along the \emph{time\_counter}. 
    911911For example, to read the second time counter from a single file the namelist would be. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11577 r11578  
    3737 
    3838Four different ways are available to provide the seven fields to the ocean. They are controlled by 
    39 namelist \nam{sbc} variables: 
     39namelist \nam{sbc}{sbc} variables: 
    4040 
    4141\begin{itemize} 
     
    842842 
    843843The optional atmospheric pressure can be used to force ocean and ice dynamics 
    844 (\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc} namelist). 
     844(\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc}{sbc} namelist). 
    845845The input atmospheric forcing defined via \np{sn_apr}{sn\_apr} structure (\nam{sbc_apr}{sbc\_apr} namelist) 
    846846can be interpolated in time to the model time step, and even in space when the interpolation on-the-fly is used. 
     
    10701070%-------------------------------------------------------------------------------------------------------- 
    10711071 
    1072 The namelist variable in \nam{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation. 
     1072The namelist variable in \nam{sbc}{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation. 
    10731073Description and result of sensitivity test to \np{nn_isf}{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}. 
    10741074The different options are illustrated in \autoref{fig:SBC_isf}. 
     
    12661266(Note that the authors kindly provided a copy of their code to act as a basis for implementation in \NEMO). 
    12671267Icebergs are initially spawned into one of ten classes which have specific mass and thickness as 
    1268 described in the \nam{berg} namelist: \np{rn_initial_mass}{rn\_initial\_mass} and \np{rn_initial_thickness}{rn\_initial\_thickness}. 
     1268described in the \nam{berg}{berg} namelist: \np{rn_initial_mass}{rn\_initial\_mass} and \np{rn_initial_thickness}{rn\_initial\_thickness}. 
    12691269Each class has an associated scaling (\np{rn_mass_scaling}{rn\_mass\_scaling}), 
    12701270which is an integer representing how many icebergs of this class are being described as one lagrangian point 
     
    13431343 
    13441344Physical processes related to ocean surface waves can be accounted by setting the logical variable 
    1345 \np{ln_wave}{ln\_wave}\forcode{=.true.} in \nam{sbc} namelist. In addition, specific flags accounting for 
     1345\np{ln_wave}{ln\_wave}\forcode{=.true.} in \nam{sbc}{sbc} namelist. In addition, specific flags accounting for 
    13461346different processes should be activated as explained in the following sections. 
    13471347 
     
    13521352Input Data generic Interface (see \autoref{sec:SBC_input}). 
    13531353\item[coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np{ln_cpl}{ln\_cpl} \forcode{= .true.} 
    1354 in \nam{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist. 
     1354in \nam{sbc}{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist. 
    13551355\end{description} 
    13561356 
     
    13641364 
    13651365The neutral surface drag coefficient provided from an external data source (\ie\ a wave model), 
    1366 can be used by setting the logical variable \np{ln_cdgw}{ln\_cdgw} \forcode{= .true.} in \nam{sbc} namelist. 
     1366can be used by setting the logical variable \np{ln_cdgw}{ln\_cdgw} \forcode{= .true.} in \nam{sbc}{sbc} namelist. 
    13671367Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided, 
    13681368the drag coefficient is computed according to the stable/unstable conditions of the 
     
    15611561assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF. 
    15621562The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO\ by 
    1563 setting \np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}} namelist variable) when 
     1563setting \np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}{sbc}} namelist variable) when 
    15641564using a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.}) or 
    15651565the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}). 
     
    16681668The presence at the sea surface of an ice covered area modifies all the fluxes transmitted to the ocean. 
    16691669There are several way to handle sea-ice in the system depending on 
    1670 the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc} namelist. 
     1670the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc}{sbc} namelist. 
    16711671\begin{description} 
    16721672\item[nn\_ice = 0] 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

    r11577 r11578  
    172172The \np{ln_sto_eos}{ln\_sto\_eos} namelist variable activates stochastic parametrisation of equation of state. 
    173173By default it set to \forcode{.false.}) and not active. 
    174 The set of parameters is available in \nam{sto} namelist 
     174The set of parameters is available in \nam{sto}{sto} namelist 
    175175(only the subset for equation of state stochastic parametrisation is listed below): 
    176176%---------------------------------------namsto-------------------------------------------------- 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11577 r11578  
    635635%-------------------------------------------------------------------------------------------------------------- 
    636636 
    637 Options are defined through the \nam{zdf} namelist variables. 
     637Options are defined through the \nam{zdf}{zdf} namelist variables. 
    638638The formulation of the vertical subgrid scale tracer physics is the same for all the vertical coordinates, 
    639639and is based on a laplacian operator. 
     
    898898(\ie\ the one associated with the Antarctic Bottom Water) by a few Sverdrups \citep{emile-geay.madec_OS09}. 
    899899 
    900 Options are defined through the \nam{bbc} namelist variables. 
     900Options are defined through the \nam{bbc}{bbc} namelist variables. 
    901901The presence of geothermal heating is controlled by setting the namelist parameter \np{ln_trabbc}{ln\_trabbc} to true. 
    902902Then, when \np{nn_geoflx}{nn\_geoflx} is set to 1, a constant geothermal heating is introduced whose value is given by 
     
    919919%-------------------------------------------------------------------------------------------------------------- 
    920920 
    921 Options are defined through the \nam{bbl} namelist variables. 
     921Options are defined through the \nam{bbl}{bbl} namelist variables. 
    922922In a $z$-coordinate configuration, the bottom topography is represented by a series of discrete steps. 
    923923This is not adequate to represent gravity driven downslope flows. 
     
    10981098The restoring term is added when the namelist parameter \np{ln_tradmp}{ln\_tradmp} is set to true. 
    10991099It also requires that both \np{ln_tsd_init}{ln\_tsd\_init} and \np{ln_tsd_dmp}{ln\_tsd\_dmp} are set to true in 
    1100 \nam{tsd} namelist as well as \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures are correctly set 
     1100\nam{tsd}{tsd} namelist as well as \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures are correctly set 
    11011101(\ie\ that $T_o$ and $S_o$ are provided in input files and read using \mdl{fldread}, 
    11021102see \autoref{subsec:SBC_fldread}). 
     
    11381138%-------------------------------------------------------------------------------------------------------------- 
    11391139 
    1140 Options are defined through the \nam{dom} namelist variables. 
     1140Options are defined through the \nam{dom}{dom} namelist variables. 
    11411141The general framework for tracer time stepping is a modified leap-frog scheme \citep{leclair.madec_OM09}, 
    11421142\ie\ a three level centred time scheme associated with a Asselin time filter (cf. \autoref{sec:TD_mLF}): 
     
    12131213density in the World Ocean varies by no more than 2$\%$ from that value \citep{gill_bk82}. 
    12141214 
    1215 Options which control the EOS used are defined through the \nam{eos} namelist variables. 
     1215Options which control the EOS used are defined through the \nam{eos}{eos} namelist variables. 
    12161216 
    12171217\begin{description} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r11577 r11578  
    6161\label{subsec:ZDF_cst} 
    6262 
    63 Options are defined through the \nam{zdf} namelist variables. 
     63Options are defined through the \nam{zdf}{zdf} namelist variables. 
    6464When \np{ln_zdfcst}{ln\_zdfcst} is defined, the momentum and tracer vertical eddy coefficients are set to 
    6565constant values over the whole ocean. 
     
    211211too weak vertical diffusion. 
    212212They must be specified at least larger than the molecular values, and are set through \np{rn_avm0}{rn\_avm0} and 
    213 \np{rn_avt0}{rn\_avt0} (\nam{zdf} namelist, see \autoref{subsec:ZDF_cst}). 
     213\np{rn_avt0}{rn\_avt0} (\nam{zdf}{zdf} namelist, see \autoref{subsec:ZDF_cst}). 
    214214 
    215215\subsubsection{Turbulent length scale} 
     
    225225which is valid in a stable stratified region with constant values of the Brunt-Vais\"{a}l\"{a} frequency. 
    226226The resulting length scale is bounded by the distance to the surface or to the bottom 
    227 (\np{nn_mxl}{nn\_mxl}\forcode{=0}) or by the local vertical scale factor (\np{nn\_mxl}\forcode{=1}). 
     227(\np{nn_mxl}{nn\_mxl}\forcode{=0}) or by the local vertical scale factor (\np{nn_mxl}{nn\_mxl}\forcode{=1}). 
    228228\citet{blanke.delecluse_JPO93} notice that this simplification has two major drawbacks: 
    229229it makes no sense for locally unstable stratification and the computation no longer uses all 
     
    312312$\alpha_{CB} = 100$ the Craig and Banner's value. 
    313313As the surface boundary condition on TKE is prescribed through $\bar{e}_o = e_{bb} |\tau| / \rho_o$, 
    314 with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter, setting \np{rn\_ebb}\forcode{ = 67.83} corresponds 
     314with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter, setting \np{rn_ebb}{rn\_ebb}\forcode{ = 67.83} corresponds 
    315315to $\alpha_{CB} = 100$. 
    316316Further setting  \np{ln_mxl0}{ln\_mxl0}\forcode{ =.true.},  applies \autoref{eq:ZDF_Lsbc} as the surface boundary condition on the length scale, 
     
    706706%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    707707 
    708 Options are defined through the \nam{zdf} namelist variables. 
     708Options are defined through the \nam{zdf}{zdf} namelist variables. 
    709709The non-penetrative convective adjustment is used when \np{ln_zdfnpc}{ln\_zdfnpc}\forcode{=.true.}. 
    710710It is applied at each \np{nn_npc}{nn\_npc} time step and mixes downwards instantaneously the statically unstable portion of 
     
    750750\label{subsec:ZDF_evd} 
    751751 
    752 Options are defined through the  \nam{zdf} namelist variables. 
     752Options are defined through the  \nam{zdf}{zdf} namelist variables. 
    753753The enhanced vertical diffusion parameterisation is used when \np{ln_zdfevd}{ln\_zdfevd}\forcode{=.true.}. 
    754754In this case, the vertical eddy mixing coefficients are assigned very large values 
     
    811811 
    812812This parameterisation has been introduced in \mdl{zdfddm} module and is controlled by the namelist parameter 
    813 \np{ln_zdfddm}{ln\_zdfddm} in \nam{zdf}. 
     813\np{ln_zdfddm}{ln\_zdfddm} in \nam{zdf}{zdf}. 
    814814Double diffusion occurs when relatively warm, salty water overlies cooler, fresher water, or vice versa. 
    815815The former condition leads to salt fingering and the latter to diffusive convection. 
     
    919919%-------------------------------------------------------------------------------------------------------------- 
    920920 
    921 Options to define the top and bottom friction are defined through the \nam{drg} namelist variables. 
     921Options to define the top and bottom friction are defined through the \nam{drg}{drg} namelist variables. 
    922922The bottom friction represents the friction generated by the bathymetry. 
    923923The top friction represents the friction generated by the ice shelf/ocean interface. 
     
    11421142An optional implicit form of bottom friction has been implemented to improve model stability. 
    11431143We recommend this option for shelf sea and coastal ocean applications. %, especially for split-explicit time splitting. 
    1144 This option can be invoked by setting \np{ln_drgimp}{ln\_drgimp} to \forcode{.true.} in the \nam{drg} namelist. 
    1145 %This option requires \np{ln_zdfexp}{ln\_zdfexp} to be \forcode{.false.} in the \nam{zdf} namelist. 
     1144This option can be invoked by setting \np{ln_drgimp}{ln\_drgimp} to \forcode{.true.} in the \nam{drg}{drg} namelist. 
     1145%This option requires \np{ln_zdfexp}{ln\_zdfexp} to be \forcode{.false.} in the \nam{zdf}{zdf} namelist. 
    11461146 
    11471147This implementation is performed in \mdl{dynzdf} where the following boundary conditions are set while solving the fully implicit diffusion step: 
     
    11701170\label{subsec:ZDF_drg_ts} 
    11711171 
    1172 With split-explicit free surface, the sub-stepping of barotropic equations needs the knowledge of top/bottom stresses. An obvious way to satisfy this is to take them as constant over the course of the barotropic integration and equal to the value used to update the baroclinic momentum trend. Provided \np{ln_drgimp}{ln\_drgimp}\forcode{= .false.} and a centred or \textit{leap-frog} like integration of barotropic equations is used (\ie\ \forcode{ln_bt_fw=.false.}, cf \autoref{subsec:DYN_spg_ts}), this does ensure that barotropic and baroclinic dynamics feel the same stresses during one leapfrog time step. However, if \np{ln\_drgimp}\forcode{= .true.},  stresses depend on the \textit{after} value of the velocities which themselves depend on the barotropic iteration result. This cyclic dependency makes difficult obtaining consistent stresses in 2d and 3d dynamics. Part of this mismatch is then removed when setting the final barotropic component of 3d velocities to the time splitting estimate. This last step can be seen as a necessary evil but should be minimized since it interferes with the adjustment to the boundary conditions. 
     1172With split-explicit free surface, the sub-stepping of barotropic equations needs the knowledge of top/bottom stresses. An obvious way to satisfy this is to take them as constant over the course of the barotropic integration and equal to the value used to update the baroclinic momentum trend. Provided \np{ln_drgimp}{ln\_drgimp}\forcode{= .false.} and a centred or \textit{leap-frog} like integration of barotropic equations is used (\ie\ \forcode{ln_bt_fw=.false.}, cf \autoref{subsec:DYN_spg_ts}), this does ensure that barotropic and baroclinic dynamics feel the same stresses during one leapfrog time step. However, if \np{ln_drgimp}{ln\_drgimp}\forcode{= .true.},  stresses depend on the \textit{after} value of the velocities which themselves depend on the barotropic iteration result. This cyclic dependency makes difficult obtaining consistent stresses in 2d and 3d dynamics. Part of this mismatch is then removed when setting the final barotropic component of 3d velocities to the time splitting estimate. This last step can be seen as a necessary evil but should be minimized since it interferes with the adjustment to the boundary conditions. 
    11731173 
    11741174The strategy to handle top/bottom stresses with split-explicit free surface in \NEMO\ is as follows: 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r11577 r11578  
    2424The reference configurations also provide a sense for some of the options available in the code, 
    2525though by no means are all options exercised in the reference configurations. 
    26 Configuration is defined manually through the \nam{cfg} namelist variables. 
     26Configuration is defined manually through the \nam{cfg}{cfg} namelist variables. 
    2727 
    2828%------------------------------------------namcfg---------------------------------------------------- 
     
    8888https://doi.org/10.5281/zenodo.2640723 
    8989 
    90 In this namelist\_cfg the name of domain input file is set in \nam{cfg} block of namelist. 
     90In this namelist\_cfg the name of domain input file is set in \nam{cfg}{cfg} block of namelist. 
    9191 
    9292%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    253253 
    254254The GYRE configuration is set like an analytical configuration. 
    255 Through \np{ln_read_cfg}{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg} namelist defined in 
     255Through \np{ln_read_cfg}{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg}{cfg} namelist defined in 
    256256the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg} 
    257257analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r11577 r11578  
    110110    \textit{Left}: a closea\_mask field; 
    111111    \textit{Right}: a closea\_mask\_rnf field. 
    112     In this example, if \protect\np{ln\_closea} is set to \forcode{.true.}, 
     112    In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.}, 
    113113    the mean freshwater flux over each of the American Great Lakes will be set to zero, 
    114114    and the total residual for all the lakes, if negative, will be put into 
     
    218218\end{cmds} 
    219219 
    220 \item Add the logical switch \np{ln_use_jattr}{ln\_use\_jattr} to \nam{cfg} in the configuration 
     220\item Add the logical switch \np{ln_use_jattr}{ln\_use\_jattr} to \nam{cfg}{cfg} in the configuration 
    221221namelist (if it is not already there) and set \forcode{.true.} 
    222222\end{itemize} 
     
    331331be set at all the locations actually required by each individual for the fold operation. 
    332332This alternative method should give identical results to the default \textsc{ALLGATHER} method and 
    333 is recommended for large values of \np{jpni}. 
    334 The new method is activated by setting \np{ln_nnogather}{ln\_nnogather} to be true (\nam{mpp}). 
     333is recommended for large values of \np{jpni}{jpni}. 
     334The new method is activated by setting \np{ln_nnogather}{ln\_nnogather} to be true (\nam{mpp}{mpp}). 
    335335The reproducibility of results using the two methods should be confirmed for each new, 
    336336non-reference configuration. 
     
    350350%-------------------------------------------------------------------------------------------------------------- 
    351351 
    352 Options are defined through the  \nam{ctl} namelist variables. 
     352Options are defined through the  \nam{ctl}{ctl} namelist variables. 
    353353 
    354354\subsection{Vector optimisation} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11577 r11578  
    141141The general idea is to solve the free surface equation with a small time step, 
    142142while the three dimensional prognostic variables are solved with a longer time step that 
    143 is a multiple of \np{rdtbt} in the \nam{dom} namelist (Figure III.3). 
     143is a multiple of \np{rdtbt}{rdtbt} in the \nam{dom}{dom} namelist (Figure III.3). 
    144144 
    145145%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
     
    296296The extra term introduced in the equations (see {\S}I.2.2) is solved implicitly. 
    297297The elliptic solvers available in the code are documented in \autoref{chap:MISC}. 
    298 The amplitude of the extra term is given by the namelist variable \np{rnu}. 
     298The amplitude of the extra term is given by the namelist variable \np{rnu}{rnu}. 
    299299The default value is 1, as recommended by \citet{Roullet2000?} 
    300300 
    301 \colorbox{red}{\np{rnu}\forcode{=1} to be suppressed from namelist !} 
     301\colorbox{red}{\np{rnu}{rnu}\forcode{=1} to be suppressed from namelist !} 
    302302 
    303303%------------------------------------------------------------- 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11577 r11578  
    298298is missing, an Euler time stepping scheme is imposed. A forward initial step can still be enforced by the user by setting 
    299299the namelist variable \np{nn_euler}{nn\_euler}\forcode{=0}. Other options to control the time integration of the model 
    300 are defined through the  \nam{run} namelist variables. 
     300are defined through the  \nam{run}{run} namelist variables. 
    301301%%% 
    302302\gmcomment{ 
     
    322322%-------------------------------------------------------------------------------------------------------------- 
    323323 
    324 Options are defined through the  \nam{dom} namelist variables. 
     324Options are defined through the  \nam{dom}{dom} namelist variables. 
    325325 \colorbox{yellow}{add here a few word on nit000 and nitend} 
    326326 
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