Changeset 11537


Ignore:
Timestamp:
2019-09-12T10:24:48+02:00 (13 months ago)
Author:
clem
Message:

make sure SI3 doc can be compiled, plus small edits

Location:
NEMO/trunk/doc/latex
Files:
26 edited
1 moved

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

    r11435 r11537  
    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}=0) employs constant weights, 
    6767\begin{align} 
    6868  \label{eq: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}=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_CONFIG.tex

    r11435 r11537  
    254254 
    255255The GYRE configuration is set like an analytical configuration. 
    256 Through \np{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg} namelist defined in 
     256Through \np{ln\_read\_cfg}\forcode{=.false.} in \nam{cfg} namelist defined in 
    257257the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg} 
    258258analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. 
     
    266266Obviously, the namelist parameters have to be adjusted to the chosen resolution, 
    267267see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations). 
    268 In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}). 
     268In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{=31}) (\autoref{fig:zgr}). 
    269269 
    270270The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and 
     
    272272For example, keeping a same model size on each processor while increasing the number of processor used is very easy, 
    273273even though the physical integrity of the solution can be compromised. 
    274 Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \nam{usr\_def} in 
     274Benchmark is activate via \np{ln\_bench}\forcode{=.true.} in \nam{usr\_def} in 
    275275namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}. 
    276276 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

    r11536 r11537  
    125125 
    126126XIOS may be used to read single file restart produced by \NEMO. Currently only the variables written to 
    127 file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np{ln\_xios\_read}\forcode{ = .true. } 
     127file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np{ln\_xios\_read}\forcode{=.true. } 
    128128in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default \NEMO 
    129129functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read 
     
    143143type of restart \NEMO\ will write. If it is set to 0, default \NEMO\ functionality will be used - each 
    144144processor writes its own restart file; if it is set to 1 XIOS will write restart into a single file; 
    145 for \np{nn\_wxios}\forcode{ = 2} the restart will be written by XIOS into multiple files, one for each XIOS server. 
    146 Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np{nn\_wxios}\forcode{ = 2}}. The restart will 
     145for \np{nn\_wxios}\forcode{=2} the restart will be written by XIOS into multiple files, one for each XIOS server. 
     146Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np{nn\_wxios}\forcode{=2}}. The restart will 
    147147have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by \NEMO\ only, 
    148148and may be useful when there is a need to change number of processors used to run simulation. 
     
    15081508\textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested. 
    15091509In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} are not working, 
    1510 and none of the options have been tested with variable volume (\ie\ \np{ln\_linssh}\forcode{ = .true.}). 
     1510and none of the options have been tested with variable volume (\ie\ \np{ln\_linssh}\forcode{=.true.}). 
    15111511 
    15121512% ------------------------------------------------------------------------------------------------------------- 
     
    15251525Options are defined by \nam{flo} namelist variables. 
    15261526The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option), 
    1527 or on a $4^th$ Runge-Hutta algorithm (\np{ln\_flork4}\forcode{ = .true.}). 
     1527or on a $4^th$ Runge-Hutta algorithm (\np{ln\_flork4}\forcode{=.true.}). 
    15281528Note that the \cite{blanke.raynaud_JPO97} algorithm have the advantage of providing trajectories which 
    15291529are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry. 
     
    15321532 
    15331533Initial coordinates can be given with Ariane Tools convention 
    1534 (IJK coordinates, (\np{ln\_ariane}\forcode{ = .true.}) ) or with longitude and latitude. 
     1534(IJK coordinates, (\np{ln\_ariane}\forcode{=.true.}) ) or with longitude and latitude. 
    15351535 
    15361536In case of Ariane convention, input filename is \textit{init\_float\_ariane}. 
     
    15831583 
    15841584\np{jpnfl} is the total number of floats during the run. 
    1585 When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{ = .true.} ), 
     1585When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{=.true.} ), 
    15861586\np{jpnflnewflo} can be added in the initialization file. 
    15871587 
     
    15911591creation of the float restart file. 
    15921592 
    1593 Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{ = .true.}). 
     1593Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{=.true.}). 
    15941594In that case, output filename is trajec\_float. 
    15951595 
    1596 Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{ = .false.}) with 
     1596Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{=.false.}) with 
    15971597\key{iomput} and outputs selected in iodef.xml. 
    15981598Here it is an example of specification to put in files description section: 
     
    19441944 
    19451945Third, the discretisation of \autoref{eq:steric_Bq} depends on the type of free surface which is considered. 
    1946 In the non linear free surface case, \ie\ \np{ln\_linssh}\forcode{ = .true.}, it is given by 
     1946In the non linear free surface case, \ie\ \np{ln\_linssh}\forcode{=.true.}, it is given by 
    19471947 
    19481948\[ 
     
    20392039sea water pressure at sea floor (botpres), dynamic sea surface height (sshdyn). 
    20402040 
    2041 In \mdl{diaptr} when \np{ln\_diaptr}\forcode{ = .true.} 
     2041In \mdl{diaptr} when \np{ln\_diaptr}\forcode{=.true.} 
    20422042(see the \nam{ptr} namelist below) can be computed on-line the poleward heat and salt transports, 
    20432043their advective and diffusive component, and the meriodional stream function . 
    2044 When \np{ln\_subbas}\forcode{ = .true.}, transports and stream function are computed for the Atlantic, Indian, 
     2044When \np{ln\_subbas}\forcode{=.true.}, transports and stream function are computed for the Atlantic, Indian, 
    20452045Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean. 
    20462046The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays, 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11435 r11537  
    492492      (d) hybrid $s-z$ coordinate, 
    493493      (e) hybrid $s-z$ coordinate with partial step, and 
    494       (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}\forcode{ = .false.}). 
     494      (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}\forcode{=.false.}). 
    495495      Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e). 
    496496    } 
     
    508508a single configuration file can support both options. 
    509509 
    510 By default a non-linear free surface is used (\np{ln\_linssh} set to \forcode{ = .false.} in \nam{dom}): 
     510By default a non-linear free surface is used (\np{ln\_linssh} set to \forcode{=.false.} in \nam{dom}): 
    511511the coordinate follow the time-variation of the free surface so that the transformation is time dependent: 
    512512$z(i,j,k,t)$ (\eg\ \autoref{fig:z_zps_s_sps}f). 
    513 When a linear free surface is assumed (\np{ln\_linssh} set to \forcode{ = .true.} in \nam{dom}), 
     513When a linear free surface is assumed (\np{ln\_linssh} set to \forcode{=.true.} in \nam{dom}), 
    514514the vertical coordinates are fixed in time, but the seawater can move up and down across the $z_0$ surface 
    515515(in other words, the top of the ocean in not a rigid lid). 
     
    530530 
    531531\begin{itemize} 
    532 \item $z$-coordinate with full step bathymetry (\np{ln\_zco}\forcode{ = .true.}), 
    533 \item $z$-coordinate with partial step ($zps$) bathymetry (\np{ln\_zps}\forcode{ = .true.}), 
    534 \item Generalized, $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}). 
     532\item $z$-coordinate with full step bathymetry (\np{ln\_zco}\forcode{=.true.}), 
     533\item $z$-coordinate with partial step ($zps$) bathymetry (\np{ln\_zps}\forcode{=.true.}), 
     534\item Generalized, $s$-coordinate (\np{ln\_sco}\forcode{=.true.}). 
    535535\end{itemize} 
    536536 
     
    550550They are updated at each model time step. 
    551551The initial fixed reference coordinate system is held in variable names with a $\_0$ suffix. 
    552 When the linear free surface option is used (\np{ln\_linssh}\forcode{ = .true.}), 
     552When the linear free surface option is used (\np{ln\_linssh}\forcode{=.true.}), 
    553553\textit{before}, \textit{now} and \textit{after} arrays are initially set to 
    554554their reference counterpart and remain fixed. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11435 r11537  
    192192 
    193193Options are defined through the \nam{dyn\_vor} namelist variables. 
    194 Four discretisations of the vorticity term (\texttt{ln\_dynvor\_xxx}\forcode{ = .true.}) are available: 
     194Four discretisations of the vorticity term (\texttt{ln\_dynvor\_xxx}\forcode{=.true.}) are available: 
    195195conserving potential enstrophy of horizontally non-divergent flow (ENS scheme); 
    196196conserving horizontal kinetic energy (ENE scheme); 
     
    200200(EEN scheme) (see \autoref{subsec:C_vorEEN}). 
    201201In the case of ENS, ENE or MIX schemes the land sea mask may be slightly modified to ensure the consistency of 
    202 vorticity term with analytical equations (\np{ln\_dynvor\_con}\forcode{ = .true.}). 
     202vorticity term with analytical equations (\np{ln\_dynvor\_con}\forcode{=.true.}). 
    203203The vorticity terms are all computed in dedicated routines that can be found in the \mdl{dynvor} module. 
    204204 
     
    206206%                 enstrophy conserving scheme 
    207207%------------------------------------------------------------- 
    208 \subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens = .true.})] 
    209 {Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{ = .true.})} 
     208\subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens=.true.})] 
     209{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{=.true.})} 
    210210\label{subsec:DYN_vor_ens} 
    211211 
     
    230230%                 energy conserving scheme 
    231231%------------------------------------------------------------- 
    232 \subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene = .true.})] 
    233 {Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{ = .true.})} 
     232\subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene=.true.})] 
     233{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{=.true.})} 
    234234\label{subsec:DYN_vor_ene} 
    235235 
     
    251251%                 mix energy/enstrophy conserving scheme 
    252252%------------------------------------------------------------- 
    253 \subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix = .true.})] 
    254 {Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{ = .true.})} 
     253\subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix=.true.})] 
     254{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{=.true.})} 
    255255\label{subsec:DYN_vor_mix} 
    256256 
     
    277277%                 energy and enstrophy conserving scheme 
    278278%------------------------------------------------------------- 
    279 \subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een = .true.})] 
    280 {Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.})} 
     279\subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een=.true.})] 
     280{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{=.true.})} 
    281281\label{subsec:DYN_vor_een} 
    282282 
     
    328328A key point in \autoref{eq:een_e3f} is how the averaging in the \textbf{i}- and \textbf{j}- directions is made. 
    329329It uses the sum of masked t-point vertical scale factor divided either by the sum of the four t-point masks 
    330 (\np{nn\_een\_e3f}\forcode{ = 1}), or just by $4$ (\np{nn\_een\_e3f}\forcode{ = .true.}). 
     330(\np{nn\_een\_e3f}\forcode{=1}), or just by $4$ (\np{nn\_een\_e3f}\forcode{=.true.}). 
    331331The latter case preserves the continuity of $e_{3f}$ when one or more of the neighbouring $e_{3t}$ tends to zero and 
    332332extends by continuity the value of $e_{3f}$ into the land areas. 
     
    410410  \right. 
    411411\] 
    412 When \np{ln\_dynzad\_zts}\forcode{ = .true.}, 
     412When \np{ln\_dynzad\_zts}\forcode{=.true.}, 
    413413a split-explicit time stepping with 5 sub-timesteps is used on the vertical advection term. 
    414414This option can be useful when the value of the timestep is limited by vertical advection \citep{lemarie.debreu.ea_OM15}. 
     
    495495%                 2nd order centred scheme 
    496496%------------------------------------------------------------- 
    497 \subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2 = .true.})] 
    498 {CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{ = .true.})} 
     497\subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2=.true.})] 
     498{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{=.true.})} 
    499499\label{subsec:DYN_adv_cen2} 
    500500 
     
    519519%                 UBS scheme 
    520520%------------------------------------------------------------- 
    521 \subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs = .true.})] 
    522 {UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{ = .true.})} 
     521\subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs=.true.})] 
     522{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{=.true.})} 
    523523\label{subsec:DYN_adv_ubs} 
    524524 
     
    542542But the amplitudes of the false extrema are significantly reduced over those in the centred second order method. 
    543543As the scheme already includes a diffusion component, it can be used without explicit lateral diffusion on momentum 
    544 (\ie\ \np{ln\_dynldf\_lap}\forcode{ = }\np{ln\_dynldf\_bilap}\forcode{ = .false.}), 
     544(\ie\ \np{ln\_dynldf\_lap}\forcode{=}\np{ln\_dynldf\_bilap}\forcode{=.false.}), 
    545545and it is recommended to do so. 
    546546 
     
    596596%           z-coordinate with full step 
    597597%-------------------------------------------------------------------------------------------------------------- 
    598 \subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco = .true.})] 
    599 {Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{ = .true.})} 
     598\subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco=.true.})] 
     599{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{=.true.})} 
    600600\label{subsec:DYN_hpg_zco} 
    601601 
     
    642642%           z-coordinate with partial step 
    643643%-------------------------------------------------------------------------------------------------------------- 
    644 \subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps = .true.})] 
    645 {Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{ = .true.})} 
     644\subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps=.true.})] 
     645{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{=.true.})} 
    646646\label{subsec:DYN_hpg_zps} 
    647647 
     
    672672density Jacobian with cubic polynomial method is currently disabled whilst known bugs are under investigation. 
    673673 
    674 $\bullet$ Traditional coding (see for example \citet{madec.delecluse.ea_JPO96}: (\np{ln\_dynhpg\_sco}\forcode{ = .true.}) 
     674$\bullet$ Traditional coding (see for example \citet{madec.delecluse.ea_JPO96}: (\np{ln\_dynhpg\_sco}\forcode{=.true.}) 
    675675\begin{equation} 
    676676  \label{eq:dynhpg_sco} 
     
    690690($e_{3w}$). 
    691691 
    692 $\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln\_dynhpg\_isf}\forcode{ = .true.}). 
    693 This scheme need the activation of ice shelf cavities (\np{ln\_isfcav}\forcode{ = .true.}). 
    694  
    695 $\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln\_dynhpg\_prj}\forcode{ = .true.}) 
     692$\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln\_dynhpg\_isf}\forcode{=.true.}). 
     693This scheme need the activation of ice shelf cavities (\np{ln\_isfcav}\forcode{=.true.}). 
     694 
     695$\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln\_dynhpg\_prj}\forcode{=.true.}) 
    696696 
    697697$\bullet$ Density Jacobian with cubic polynomial scheme (DJC) \citep{shchepetkin.mcwilliams_OM05} 
    698 (\np{ln\_dynhpg\_djc}\forcode{ = .true.}) (currently disabled; under development) 
     698(\np{ln\_dynhpg\_djc}\forcode{=.true.}) (currently disabled; under development) 
    699699 
    700700Note that expression \autoref{eq:dynhpg_sco} is commonly used when the variable volume formulation is activated 
    701701(\texttt{vvl?}) because in that case, even with a flat bottom, 
    702702the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_rpt07}. 
    703 The pressure jacobian scheme (\np{ln\_dynhpg\_prj}\forcode{ = .true.}) is available as 
    704 an improved option to \np{ln\_dynhpg\_sco}\forcode{ = .true.} when \texttt{vvl?} is active. 
     703The pressure jacobian scheme (\np{ln\_dynhpg\_prj}\forcode{=.true.}) is available as 
     704an improved option to \np{ln\_dynhpg\_sco}\forcode{=.true.} when \texttt{vvl?} is active. 
    705705The pressure Jacobian scheme uses a constrained cubic spline to 
    706706reconstruct the density profile across the water column. 
     
    713713\label{subsec:DYN_hpg_isf} 
    714714Beneath an ice shelf, the total pressure gradient is the sum of the pressure gradient due to the ice shelf load and 
    715 the pressure gradient due to the ocean load (\np{ln\_dynhpg\_isf}\forcode{ = .true.}).\\ 
     715the pressure gradient due to the ocean load (\np{ln\_dynhpg\_isf}\forcode{=.true.}).\\ 
    716716 
    717717The main hypothesis to compute the ice shelf load is that the ice shelf is in an isostatic equilibrium. 
     
    728728%           Time-scheme 
    729729%-------------------------------------------------------------------------------------------------------------- 
    730 \subsection[Time-scheme (\forcode{ln_dynhpg_imp = .{true,false}.})] 
    731 {Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{ = .\{true,false\}}.)} 
     730\subsection[Time-scheme (\forcode{ln_dynhpg_imp={.true.,.false.}})] 
     731{Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{=.true.,.false.})} 
    732732\label{subsec:DYN_hpg_imp} 
    733733 
     
    745745rather than at the central time level $t$ only, as in the standard leapfrog scheme. 
    746746 
    747 $\bullet$ leapfrog scheme (\np{ln\_dynhpg\_imp}\forcode{ = .true.}): 
     747$\bullet$ leapfrog scheme (\np{ln\_dynhpg\_imp}\forcode{=.true.}): 
    748748 
    749749\begin{equation} 
     
    753753\end{equation} 
    754754 
    755 $\bullet$ semi-implicit scheme (\np{ln\_dynhpg\_imp}\forcode{ = .true.}): 
     755$\bullet$ semi-implicit scheme (\np{ln\_dynhpg\_imp}\forcode{=.true.}): 
    756756\begin{equation} 
    757757  \label{eq:dynhpg_imp} 
     
    771771such as the stability limits associated with advection or diffusion. 
    772772 
    773 In practice, the semi-implicit scheme is used when \np{ln\_dynhpg\_imp}\forcode{ = .true.}. 
     773In practice, the semi-implicit scheme is used when \np{ln\_dynhpg\_imp}\forcode{=.true.}. 
    774774In this case, we choose to apply the time filter to temperature and salinity used in the equation of state, 
    775775instead of applying it to the hydrostatic pressure or to the density, 
     
    829829% Explicit free surface formulation 
    830830%-------------------------------------------------------------------------------------------------------------- 
    831 \subsection[Explicit free surface (\texttt{ln\_dynspg\_exp}\forcode{ = .true.})] 
    832 {Explicit free surface (\protect\np{ln\_dynspg\_exp}\forcode{ = .true.})} 
     831\subsection[Explicit free surface (\texttt{ln\_dynspg\_exp}\forcode{=.true.})] 
     832{Explicit free surface (\protect\np{ln\_dynspg\_exp}\forcode{=.true.})} 
    833833\label{subsec:DYN_spg_exp} 
    834834 
     
    856856% Split-explict free surface formulation 
    857857%-------------------------------------------------------------------------------------------------------------- 
    858 \subsection[Split-explicit free surface (\texttt{ln\_dynspg\_ts}\forcode{ = .true.})] 
    859 {Split-explicit free surface (\protect\np{ln\_dynspg\_ts}\forcode{ = .true.})} 
     858\subsection[Split-explicit free surface (\texttt{ln\_dynspg\_ts}\forcode{=.true.})] 
     859{Split-explicit free surface (\protect\np{ln\_dynspg\_ts}\forcode{=.true.})} 
    860860\label{subsec:DYN_spg_ts} 
    861861%------------------------------------------namsplit----------------------------------------------------------- 
     
    871871The size of the small time step, $\rdt_e$ (the external mode or barotropic time step) is provided through 
    872872the \np{nn\_baro} namelist parameter as: $\rdt_e = \rdt / nn\_baro$. 
    873 This parameter can be optionally defined automatically (\np{ln\_bt\_nn\_auto}\forcode{ = .true.}) considering that 
     873This parameter can be optionally defined automatically (\np{ln\_bt\_nn\_auto}\forcode{=.true.}) considering that 
    874874the stability of the barotropic system is essentially controled by external waves propagation. 
    875875Maximum Courant number is in that case time independent, and easily computed online from the input bathymetry. 
     
    916916      The former are used to obtain time filtered quantities at $t+\rdt$ while 
    917917      the latter are used to obtain time averaged transports to advect tracers. 
    918       a) Forward time integration: \protect\np{ln\_bt\_fw}\forcode{ = .true.}, 
    919       \protect\np{ln\_bt\_av}\forcode{ = .true.}. 
    920       b) Centred time integration: \protect\np{ln\_bt\_fw}\forcode{ = .false.}, 
    921       \protect\np{ln\_bt\_av}\forcode{ = .true.}. 
     918      a) Forward time integration: \protect\np{ln\_bt\_fw}\forcode{=.true.}, 
     919      \protect\np{ln\_bt\_av}\forcode{=.true.}. 
     920      b) Centred time integration: \protect\np{ln\_bt\_fw}\forcode{=.false.}, 
     921      \protect\np{ln\_bt\_av}\forcode{=.true.}. 
    922922      c) Forward time integration with no time filtering (POM-like scheme): 
    923       \protect\np{ln\_bt\_fw}\forcode{ = .true.}, \protect\np{ln\_bt\_av}\forcode{ = .false.}. 
     923      \protect\np{ln\_bt\_fw}\forcode{=.true.}, \protect\np{ln\_bt\_av}\forcode{=.false.}. 
    924924    } 
    925925  \end{center} 
     
    927927%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    928928 
    929 In the default case (\np{ln\_bt\_fw}\forcode{ = .true.}), 
     929In the default case (\np{ln\_bt\_fw}\forcode{=.true.}), 
    930930the external mode is integrated between \textit{now} and \textit{after} baroclinic time-steps 
    931931(\autoref{fig:DYN_dynspg_ts}a). 
    932932To avoid aliasing of fast barotropic motions into three dimensional equations, 
    933 time filtering is eventually applied on barotropic quantities (\np{ln\_bt\_av}\forcode{ = .true.}). 
     933time filtering is eventually applied on barotropic quantities (\np{ln\_bt\_av}\forcode{=.true.}). 
    934934In that case, the integration is extended slightly beyond \textit{after} time step to 
    935935provide time filtered quantities. 
     
    938938asselin filtering is not applied to barotropic quantities.\\ 
    939939Alternatively, one can choose to integrate barotropic equations starting from \textit{before} time step 
    940 (\np{ln\_bt\_fw}\forcode{ = .false.}). 
     940(\np{ln\_bt\_fw}\forcode{=.false.}). 
    941941Although more computationaly expensive ( \np{nn\_baro} additional iterations are indeed necessary), 
    942942the baroclinic to barotropic forcing term given at \textit{now} time step become centred in 
     
    963963 
    964964One can eventually choose to feedback instantaneous values by not using any time filter 
    965 (\np{ln\_bt\_av}\forcode{ = .false.}). 
     965(\np{ln\_bt\_av}\forcode{=.false.}). 
    966966In that case, external mode equations are continuous in time, 
    967967\ie\ they are not re-initialized when starting a new sub-stepping sequence. 
     
    11651165 
    11661166% ================================================================ 
    1167 \subsection[Iso-level laplacian (\forcode{ln_dynldf_lap = .true.})] 
    1168 {Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})} 
     1167\subsection[Iso-level laplacian (\forcode{ln_dynldf_lap=.true.})] 
     1168{Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{=.true.})} 
    11691169\label{subsec:DYN_ldf_lap} 
    11701170 
     
    11911191%           Rotated laplacian operator 
    11921192%-------------------------------------------------------------------------------------------------------------- 
    1193 \subsection[Rotated laplacian (\forcode{ln_dynldf_iso = .true.})] 
    1194 {Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})} 
     1193\subsection[Rotated laplacian (\forcode{ln_dynldf_iso=.true.})] 
     1194{Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{=.true.})} 
    11951195\label{subsec:DYN_ldf_iso} 
    11961196 
    11971197A rotation of the lateral momentum diffusion operator is needed in several cases: 
    1198 for iso-neutral diffusion in the $z$-coordinate (\np{ln\_dynldf\_iso}\forcode{ = .true.}) and 
    1199 for either iso-neutral (\np{ln\_dynldf\_iso}\forcode{ = .true.}) or 
    1200 geopotential (\np{ln\_dynldf\_hor}\forcode{ = .true.}) diffusion in the $s$-coordinate. 
     1198for iso-neutral diffusion in the $z$-coordinate (\np{ln\_dynldf\_iso}\forcode{=.true.}) and 
     1199for either iso-neutral (\np{ln\_dynldf\_iso}\forcode{=.true.}) or 
     1200geopotential (\np{ln\_dynldf\_hor}\forcode{=.true.}) diffusion in the $s$-coordinate. 
    12011201In the partial step case, coordinates are horizontal except at the deepest level and 
    1202 no rotation is performed when \np{ln\_dynldf\_hor}\forcode{ = .true.}. 
     1202no rotation is performed when \np{ln\_dynldf\_hor}\forcode{=.true.}. 
    12031203The diffusion operator is defined simply as the divergence of down gradient momentum fluxes on 
    12041204each momentum component. 
     
    12501250%           Iso-level bilaplacian operator 
    12511251%-------------------------------------------------------------------------------------------------------------- 
    1252 \subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap = .true.})] 
    1253 {Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})} 
     1252\subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap=.true.})] 
     1253{Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{=.true.})} 
    12541254\label{subsec:DYN_ldf_bilap} 
    12551255 
     
    12771277Two time stepping schemes can be used for the vertical diffusion term: 
    12781278$(a)$ a forward time differencing scheme 
    1279 (\np{ln\_zdfexp}\forcode{ = .true.}) using a time splitting technique (\np{nn\_zdfexp} $>$ 1) or 
    1280 $(b)$ a backward (or implicit) time differencing scheme (\np{ln\_zdfexp}\forcode{ = .false.}) 
     1279(\np{ln\_zdfexp}\forcode{=.true.}) using a time splitting technique (\np{nn\_zdfexp} $>$ 1) or 
     1280$(b)$ a backward (or implicit) time differencing scheme (\np{ln\_zdfexp}\forcode{=.false.}) 
    12811281(see \autoref{chap:STP}). 
    12821282Note that namelist variables \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics. 
     
    13281328three other forcings may enter the dynamical equations by affecting the surface pressure gradient. 
    13291329 
    1330 (1) When \np{ln\_apr\_dyn}\forcode{ = .true.} (see \autoref{sec:SBC_apr}), 
     1330(1) When \np{ln\_apr\_dyn}\forcode{=.true.} (see \autoref{sec:SBC_apr}), 
    13311331the atmospheric pressure is taken into account when computing the surface pressure gradient. 
    13321332 
    1333 (2) When \np{ln\_tide\_pot}\forcode{ = .true.} and \np{ln\_tide}\forcode{ = .true.} (see \autoref{sec:SBC_tide}), 
     1333(2) When \np{ln\_tide\_pot}\forcode{=.true.} and \np{ln\_tide}\forcode{=.true.} (see \autoref{sec:SBC_tide}), 
    13341334the tidal potential is taken into account when computing the surface pressure gradient. 
    13351335 
    1336 (3) When \np{nn\_ice\_embd}\forcode{ = 2} and LIM or CICE is used 
     1336(3) When \np{nn\_ice\_embd}\forcode{=2} and LIM or CICE is used 
    13371337(\ie\ when the sea-ice is embedded in the ocean), 
    13381338the snow-ice mass is taken into account when computing the surface pressure gradient. 
     
    14091409 
    14101410The flux across each $u$-face of a tracer cell is multiplied by a factor zuwdmask (an array which depends on ji and jj). 
    1411 If the user sets \np{ln\_wd\_dl\_ramp}\forcode{ = .false.} then zuwdmask is 1 when the 
     1411If the user sets \np{ln\_wd\_dl\_ramp}\forcode{=.false.} then zuwdmask is 1 when the 
    14121412flux is from a cell with water depth greater than \np{rn\_wdmin1} and 0 otherwise. If the user sets 
    1413 \np{ln\_wd\_dl\_ramp}\forcode{ = .true.} the flux across the face is ramped down as the water depth decreases 
     1413\np{ln\_wd\_dl\_ramp}\forcode{=.true.} the flux across the face is ramped down as the water depth decreases 
    14141414from 2 * \np{rn\_wdmin1} to \np{rn\_wdmin1}. The use of this ramp reduced grid-scale noise in idealised test cases. 
    14151415 
     
    14281428fields (tracers independent of $x$, $y$ and $z$). Our scheme conserves constant tracers because 
    14291429the velocities used at the tracer cell faces on the baroclinic timesteps are carefully calculated by dynspg\_ts 
    1430 to equal their mean value during the barotropic steps. If the user sets \np{ln\_wd\_dl\_bc}\forcode{ = .true.}, the 
     1430to equal their mean value during the barotropic steps. If the user sets \np{ln\_wd\_dl\_bc}\forcode{=.true.}, the 
    14311431baroclinic velocities are also multiplied by a suitably weighted average of zuwdmask. 
    14321432 
     
    16551655 
    16561656$\bullet$ vector invariant form or linear free surface 
    1657 (\np{ln\_dynhpg\_vec}\forcode{ = .true.} ; \texttt{vvl?} not defined): 
     1657(\np{ln\_dynhpg\_vec}\forcode{=.true.} ; \texttt{vvl?} not defined): 
    16581658\[ 
    16591659  % \label{eq:dynnxt_vec} 
     
    16671667 
    16681668$\bullet$ flux form and nonlinear free surface 
    1669 (\np{ln\_dynhpg\_vec}\forcode{ = .false.} ; \texttt{vvl?} defined): 
     1669(\np{ln\_dynhpg\_vec}\forcode{=.false.} ; \texttt{vvl?} defined): 
    16701670\[ 
    16711671  % \label{eq:dynnxt_flux} 
     
    16811681the subscript $f$ denotes filtered values and $\gamma$ is the Asselin coefficient. 
    16821682$\gamma$ is initialized as \np{nn\_atfp} (namelist parameter). 
    1683 Its default value is \np{nn\_atfp}\forcode{ = 10.e-3}. 
     1683Its default value is \np{nn\_atfp}\forcode{=10.e-3}. 
    16841684In both cases, the modified Asselin filter is not applied since perfect conservation is not an issue for 
    16851685the momentum equations. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11536 r11537  
    171171%        Closed, cyclic (\jp{jperio}\forcode{ = 0..2}) 
    172172% ------------------------------------------------------------------------------------------------------------- 
    173 \subsection[Closed, cyclic (\forcode{jperio = [0127]})] 
    174 {Closed, cyclic (\protect\jp{jperio}\forcode{ = [0127]})} 
     173\subsection[Closed, cyclic (\forcode{jperio=[0127]})] 
     174{Closed, cyclic (\protect\jp{jperio}\forcode{=[0127]})} 
    175175\label{subsec:LBC_jperio012} 
    176176 
     
    185185\begin{description} 
    186186 
    187 \item[For closed boundary (\jp{jperio}\forcode{ = 0})], 
     187\item[For closed boundary (\jp{jperio}\forcode{=0})], 
    188188  solid walls are imposed at all model boundaries: 
    189189  first and last rows and columns are set to zero. 
    190190 
    191 \item[For cyclic east-west boundary (\jp{jperio}\forcode{ = 1})], 
     191\item[For cyclic east-west boundary (\jp{jperio}\forcode{=1})], 
    192192  first and last rows are set to zero (closed) whilst the first column is set to 
    193193  the value of the last-but-one column and the last column to the value of the second one 
     
    195195  Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end. 
    196196 
    197 \item[For cyclic north-south boundary (\jp{jperio}\forcode{ = 2})], 
     197\item[For cyclic north-south boundary (\jp{jperio}\forcode{=2})], 
    198198  first and last columns are set to zero (closed) whilst the first row is set to 
    199199  the value of the last-but-one row and the last row to the value of the second one 
     
    201201  Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end. 
    202202 
    203 \item[Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{ = 7})] combines cases 1 and 2. 
     203\item[Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{=7})] combines cases 1 and 2. 
    204204 
    205205\end{description} 
     
    220220%        North fold (\textit{jperio = 3 }to $6)$ 
    221221% ------------------------------------------------------------------------------------------------------------- 
    222 \subsection[North-fold (\forcode{jperio = [3-6]})] 
    223 {North-fold (\protect\jp{jperio}\forcode{ = [3-6]})} 
     222\subsection[North-fold (\forcode{jperio=[3-6]})] 
     223{North-fold (\protect\jp{jperio}\forcode{=[3-6]})} 
    224224\label{subsec:LBC_north_fold} 
    225225 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11435 r11537  
    2424(see the \nam{tra\_ldf} and \nam{dyn\_ldf} below). 
    2525Note that this chapter describes the standard implementation of iso-neutral tracer mixing.  
    26 Griffies's implementation, which is used if \np{ln\_traldf\_triad}\forcode{ = .true.}, 
     26Griffies's implementation, which is used if \np{ln\_traldf\_triad}\forcode{=.true.}, 
    2727is described in \autoref{apdx:triad} 
    2828 
     
    4545{No lateral mixing (\protect\np{ln\_traldf\_OFF}, \protect\np{ln\_dynldf\_OFF})} 
    4646 
    47 It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln\_traldf\_OFF}\forcode{ = .true.}) and/or  
    48 momentum (\protect\np{ln\_dynldf\_OFF}\forcode{ = .true.}). The latter option is even recommended if using the  
    49 UBS advection scheme on momentum (\np{ln\_dynadv\_ubs}\forcode{ = .true.}, 
     47It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln\_traldf\_OFF}\forcode{=.true.}) and/or  
     48momentum (\protect\np{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the  
     49UBS advection scheme on momentum (\np{ln\_dynadv\_ubs}\forcode{=.true.}, 
    5050see \autoref{subsec:DYN_adv_ubs}) and can be useful for testing purposes. 
    5151 
    5252\subsection[Laplacian mixing (\forcode{ln_traldf_lap}, \forcode{ln_dynldf_lap})] 
    5353{Laplacian mixing (\protect\np{ln\_traldf\_lap}, \protect\np{ln\_dynldf\_lap})} 
    54 Setting \protect\np{ln\_traldf\_lap}\forcode{ = .true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{ = .true.} enables  
     54Setting \protect\np{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{=.true.} enables  
    5555a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine  
    5656Laplacian and Bilaplacian operators for the same variable. 
     
    5858\subsection[Bilaplacian mixing (\forcode{ln_traldf_blp}, \forcode{ln_dynldf_blp})] 
    5959{Bilaplacian mixing (\protect\np{ln\_traldf\_blp}, \protect\np{ln\_dynldf\_blp})} 
    60 Setting \protect\np{ln\_traldf\_blp}\forcode{ = .true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{ = .true.} enables  
     60Setting \protect\np{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{=.true.} enables  
    6161a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice.  
    6262We stress again that from \NEMO\ 4, the simultaneous use Laplacian and Bilaplacian operators is not allowed. 
     
    115115%gm%  caution I'm not sure the simplification was a good idea!  
    116116 
    117 These slopes are computed once in \rou{ldf\_slp\_init} when \np{ln\_sco}\forcode{ = .true.}, 
    118 and either \np{ln\_traldf\_hor}\forcode{ = .true.} or \np{ln\_dynldf\_hor}\forcode{ = .true.}.  
     117These slopes are computed once in \rou{ldf\_slp\_init} when \np{ln\_sco}\forcode{=.true.}, 
     118and either \np{ln\_traldf\_hor}\forcode{=.true.} or \np{ln\_dynldf\_hor}\forcode{=.true.}.  
    119119 
    120120\subsection{Slopes for tracer iso-neutral mixing} 
     
    172172\item[$s$- or hybrid $s$-$z$- coordinate: ] 
    173173  in the current release of \NEMO, iso-neutral mixing is only employed for $s$-coordinates if 
    174   the Griffies scheme is used (\np{ln\_traldf\_triad}\forcode{ = .true.}; 
     174  the Griffies scheme is used (\np{ln\_traldf\_triad}\forcode{=.true.}; 
    175175  see \autoref{apdx:triad}). 
    176176  In other words, iso-neutral mixing will only be accurately represented with a linear equation of state 
    177   (\np{ln\_seos}\forcode{ = .true.}). 
     177  (\np{ln\_seos}\forcode{=.true.}). 
    178178  In the case of a "true" equation of state, the evaluation of $i$ and $j$ derivatives in \autoref{eq:ldfslp_iso} 
    179179  will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes. 
     
    230230To overcome this problem, several techniques have been proposed in which the numerical schemes of 
    231231the ocean model are modified \citep{weaver.eby_JPO97, griffies.gnanadesikan.ea_JPO98}. 
    232 Griffies's scheme is now available in \NEMO\ if \np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:triad}. 
     232Griffies's scheme is now available in \NEMO\ if \np{ln\_traldf\_triad}\forcode{=.true.}; see \autoref{apdx:triad}. 
    233233Here, another strategy is presented \citep{lazar_phd97}: 
    234234a local filtering of the iso-neutral slopes (made on 9 grid-points) prevents the development of 
     
    337337The way the mixing coefficients are set in the reference version can be described as follows: 
    338338 
    339 \subsection[Mixing coefficients read from file (\forcode{nn_aht_ijk_t = -20, -30}, \forcode{nn_ahm_ijk_t = -20,-30})] 
    340 { Mixing coefficients read from file (\protect\np{nn\_aht\_ijk\_t}\forcode{ = -20, -30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{ = -20, -30})} 
     339\subsection[Mixing coefficients read from file (\forcode{nn_aht_ijk_t=-20, -30}, \forcode{nn_ahm_ijk_t=-20,-30})] 
     340{ Mixing coefficients read from file (\protect\np{nn\_aht\_ijk\_t}\forcode{=-20, -30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=-20, -30})} 
    341341 
    342342Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model,  
     
    344344decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}.  
    345345Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05.  
    346 The provided fields can either be 2d (\np{nn\_aht\_ijk\_t}\forcode{ = -20}, \np{nn\_ahm\_ijk\_t}\forcode{ = -20}) or 3d (\np{nn\_aht\_ijk\_t}\forcode{ = -30},  \np{nn\_ahm\_ijk\_t}\forcode{ = -30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}). 
     346The provided fields can either be 2d (\np{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn\_aht\_ijk\_t}\forcode{=-30},  \np{nn\_ahm\_ijk\_t}\forcode{=-30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}). 
    347347 
    348348%-------------------------------------------------TABLE--------------------------------------------------- 
     
    352352      \hline 
    353353      Namelist parameter                        & Input filename                               & dimensions & variable names                      \\  \hline 
    354       \np{nn\_ahm\_ijk\_t}\forcode{ = -20}       & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline 
    355       \np{nn\_aht\_ijk\_t}\forcode{ = -20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$          & \forcode{ahtu_2d, ahtv_2d}    \\   \hline 
    356       \np{nn\_ahm\_ijk\_t}\forcode{ = -30}       & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline 
    357       \np{nn\_aht\_ijk\_t}\forcode{ = -30}       & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline 
     354      \np{nn\_ahm\_ijk\_t}\forcode{=-20}      & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline 
     355      \np{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$         & \forcode{ahtu_2d, ahtv_2d}    \\   \hline 
     356      \np{nn\_ahm\_ijk\_t}\forcode{=-30}      & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline 
     357      \np{nn\_aht\_ijk\_t}\forcode{=-30}      & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline 
    358358    \end{tabular} 
    359359    \caption{ 
     
    365365%-------------------------------------------------------------------------------------------------------------- 
    366366 
    367 \subsection[Constant mixing coefficients (\forcode{nn_aht_ijk_t = 0}, \forcode{nn_ahm_ijk_t = 0})] 
    368 { Constant mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{ = 0}, \protect\np{nn\_ahm\_ijk\_t}\forcode{ = 0})} 
     367\subsection[Constant mixing coefficients (\forcode{nn_aht_ijk_t=0}, \forcode{nn_ahm_ijk_t=0})] 
     368{ Constant mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=0}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=0})} 
    369369 
    370370If constant, mixing coefficients are set thanks to a velocity and a length scales ($U_{scl}$, $L_{scl}$) such that: 
     
    382382 $U_{scl}$ and $L_{scl}$ are given by the namelist parameters \np{rn\_Ud}, \np{rn\_Uv}, \np{rn\_Ld} and \np{rn\_Lv}. 
    383383 
    384 \subsection[Vertically varying mixing coefficients (\forcode{nn_aht_ijk_t = 10}, \forcode{nn_ahm_ijk_t = 10})] 
    385 {Vertically varying mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{ = 10}, \protect\np{nn\_ahm\_ijk\_t}\forcode{ = 10})} 
     384\subsection[Vertically varying mixing coefficients (\forcode{nn_aht_ijk_t=10}, \forcode{nn_ahm_ijk_t=10})] 
     385{Vertically varying mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=10}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=10})} 
    386386 
    387387In the vertically varying case, a hyperbolic variation of the lateral mixing coefficient is introduced in which 
     
    390390This profile is hard coded in module \mdl{ldfc1d\_c2d}, but can be easily modified by users. 
    391391 
    392 \subsection[Mesh size dependent mixing coefficients (\forcode{nn_aht_ijk_t = 20}, \forcode{nn_ahm_ijk_t = 20})] 
    393 {Mesh size dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{ = 20}, \protect\np{nn\_ahm\_ijk\_t}\forcode{ = 20})} 
     392\subsection[Mesh size dependent mixing coefficients (\forcode{nn_aht_ijk_t=20}, \forcode{nn_ahm_ijk_t=20})] 
     393{Mesh size dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=20}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=20})} 
    394394 
    395395In that case, the horizontal variation of the eddy coefficient depends on the local mesh size and 
     
    416416\colorbox{yellow}{CASE \np{nn\_aht\_ijk\_t} = 21 to be added} 
    417417 
    418 \subsection[Mesh size and depth dependent mixing coefficients (\forcode{nn_aht_ijk_t = 30}, \forcode{nn_ahm_ijk_t = 30})] 
    419 {Mesh size and depth dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{ = 30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{ = 30})} 
     418\subsection[Mesh size and depth dependent mixing coefficients (\forcode{nn_aht_ijk_t=30}, \forcode{nn_ahm_ijk_t=30})] 
     419{Mesh size and depth dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=30})} 
    420420 
    421421The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases above, 
     
    423423the magnitude of the coefficient.  
    424424 
    425 \subsection[Velocity dependent mixing coefficients (\forcode{nn_aht_ijk_t = 31}, \forcode{nn_ahm_ijk_t = 31})] 
    426 {Flow dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{ = 31}, \protect\np{nn\_ahm\_ijk\_t}\forcode{ = 31})} 
     425\subsection[Velocity dependent mixing coefficients (\forcode{nn_aht_ijk_t=31}, \forcode{nn_ahm_ijk_t=31})] 
     426{Flow dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=31}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=31})} 
    427427In that case, the eddy coefficient is proportional to the local velocity magnitude so that the Reynolds number $Re =  \lvert U \rvert  e / A_l$ is constant (and here hardcoded to $12$): 
    428428\colorbox{yellow}{JC comment: The Reynolds is effectively set to 12 in the code for both operators but shouldn't it be 2 for Laplacian ?} 
     
    438438\end{equation} 
    439439 
    440 \subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t = 32})] 
    441 {Deformation rate dependent viscosities (\protect\np{nn\_ahm\_ijk\_t}\forcode{ = 32})} 
     440\subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})] 
     441{Deformation rate dependent viscosities (\protect\np{nn\_ahm\_ijk\_t}\forcode{=32})} 
    442442 
    443443This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a  
     
    491491% Eddy Induced Mixing 
    492492% ================================================================ 
    493 \section[Eddy induced velocity (\forcode{ln_ldfeiv = .true.})] 
    494 {Eddy induced velocity (\protect\np{ln\_ldfeiv}\forcode{ = .true.})} 
     493\section[Eddy induced velocity (\forcode{ln_ldfeiv=.true.})] 
     494{Eddy induced velocity (\protect\np{ln\_ldfeiv}\forcode{=.true.})} 
    495495 
    496496\label{sec:LDF_eiv} 
     
    523523} 
    524524 
    525 When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np{ln\_ldfeiv}\forcode{ = .true.}), 
     525When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np{ln\_ldfeiv}\forcode{=.true.}), 
    526526an eddy induced tracer advection term is added, 
    527527the formulation of which depends on the slopes of iso-neutral surfaces. 
     
    530530and the sum \autoref{eq:ldfslp_geo} + \autoref{eq:ldfslp_iso} in $s$-coordinates. 
    531531 
    532 If isopycnal mixing is used in the standard way, \ie\ \np{ln\_traldf\_triad}\forcode{ = .false.}, the eddy induced velocity is given by:  
     532If isopycnal mixing is used in the standard way, \ie\ \np{ln\_traldf\_triad}\forcode{=.false.}, the eddy induced velocity is given by:  
    533533\begin{equation} 
    534534  \label{eq:ldfeiv} 
     
    554554\colorbox{yellow}{CASE \np{nn\_aei\_ijk\_t} = 21 to be added} 
    555555 
    556 In case of setting \np{ln\_traldf\_triad}\forcode{ = .true.}, a skew form of the eddy induced advective fluxes is used, which is described in \autoref{apdx:triad}. 
     556In case of setting \np{ln\_traldf\_triad}\forcode{=.true.}, a skew form of the eddy induced advective fluxes is used, which is described in \autoref{apdx:triad}. 
    557557 
    558558% ================================================================ 
    559559% Mixed layer eddies 
    560560% ================================================================ 
    561 \section[Mixed layer eddies (\forcode{ln_mle = .true.})] 
    562 {Mixed layer eddies (\protect\np{ln\_mle}\forcode{ = .true.})} 
     561\section[Mixed layer eddies (\forcode{ln_mle=.true.})] 
     562{Mixed layer eddies (\protect\np{ln\_mle}\forcode{=.true.})} 
    563563 
    564564\label{sec:LDF_mle} 
     
    570570%-------------------------------------------------------------------------------------------------------------- 
    571571 
    572 If  \np{ln\_mle}\forcode{ = .true.} in \nam{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection. 
     572If  \np{ln\_mle}\forcode{=.true.} in \nam{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection. 
    573573 
    574574\colorbox{yellow}{TBC} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11435 r11537  
    3737\begin{itemize} 
    3838\item 
    39   a bulk formulation (\np{ln\_blk}\forcode{ = .true.} with four possible bulk algorithms), 
    40 \item 
    41   a flux formulation (\np{ln\_flx}\forcode{ = .true.}), 
     39  a bulk formulation (\np{ln\_blk}\forcode{=.true.} with four possible bulk algorithms), 
     40\item 
     41  a flux formulation (\np{ln\_flx}\forcode{=.true.}), 
    4242\item 
    4343  a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler), 
    44 (\np{ln\_cpl} or \np{ln\_mixcpl}\forcode{ = .true.}), 
    45 \item 
    46   a user defined formulation (\np{ln\_usr}\forcode{ = .true.}). 
     44(\np{ln\_cpl} or \np{ln\_mixcpl}\forcode{=.true.}), 
     45\item 
     46  a user defined formulation (\np{ln\_usr}\forcode{=.true.}). 
    4747\end{itemize} 
    4848 
     
    6565  the local grid directions in the model, 
    6666\item 
    67   the use of a land/sea mask for input fields (\np{nn\_lsm}\forcode{ = .true.}), 
    68 \item 
    69   the addition of a surface restoring term to observed SST and/or SSS (\np{ln\_ssr}\forcode{ = .true.}), 
     67  the use of a land/sea mask for input fields (\np{nn\_lsm}\forcode{=.true.}), 
     68\item 
     69  the addition of a surface restoring term to observed SST and/or SSS (\np{ln\_ssr}\forcode{=.true.}), 
    7070\item 
    7171  the modification of fluxes below ice-covered areas (using climatological ice-cover or a sea-ice model) 
    72   (\np{nn\_ice}\forcode{ = 0..3}), 
    73 \item 
    74   the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln\_rnf}\forcode{ = .true.}), 
     72  (\np{nn\_ice}\forcode{=0..3}), 
     73\item 
     74  the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln\_rnf}\forcode{=.true.}), 
    7575\item 
    7676  the addition of ice-shelf melting as lateral inflow (parameterisation) or 
    77   as fluxes applied at the land-ice ocean interface (\np{ln\_isf}\forcode{ = .true.}), 
     77  as fluxes applied at the land-ice ocean interface (\np{ln\_isf}\forcode{=.true.}), 
    7878\item 
    7979  the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift 
    80   (\np{nn\_fwb}\forcode{ = 0..2}), 
     80  (\np{nn\_fwb}\forcode{=0..2}), 
    8181\item 
    8282  the transformation of the solar radiation (if provided as daily mean) into an analytical diurnal cycle 
    83   (\np{ln\_dm2dc}\forcode{ = .true.}), 
    84 \item 
    85   the activation of wave effects from an external wave model  (\np{ln\_wave}\forcode{ = .true.}), 
    86 \item 
    87   a neutral drag coefficient is read from an external wave model (\np{ln\_cdgw}\forcode{ = .true.}), 
    88 \item 
    89   the Stokes drift from an external wave model is accounted for (\np{ln\_sdw}\forcode{ = .true.}), 
    90 \item 
    91   the choice of the Stokes drift profile parameterization (\np{nn\_sdrift}\forcode{ = 0..2}), 
    92 \item 
    93   the surface stress given to the ocean is modified by surface waves (\np{ln\_tauwoc}\forcode{ = .true.}), 
    94 \item 
    95   the surface stress given to the ocean is read from an external wave model (\np{ln\_tauw}\forcode{ = .true.}), 
    96 \item 
    97   the Stokes-Coriolis term is included (\np{ln\_stcor}\forcode{ = .true.}), 
    98 \item 
    99   the light penetration in the ocean (\np{ln\_traqsr}\forcode{ = .true.} with namelist \nam{tra\_qsr}), 
    100 \item 
    101   the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np{ln\_apr\_dyn}\forcode{ = .true.} with namelist \nam{sbc\_apr}), 
    102 \item 
    103   the effect of sea-ice pressure on the ocean (\np{ln\_ice\_embd}\forcode{ = .true.}). 
     83  (\np{ln\_dm2dc}\forcode{=.true.}), 
     84\item 
     85  the activation of wave effects from an external wave model  (\np{ln\_wave}\forcode{=.true.}), 
     86\item 
     87  a neutral drag coefficient is read from an external wave model (\np{ln\_cdgw}\forcode{=.true.}), 
     88\item 
     89  the Stokes drift from an external wave model is accounted for (\np{ln\_sdw}\forcode{=.true.}), 
     90\item 
     91  the choice of the Stokes drift profile parameterization (\np{nn\_sdrift}\forcode{=0..2}), 
     92\item 
     93  the surface stress given to the ocean is modified by surface waves (\np{ln\_tauwoc}\forcode{=.true.}), 
     94\item 
     95  the surface stress given to the ocean is read from an external wave model (\np{ln\_tauw}\forcode{=.true.}), 
     96\item 
     97  the Stokes-Coriolis term is included (\np{ln\_stcor}\forcode{=.true.}), 
     98\item 
     99  the light penetration in the ocean (\np{ln\_traqsr}\forcode{=.true.} with namelist \nam{tra\_qsr}), 
     100\item 
     101  the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np{ln\_apr\_dyn}\forcode{=.true.} with namelist \nam{sbc\_apr}), 
     102\item 
     103  the effect of sea-ice pressure on the ocean (\np{ln\_ice\_embd}\forcode{=.true.}). 
    104104\end{itemize} 
    105105 
     
    138138The latter is the penetrative part of the heat flux. 
    139139It is applied as a 3D trend of the temperature equation (\mdl{traqsr} module) when 
    140 \np{ln\_traqsr}\forcode{ = .true.}. 
     140\np{ln\_traqsr}\forcode{=.true.}. 
    141141The way the light penetrates inside the water column is generally a sum of decreasing exponentials 
    142142(see \autoref{subsec:TRA_qsr}). 
     
    273273        \hline 
    274274                                        &  daily or weekLL     &  monthly           &  yearly        \\   \hline 
    275         \np{clim}\forcode{ = .false.}  &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\   \hline 
    276         \np{clim}\forcode{ = .true.}   &  not possible        &  fn\_m??.nc        &  fn            \\   \hline 
     275        \np{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\   \hline 
     276        \np{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\   \hline 
    277277      \end{tabular} 
    278278    \end{center} 
     
    342342However, for forcing data related to the surface module, 
    343343values are not needed at every time-step but at every \np{nn\_fsbc} time-step. 
    344 For example with \np{nn\_fsbc}\forcode{ = 3}, the surface module will be called at time-steps 1, 4, 7, etc. 
     344For example with \np{nn\_fsbc}\forcode{=3}, the surface module will be called at time-steps 1, 4, 7, etc. 
    345345The date used for the time interpolation is thus redefined to the middle of \np{nn\_fsbc} time-step period. 
    346346In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\ 
     
    537537  Spinup of the iceberg floats 
    538538\item 
    539   Ocean/sea-ice simulation with both models running in parallel (\np{ln\_mixcpl}\forcode{ = .true.}) 
     539  Ocean/sea-ice simulation with both models running in parallel (\np{ln\_mixcpl}\forcode{=.true.}) 
    540540\end{itemize} 
    541541 
     
    592592 
    593593The user can also choose in the \nam{sbc\_sas} namelist to read the mean (nn\_fsbc time-step) fraction of solar net radiation absorbed in the 1st T level using 
    594  (\np{ln\_flx}\forcode{ = .true.}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln\_flx}\forcode{ = .true.}). In that last case, only the 1st level will be read in. 
     594 (\np{ln\_flx}\forcode{=.true.}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln\_flx}\forcode{=.true.}). In that last case, only the 1st level will be read in. 
    595595 
    596596 
     
    607607%------------------------------------------------------------------------------------------------------------- 
    608608 
    609 In the flux formulation (\np{ln\_flx}\forcode{ = .true.}), 
     609In the flux formulation (\np{ln\_flx}\forcode{=.true.}), 
    610610the surface boundary condition fields are directly read from input files. 
    611611The user has to define in the namelist \nam{sbc\_flx} the name of the file, 
     
    706706\begin{itemize} 
    707707\item 
    708   NCAR (\np{ln\_NCAR}\forcode{ = .true.}): 
     708  NCAR (\np{ln\_NCAR}\forcode{=.true.}): 
    709709  The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
    710710  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
     
    716716  This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
    717717\item 
    718   COARE 3.0 (\np{ln\_COARE\_3p0}\forcode{ = .true.}): 
     718  COARE 3.0 (\np{ln\_COARE\_3p0}\forcode{=.true.}): 
    719719  See \citet{fairall.bradley.ea_JC03} for more details 
    720720\item 
    721   COARE 3.5 (\np{ln\_COARE\_3p5}\forcode{ = .true.}): 
     721  COARE 3.5 (\np{ln\_COARE\_3p5}\forcode{=.true.}): 
    722722  See \citet{edson.jampana.ea_JPO13} for more details 
    723723\item 
    724   ECMWF (\np{ln\_ECMWF}\forcode{ = .true.}): 
     724  ECMWF (\np{ln\_ECMWF}\forcode{=.true.}): 
    725725  Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation. 
    726726  Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}. 
     
    740740  default constant value used for momentum and heat neutral transfer coefficients 
    741741\item 
    742   \citet{lupkes.gryanik.ea_JGR12} (\np{ln\_Cd\_L12}\forcode{ = .true.}): 
     742  \citet{lupkes.gryanik.ea_JGR12} (\np{ln\_Cd\_L12}\forcode{=.true.}): 
    743743  This scheme adds a dependency on edges at leads, melt ponds and flows 
    744744  of the constant neutral air-ice drag. After some approximations, 
     
    748748  It is theoretically applicable to all ice conditions (not only MIZ). 
    749749\item 
    750   \citet{lupkes.gryanik_JGR15} (\np{ln\_Cd\_L15}\forcode{ = .true.}): 
     750  \citet{lupkes.gryanik_JGR15} (\np{ln\_Cd\_L15}\forcode{=.true.}): 
    751751  Alternative turbulent transfer coefficients formulation between sea-ice 
    752752  and atmosphere with distinct momentum and heat coefficients depending 
     
    811811 
    812812The optional atmospheric pressure can be used to force ocean and ice dynamics 
    813 (\np{ln\_apr\_dyn}\forcode{ = .true.}, \nam{sbc} namelist). 
     813(\np{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc} namelist). 
    814814The input atmospheric forcing defined via \np{sn\_apr} structure (\nam{sbc\_apr} namelist) 
    815815can be interpolated in time to the model time step, and even in space when the interpolation on-the-fly is used. 
     
    867867  Msqm, Mtm, S1, MU2, NU2, L2}, and \textit{T2}). Individual 
    868868constituents are selected by including their names in the array 
    869 \np{clname} in \nam{\_tide} (e.g., \np{clname}\forcode{(1) = 'M2', } 
    870 \np{clname}\forcode{(2) = 'S2'} to select solely the tidal consituents \textit{M2} 
     869\np{clname} in \nam{\_tide} (e.g., \np{clname}\forcode{(1)='M2', } 
     870\np{clname}\forcode{(2)='S2'} to select solely the tidal consituents \textit{M2} 
    871871and \textit{S2}). Optionally, when \np{ln\_tide\_ramp} is set to 
    872872\forcode{.true.}, the equilibrium tidal forcing can be ramped up 
     
    10361036\begin{description} 
    10371037 
    1038   \item[\np{nn\_isf}\forcode{ = 1}]: 
    1039   The ice shelf cavity is represented (\np{ln\_isfcav}\forcode{ = .true.} needed). 
     1038  \item[\np{nn\_isf}\forcode{=1}]: 
     1039  The ice shelf cavity is represented (\np{ln\_isfcav}\forcode{=.true.} needed). 
    10401040  The fwf and heat flux are depending of the local water properties. 
    10411041 
     
    10431043 
    10441044   \begin{description} 
    1045    \item[\np{nn\_isfblk}\forcode{ = 1}]: 
     1045   \item[\np{nn\_isfblk}\forcode{=1}]: 
    10461046     The melt rate is based on a balance between the upward ocean heat flux and 
    10471047     the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
    1048    \item[\np{nn\_isfblk}\forcode{ = 2}]: 
     1048   \item[\np{nn\_isfblk}\forcode{=2}]: 
    10491049     The melt rate and the heat flux are based on a 3 equations formulation 
    10501050     (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
     
    10631063     There are 3 different ways to compute the exchange coeficient: 
    10641064   \begin{description} 
    1065         \item[\np{nn\_gammablk}\forcode{ = 0}]: 
     1065        \item[\np{nn\_gammablk}\forcode{=0}]: 
    10661066     The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}. 
    10671067\[ 
     
    10731073\] 
    10741074     This is the recommended formulation for ISOMIP. 
    1075    \item[\np{nn\_gammablk}\forcode{ = 1}]: 
     1075   \item[\np{nn\_gammablk}\forcode{=1}]: 
    10761076     The salt and heat exchange coefficients are velocity dependent and defined as 
    10771077\[ 
     
    10831083     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters). 
    10841084     See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
    1085    \item[\np{nn\_gammablk}\forcode{ = 2}]: 
     1085   \item[\np{nn\_gammablk}\forcode{=2}]: 
    10861086     The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    10871087\[ 
     
    10941094     This formulation has not been extensively tested in \NEMO\ (not recommended). 
    10951095   \end{description} 
    1096   \item[\np{nn\_isf}\forcode{ = 2}]: 
     1096  \item[\np{nn\_isf}\forcode{=2}]: 
    10971097   The ice shelf cavity is not represented. 
    10981098   The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    10991099   The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
    11001100   (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
    1101    (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}\forcode{ = 3}). 
     1101   (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}\forcode{=3}). 
    11021102   The effective melting length (\np{sn\_Leff\_isf}) is read from a file. 
    1103   \item[\np{nn\_isf}\forcode{ = 3}]: 
     1103  \item[\np{nn\_isf}\forcode{=3}]: 
    11041104   The ice shelf cavity is not represented. 
    11051105   The fwf (\np{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
     
    11071107   the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}). 
    11081108   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    1109   \item[\np{nn\_isf}\forcode{ = 4}]: 
    1110    The ice shelf cavity is opened (\np{ln\_isfcav}\forcode{ = .true.} needed). 
     1109  \item[\np{nn\_isf}\forcode{=4}]: 
     1110   The ice shelf cavity is opened (\np{ln\_isfcav}\forcode{=.true.} needed). 
    11111111   However, the fwf is not computed but specified from file \np{sn\_fwfisf}). 
    11121112   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    1113    As in \np{nn\_isf}\forcode{ = 1}, the fluxes are spread over the top boundary layer thickness (\np{rn\_hisf\_tbl})\\ 
     1113   As in \np{nn\_isf}\forcode{=1}, the fluxes are spread over the top boundary layer thickness (\np{rn\_hisf\_tbl})\\ 
    11141114\end{description} 
    11151115 
    1116 $\bullet$ \np{nn\_isf}\forcode{ = 1} and \np{nn\_isf}\forcode{ = 2} compute a melt rate based on 
     1116$\bullet$ \np{nn\_isf}\forcode{=1} and \np{nn\_isf}\forcode{=2} compute a melt rate based on 
    11171117the water mass properties, ocean velocities and depth. 
    11181118This flux is thus highly dependent of the model resolution (horizontal and vertical), 
    11191119realism of the water masses onto the shelf ...\\ 
    11201120 
    1121 $\bullet$ \np{nn\_isf}\forcode{ = 3} and \np{nn\_isf}\forcode{ = 4} read the melt rate from a file. 
     1121$\bullet$ \np{nn\_isf}\forcode{=3} and \np{nn\_isf}\forcode{=4} read the melt rate from a file. 
    11221122You have total control of the fwf forcing. 
    11231123This can be useful if the water masses on the shelf are not realistic or 
     
    11651165\end{description} 
    11661166 
    1167 If \np{ln\_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with 
     1167If \np{ln\_iscpl}\forcode{=.true.}, the isf draft is assume to be different at each restart step with 
    11681168potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics. 
    11691169The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases: 
     
    12011201 
    12021202In order to remove the trend and keep the conservation level as close to 0 as possible, 
    1203 a simple conservation scheme is available with \np{ln\_hsb}\forcode{ = .true.}. 
     1203a simple conservation scheme is available with \np{ln\_hsb}\forcode{=.true.}. 
    12041204The heat/salt/vol. gain/loss is diagnosed, as well as the location. 
    12051205A correction increment is computed and apply each time step during the next \np{rn\_fiscpl} time steps. 
     
    12271227which is an integer representing how many icebergs of this class are being described as one lagrangian point 
    12281228(this reduces the numerical problem of tracking every single iceberg). 
    1229 They are enabled by setting \np{ln\_icebergs}\forcode{ = .true.}. 
     1229They are enabled by setting \np{ln\_icebergs}\forcode{=.true.}. 
    12301230 
    12311231Two initialisation schemes are possible. 
     
    12381238  \np{nn\_test\_icebergs} is defined by four numbers in \np{nn\_test\_box} representing the corners of 
    12391239  the geographical box: lonmin,lonmax,latmin,latmax 
    1240 \item[\np{nn\_test\_icebergs}\forcode{ = -1}] 
     1240\item[\np{nn\_test\_icebergs}\forcode{=-1}] 
    12411241  In this scheme, the model reads a calving file supplied in the \np{sn\_icb} parameter. 
    12421242  This should be a file with a field on the configuration grid (typically ORCA) 
     
    12971297 
    12981298Physical processes related to ocean surface waves can be accounted by setting the logical variable 
    1299 \np{ln\_wave}\forcode{ = .true.} in \nam{sbc} namelist. In addition, specific flags accounting for 
     1299\np{ln\_wave}\forcode{=.true.} in \nam{sbc} namelist. In addition, specific flags accounting for 
    13001300different processes should be activated as explained in the following sections. 
    13011301 
     
    14341434In order to include this term, once evaluated the Stokes drift (using one of the 3 possible 
    14351435approximations described in \autoref{subsec:SBC_wave_sdw}), 
    1436 \np{ln\_stcor}\forcode{ = .true.} has to be set. 
     1436\np{ln\_stcor}\forcode{=.true.} has to be set. 
    14371437 
    14381438 
     
    14751475 
    14761476The wave stress derived from an external wave model can be provided either through the normalized 
    1477 wave stress into the ocean by setting \np{ln\_tauwoc}\forcode{ = .true.}, or through the zonal and 
    1478 meridional stress components by setting \np{ln\_tauw}\forcode{ = .true.}. 
     1477wave stress into the ocean by setting \np{ln\_tauwoc}\forcode{=.true.}, or through the zonal and 
     1478meridional stress components by setting \np{ln\_tauw}\forcode{=.true.}. 
    14791479 
    14801480 
     
    15211521assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF. 
    15221522The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO\ by 
    1523 setting \np{ln\_dm2dc}\forcode{ = .true.} (a \textit{\nam{sbc}} namelist variable) when 
    1524 using a bulk formulation (\np{ln\_blk}\forcode{ = .true.}) or 
    1525 the flux formulation (\np{ln\_flx}\forcode{ = .true.}). 
     1523setting \np{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}} namelist variable) when 
     1524using a bulk formulation (\np{ln\_blk}\forcode{=.true.}) or 
     1525the flux formulation (\np{ln\_flx}\forcode{=.true.}). 
    15261526The reconstruction is performed in the \mdl{sbcdcy} module. 
    15271527The detail of the algoritm used can be found in the appendix~A of \cite{bernie.guilyardi.ea_CD07}. 
     
    15601560\label{subsec:SBC_rotation} 
    15611561 
    1562 When using a flux (\np{ln\_flx}\forcode{ = .true.}) or bulk (\np{ln\_blk}\forcode{ = .true.}) formulation, 
     1562When using a flux (\np{ln\_flx}\forcode{=.true.}) or bulk (\np{ln\_blk}\forcode{=.true.}) formulation, 
    15631563pairs of vector components can be rotated from east-north directions onto the local grid directions. 
    15641564This is particularly useful when interpolation on the fly is used since here any vectors are likely to 
     
    15861586 
    15871587Options are defined through the \nam{sbc\_ssr} namelist variables. 
    1588 On forced mode using a flux formulation (\np{ln\_flx}\forcode{ = .true.}), 
     1588On forced mode using a flux formulation (\np{ln\_flx}\forcode{=.true.}), 
    15891589a feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$: 
    15901590\[ 
     
    16751675(seek advice from UKMO if necessary). 
    16761676Currently, the code is only designed to work when using the NCAR forcing option for \NEMO\ %GS: still true ? 
    1677 (with \textit{calc\_strair}\forcode{ = .true.} and \textit{calc\_Tsfc}\forcode{ = .true.} in the CICE name-list), 
     1677(with \textit{calc\_strair}\forcode{=.true.} and \textit{calc\_Tsfc}\forcode{=.true.} in the CICE name-list), 
    16781678or alternatively when \NEMO\ is coupled to the HadGAM3 atmosphere model 
    1679 (with \textit{calc\_strair}\forcode{ = .false.} and \textit{calc\_Tsfc}\forcode{ = false}). 
     1679(with \textit{calc\_strair}\forcode{=.false.} and \textit{calc\_Tsfc}\forcode{=false}). 
    16801680The code is intended to be used with \np{nn\_fsbc} set to 1 
    16811681(although coupling ocean and ice less frequently should work, 
     
    17071707 
    17081708\begin{description} 
    1709 \item[\np{nn\_fwb}\forcode{ = 0}] 
     1709\item[\np{nn\_fwb}\forcode{=0}] 
    17101710  no control at all. 
    17111711  The mean sea level is free to drift, and will certainly do so. 
    1712 \item[\np{nn\_fwb}\forcode{ = 1}] 
     1712\item[\np{nn\_fwb}\forcode{=1}] 
    17131713  global mean \textit{emp} set to zero at each model time step. 
    17141714  %GS: comment below still relevant ? 
    17151715  %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling). 
    1716 \item[\np{nn\_fwb}\forcode{ = 2}] 
     1716\item[\np{nn\_fwb}\forcode{=2}] 
    17171717  freshwater budget is adjusted from the previous year annual mean budget which 
    17181718  is read in the \textit{EMPave\_old.dat} file. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11524 r11537  
    5555 
    5656The user has the option of extracting each tendency term on the RHS of the tracer equation for output 
    57 (\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}\forcode{ = .true.}), as described in \autoref{chap:DIA}. 
     57(\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}\forcode{=.true.}), as described in \autoref{chap:DIA}. 
    5858 
    5959% ================================================================ 
     
    8282Indeed, it is obtained by using the following equality: $\nabla \cdot (\vect U \, T) = \vect U \cdot \nabla T$ which 
    8383results from the use of the continuity equation, $\partial_t e_3 + e_3 \; \nabla \cdot \vect U = 0$ 
    84 (which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie\ \np{ln\_linssh}\forcode{ = .true.}). 
     84(which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie\ \np{ln\_linssh}\forcode{=.true.}). 
    8585Therefore it is of paramount importance to design the discrete analogue of the advection tendency so that 
    8686it is consistent with the continuity equation in order to enforce the conservation properties of 
    8787the continuous equations. 
    88 In other words, by setting $\tau = 1$ in (\autoref{eq:tra_adv}) we recover the discrete form of 
     88In other words, by setting $\tau=1$ in (\autoref{eq:tra_adv}) we recover the discrete form of 
    8989the continuity equation which is used to calculate the vertical velocity. 
    9090%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    120120\begin{description} 
    121121\item[linear free surface:] 
    122   (\np{ln\_linssh}\forcode{ = .true.}) 
     122  (\np{ln\_linssh}\forcode{=.true.}) 
    123123  the first level thickness is constant in time: 
    124124  the vertical boundary condition is applied at the fixed surface $z = 0$ rather than on 
     
    128128  the first level tracer value. 
    129129\item[non-linear free surface:] 
    130   (\np{ln\_linssh}\forcode{ = .false.}) 
     130  (\np{ln\_linssh}\forcode{=.false.}) 
    131131  convergence/divergence in the first ocean level moves the free surface up/down. 
    132132  There is no tracer advection through it so that the advective fluxes through the surface are also zero. 
     
    184184%        2nd and 4th order centred schemes 
    185185% ------------------------------------------------------------------------------------------------------------- 
    186 \subsection[CEN: Centred scheme (\forcode{ln_traadv_cen = .true.})] 
    187 {CEN: Centred scheme (\protect\np{ln\_traadv\_cen}\forcode{ = .true.})} 
     186\subsection[CEN: Centred scheme (\forcode{ln_traadv_cen=.true.})] 
     187{CEN: Centred scheme (\protect\np{ln\_traadv\_cen}\forcode{=.true.})} 
    188188\label{subsec:TRA_adv_cen} 
    189189 
    190190%        2nd order centred scheme 
    191191 
    192 The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen}\forcode{ = .true.}. 
     192The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen}\forcode{=.true.}. 
    193193Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by 
    194194setting \np{nn\_cen\_h} and \np{nn\_cen\_v} to $2$ or $4$. 
     
    222222  \tau_u^{cen4} = \overline{T - \frac{1}{6} \, \delta_i \Big[ \delta_{i + 1/2}[T] \, \Big]}^{\,i + 1/2} 
    223223\end{equation} 
    224 In the vertical direction (\np{nn\_cen\_v}\forcode{ = 4}), 
     224In the vertical direction (\np{nn\_cen\_v}\forcode{=4}), 
    225225a $4^{th}$ COMPACT interpolation has been prefered \citep{demange_phd14}. 
    226226In the COMPACT scheme, both the field and its derivative are interpolated, which leads, after a matrix inversion, 
     
    252252%        FCT scheme 
    253253% ------------------------------------------------------------------------------------------------------------- 
    254 \subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct = .true.})] 
    255 {FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}\forcode{ = .true.})} 
     254\subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct=.true.})] 
     255{FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}\forcode{=.true.})} 
    256256\label{subsec:TRA_adv_tvd} 
    257257 
    258 The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct}\forcode{ = .true.}. 
     258The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct}\forcode{=.true.}. 
    259259Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by 
    260260setting \np{nn\_fct\_h} and \np{nn\_fct\_v} to $2$ or $4$. 
     
    296296%        MUSCL scheme 
    297297% ------------------------------------------------------------------------------------------------------------- 
    298 \subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus = .true.})] 
    299 {MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}\forcode{ = .true.})} 
     298\subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus=.true.})] 
     299{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}\forcode{=.true.})} 
    300300\label{subsec:TRA_adv_mus} 
    301301 
    302 The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus}\forcode{ = .true.}. 
     302The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus}\forcode{=.true.}. 
    303303MUSCL implementation can be found in the \mdl{traadv\_mus} module. 
    304304 
     
    328328This choice ensure the \textit{positive} character of the scheme. 
    329329In addition, fluxes round a grid-point where a runoff is applied can optionally be computed using upstream fluxes 
    330 (\np{ln\_mus\_ups}\forcode{ = .true.}). 
     330(\np{ln\_mus\_ups}\forcode{=.true.}). 
    331331 
    332332% ------------------------------------------------------------------------------------------------------------- 
    333333%        UBS scheme 
    334334% ------------------------------------------------------------------------------------------------------------- 
    335 \subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs = .true.})] 
    336 {UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}\forcode{ = .true.})} 
     335\subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs=.true.})] 
     336{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}\forcode{=.true.})} 
    337337\label{subsec:TRA_adv_ubs} 
    338338 
    339 The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs}\forcode{ = .true.}. 
     339The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs}\forcode{=.true.}. 
    340340UBS implementation can be found in the \mdl{traadv\_mus} module. 
    341341 
     
    367367\citep{shchepetkin.mcwilliams_OM05, demange_phd14}. 
    368368Therefore the vertical flux is evaluated using either a $2^nd$ order FCT scheme or a $4^th$ order COMPACT scheme 
    369 (\np{nn\_ubs\_v}\forcode{ = 2 or 4}). 
     369(\np{nn\_ubs\_v}\forcode{=2 or 4}). 
    370370 
    371371For stability reasons (see \autoref{chap:STP}), the first term  in \autoref{eq:tra_adv_ubs} 
     
    406406%        QCK scheme 
    407407% ------------------------------------------------------------------------------------------------------------- 
    408 \subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck = .true.})] 
    409 {QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}\forcode{ = .true.})} 
     408\subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck=.true.})] 
     409{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}\forcode{=.true.})} 
    410410\label{subsec:TRA_adv_qck} 
    411411 
    412412The Quadratic Upstream Interpolation for Convective Kinematics with Estimated Streaming Terms (QUICKEST) scheme 
    413 proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck}\forcode{ = .true.}. 
     413proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck}\forcode{=.true.}. 
    414414QUICKEST implementation can be found in the \mdl{traadv\_qck} module. 
    415415 
     
    453453except for the pure vertical component that appears when a rotation tensor is used. 
    454454This latter component is solved implicitly together with the vertical diffusion term (see \autoref{chap:STP}). 
    455 When \np{ln\_traldf\_msc}\forcode{ = .true.}, a Method of Stabilizing Correction is used in which 
     455When \np{ln\_traldf\_msc}\forcode{=.true.}, a Method of Stabilizing Correction is used in which 
    456456the pure vertical component is split into an explicit and an implicit part \citep{lemarie.debreu.ea_OM12}. 
    457457 
     
    466466 
    467467\begin{description} 
    468 \item[\np{ln\_traldf\_OFF}\forcode{ = .true.}:] 
     468\item[\np{ln\_traldf\_OFF}\forcode{=.true.}:] 
    469469  no operator selected, the lateral diffusive tendency will not be applied to the tracer equation. 
    470470  This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example). 
    471 \item[\np{ln\_traldf\_lap}\forcode{ = .true.}:] 
     471\item[\np{ln\_traldf\_lap}\forcode{=.true.}:] 
    472472  a laplacian operator is selected. 
    473473  This harmonic operator takes the following expression:  $\mathcal{L}(T) = \nabla \cdot A_{ht} \; \nabla T $, 
    474474  where the gradient operates along the selected direction (see \autoref{subsec:TRA_ldf_dir}), 
    475475  and $A_{ht}$ is the eddy diffusivity coefficient expressed in $m^2/s$ (see \autoref{chap:LDF}). 
    476 \item[\np{ln\_traldf\_blp}\forcode{ = .true.}]: 
     476\item[\np{ln\_traldf\_blp}\forcode{=.true.}]: 
    477477  a bilaplacian operator is selected. 
    478478  This biharmonic operator takes the following expression: 
     
    500500The choice of a direction of action determines the form of operator used. 
    501501The operator is a simple (re-entrant) laplacian acting in the (\textbf{i},\textbf{j}) plane when 
    502 iso-level option is used (\np{ln\_traldf\_lev}\forcode{ = .true.}) or 
     502iso-level option is used (\np{ln\_traldf\_lev}\forcode{=.true.}) or 
    503503when a horizontal (\ie\ geopotential) operator is demanded in \textit{z}-coordinate 
    504 (\np{ln\_traldf\_hor} and \np{ln\_zco} equal \forcode{.true.}). 
     504(\np{ln\_traldf\_hor} and \np{ln\_zco}\forcode{=.true.}). 
    505505The associated code can be found in the \mdl{traldf\_lap\_blp} module. 
    506506The operator is a rotated (re-entrant) laplacian when 
    507507the direction along which it acts does not coincide with the iso-level surfaces, 
    508508that is when standard or triad iso-neutral option is used 
    509 (\np{ln\_traldf\_iso} or \np{ln\_traldf\_triad} equals \forcode{.true.}, 
     509(\np{ln\_traldf\_iso} or \np{ln\_traldf\_triad} = \forcode{.true.}, 
    510510see \mdl{traldf\_iso} or \mdl{traldf\_triad} module, resp.), or 
    511511when a horizontal (\ie\ geopotential) operator is demanded in \textit{s}-coordinate 
    512 (\np{ln\_traldf\_hor} and \np{ln\_sco} equal \forcode{.true.}) 
     512(\np{ln\_traldf\_hor} and \np{ln\_sco} = \forcode{.true.}) 
    513513\footnote{In this case, the standard iso-neutral operator will be automatically selected}. 
    514514In that case, a rotation is applied to the gradient(s) that appears in the operator so that 
     
    540540It is a \textit{horizontal} operator (\ie acting along geopotential surfaces) in 
    541541the $z$-coordinate with or without partial steps, but is simply an iso-level operator in the $s$-coordinate. 
    542 It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}\forcode{ = .true.}, 
    543 we have \np{ln\_traldf\_lev}\forcode{ = .true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}\forcode{ = .true.}. 
     542It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}\forcode{=.true.}, 
     543we have \np{ln\_traldf\_lev}\forcode{=.true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}\forcode{=.true.}. 
    544544In both cases, it significantly contributes to diapycnal mixing. 
    545545It is therefore never recommended, even when using it in the bilaplacian case. 
    546546 
    547 Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{ = .true.}), 
     547Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{=.true.}), 
    548548tracers in horizontally adjacent cells are located at different depths in the vicinity of the bottom. 
    549549In this case, horizontal derivatives in (\autoref{eq:tra_ldf_lap}) at the bottom level require a specific treatment. 
     
    578578$r_1$ and $r_2$ are the slopes between the surface of computation ($z$- or $s$-surfaces) and 
    579579the surface along which the diffusion operator acts (\ie\ horizontal or iso-neutral surfaces). 
    580 It is thus used when, in addition to \np{ln\_traldf\_lap}\forcode{ = .true.}, 
    581 we have \np{ln\_traldf\_iso}\forcode{ = .true.}, 
    582 or both \np{ln\_traldf\_hor}\forcode{ = .true.} and \np{ln\_zco}\forcode{ = .true.}. 
     580It is thus used when, in addition to \np{ln\_traldf\_lap}\forcode{=.true.}, 
     581we have \np{ln\_traldf\_iso}\forcode{=.true.}, 
     582or both \np{ln\_traldf\_hor}\forcode{=.true.} and \np{ln\_zco}\forcode{=.true.}. 
    583583The way these slopes are evaluated is given in \autoref{sec:LDF_slp}. 
    584584At the surface, bottom and lateral boundaries, the turbulent fluxes of heat and salt are set to zero using 
     
    596596any additional background horizontal diffusion \citep{guilyardi.madec.ea_CD01}. 
    597597 
    598 Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{ = .true.}), 
     598Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{=.true.}), 
    599599the horizontal derivatives at the bottom level in \autoref{eq:tra_ldf_iso} require a specific treatment. 
    600600They are calculated in module zpshde, described in \autoref{sec:TRA_zpshde}. 
     
    607607 
    608608An alternative scheme developed by \cite{griffies.gnanadesikan.ea_JPO98} which ensures tracer variance decreases 
    609 is also available in \NEMO\ (\np{ln\_traldf\_triad}\forcode{ = .true.}). 
     609is also available in \NEMO\ (\np{ln\_traldf\_triad}\forcode{=.true.}). 
    610610A complete description of the algorithm is given in \autoref{apdx:triad}. 
    611611 
     
    655655respectively. 
    656656Generally, $A_w^{vT} = A_w^{vS}$ except when double diffusive mixing is parameterised 
    657 (\ie\ \np{ln\_zdfddm} equals \forcode{.true.},). 
     657(\ie\ \np{ln\_zdfddm}\forcode{=.true.},). 
    658658The way these coefficients are evaluated is given in \autoref{chap:ZDF} (ZDF). 
    659659Furthermore, when iso-neutral mixing is used, both mixing coefficients are increased by 
     
    731731Such time averaging prevents the divergence of odd and even time step (see \autoref{chap:STP}). 
    732732 
    733 In the linear free surface case (\np{ln\_linssh}\forcode{ = .true.}), an additional term has to be added on 
     733In the linear free surface case (\np{ln\_linssh}\forcode{=.true.}), an additional term has to be added on 
    734734both temperature and salinity. 
    735735On temperature, this term remove the heat content associated with mass exchange that has been added to $Q_{ns}$. 
     
    763763 
    764764Options are defined through the \nam{tra\_qsr} namelist variables. 
    765 When the penetrative solar radiation option is used (\np{ln\_traqsr}\forcode{ = .true.}), 
     765When the penetrative solar radiation option is used (\np{ln\_traqsr}\forcode{=.true.}), 
    766766the solar radiation penetrates the top few tens of meters of the ocean. 
    767 If it is not used (\np{ln\_traqsr}\forcode{ = .false.}) all the heat flux is absorbed in the first ocean level. 
     767If it is not used (\np{ln\_traqsr}\forcode{=.false.}) all the heat flux is absorbed in the first ocean level. 
    768768Thus, in the former case a term is added to the time evolution equation of temperature \autoref{eq:PE_tra_T} and 
    769769the surface boundary condition is modified to take into account only the non-penetrative part of the surface 
     
    794794larger depths where it contributes to local heating. 
    795795The way this second part of the solar energy penetrates into the ocean depends on which formulation is chosen. 
    796 In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd}\forcode{ = .true.}) 
     796In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd}\forcode{=.true.}) 
    797797a chlorophyll-independent monochromatic formulation is chosen for the shorter wavelengths, 
    798798leading to the following expression \citep{paulson.simpson_JPO77}: 
     
    822822The 2-bands formulation does not reproduce the full model very well. 
    823823 
    824 The RGB formulation is used when \np{ln\_qsr\_rgb}\forcode{ = .true.}. 
     824The RGB formulation is used when \np{ln\_qsr\_rgb}\forcode{=.true.}. 
    825825The RGB attenuation coefficients (\ie\ the inverses of the extinction length scales) are tabulated over 
    82682661 nonuniform chlorophyll classes ranging from 0.01 to 10 g.Chl/L 
     
    829829 
    830830\begin{description} 
    831 \item[\np{nn\_chldta}\forcode{ = 0}] 
     831\item[\np{nn\_chldta}\forcode{=0}] 
    832832  a constant 0.05 g.Chl/L value everywhere ; 
    833 \item[\np{nn\_chldta}\forcode{ = 1}] 
     833\item[\np{nn\_chldta}\forcode{=1}] 
    834834  an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in 
    835835  the vertical direction; 
    836 \item[\np{nn\_chldta}\forcode{ = 2}] 
     836\item[\np{nn\_chldta}\forcode{=2}] 
    837837  same as previous case except that a vertical profile of chlorophyl is used. 
    838838  Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value; 
    839 \item[\np{ln\_qsr\_bio}\forcode{ = .true.}] 
     839\item[\np{ln\_qsr\_bio}\forcode{=.true.}] 
    840840  simulated time varying chlorophyll by TOP biogeochemical model. 
    841841  In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in 
     
    876876%        Bottom Boundary Condition 
    877877% ------------------------------------------------------------------------------------------------------------- 
    878 \subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc = .true.})] 
     878\subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc=.true.})] 
    879879{Bottom boundary condition (\protect\mdl{trabbc})} 
    880880\label{subsec:TRA_bbc} 
     
    915915% Bottom Boundary Layer 
    916916% ================================================================ 
    917 \section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl = .true.})] 
    918 {Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln\_trabbl}\forcode{ = .true.})} 
     917\section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl=.true.})] 
     918{Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln\_trabbl}\forcode{=.true.})} 
    919919\label{sec:TRA_bbl} 
    920920%--------------------------------------------nambbl--------------------------------------------------------- 
     
    948948%        Diffusive BBL 
    949949% ------------------------------------------------------------------------------------------------------------- 
    950 \subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf = 1})] 
    951 {Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}\forcode{ = 1})} 
     950\subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf=1})] 
     951{Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}\forcode{=1})} 
    952952\label{subsec:TRA_bbl_diff} 
    953953 
    954 When applying sigma-diffusion (\np{ln\_trabbl}\forcode{ = .true.} and \np{nn\_bbl\_ldf} set to 1), 
     954When applying sigma-diffusion (\np{ln\_trabbl}\forcode{=.true.} and \np{nn\_bbl\_ldf} set to 1), 
    955955the diffusive flux between two adjacent cells at the ocean floor is given by 
    956956\[ 
     
    988988%        Advective BBL 
    989989% ------------------------------------------------------------------------------------------------------------- 
    990 \subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv = [12]})] 
    991 {Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{ = [12]})} 
     990\subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=[12]})] 
     991{Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{=[12]})} 
    992992\label{subsec:TRA_bbl_adv} 
    993993 
     
    10201020%%%gmcomment   :  this section has to be really written 
    10211021 
    1022 When applying an advective BBL (\np{nn\_bbl\_adv}\forcode{ = 1..2}), an overturning circulation is added which 
     1022When applying an advective BBL (\np{nn\_bbl\_adv}\forcode{=1..2}), an overturning circulation is added which 
    10231023connects two adjacent bottom grid-points only if dense water overlies less dense water on the slope. 
    10241024The density difference causes dense water to move down the slope. 
    10251025 
    1026 \np{nn\_bbl\_adv}\forcode{ = 1}: 
     1026\np{nn\_bbl\_adv}\forcode{=1}: 
    10271027the downslope velocity is chosen to be the Eulerian ocean velocity just above the topographic step 
    10281028(see black arrow in \autoref{fig:bbl}) \citep{beckmann.doscher_JPO97}. 
     
    10311031if the velocity is directed towards greater depth (\ie\ $\vect U \cdot \nabla H > 0$). 
    10321032 
    1033 \np{nn\_bbl\_adv}\forcode{ = 2}: 
     1033\np{nn\_bbl\_adv}\forcode{=2}: 
    10341034the downslope velocity is chosen to be proportional to $\Delta \rho$, 
    10351035the density difference between the higher cell and lower cell densities \citep{campin.goosse_T99}. 
     
    11591159(\ie\ fluxes plus content in mass exchanges). 
    11601160$\gamma$ is initialized as \np{rn\_atfp} (\textbf{namelist} parameter). 
    1161 Its default value is \np{rn\_atfp}\forcode{ = 10.e-3}. 
     1161Its default value is \np{rn\_atfp}\forcode{=10.e-3}. 
    11621162Note that the forcing correction term in the filter is not applied in linear free surface 
    1163 (\jp{ln\_linssh}\forcode{ = .true.}) (see \autoref{subsec:TRA_sbc}). 
     1163(\jp{ln\_linssh}\forcode{=.true.}) (see \autoref{subsec:TRA_sbc}). 
    11641164Not also that in constant volume case, the time stepping is performed on $T$, not on its content, $e_{3t}T$. 
    11651165 
     
    12201220 
    12211221\begin{description} 
    1222 \item[\np{ln\_teos10}\forcode{ = .true.}] 
     1222\item[\np{ln\_teos10}\forcode{=.true.}] 
    12231223  the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used. 
    12241224  The accuracy of this approximation is comparable to the TEOS-10 rational function approximation, 
     
    12391239  either computing the air-sea and ice-sea fluxes (forced mode) or 
    12401240  sending the SST field to the atmosphere (coupled mode). 
    1241 \item[\np{ln\_eos80}\forcode{ = .true.}] 
     1241\item[\np{ln\_eos80}\forcode{=.true.}] 
    12421242  the polyEOS80-bsq equation of seawater is used. 
    12431243  It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to 
     
    12511251  Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which 
    12521252  is conserved by the model: $C_p$ is set to a constant value, the TEOS10 value. 
    1253 \item[\np{ln\_seos}\forcode{ = .true.}] 
     1253\item[\np{ln\_seos}\forcode{=.true.}] 
    12541254  a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen, 
    12551255  the coefficients of which has been optimized to fit the behavior of TEOS10 
     
    13761376I've changed "derivative" to "difference" and "mean" to "average"} 
    13771377 
    1378 With partial cells (\np{ln\_zps}\forcode{ = .true.}) at bottom and top (\np{ln\_isfcav}\forcode{ = .true.}), 
     1378With partial cells (\np{ln\_zps}\forcode{=.true.}) at bottom and top (\np{ln\_isfcav}\forcode{=.true.}), 
    13791379in general, tracers in horizontally adjacent cells live at different depths. 
    13801380Horizontal gradients of tracers are needed for horizontal diffusion (\mdl{traldf} module) and 
    13811381the hydrostatic pressure gradient calculations (\mdl{dynhpg} module). 
    1382 The partial cell properties at the top (\np{ln\_isfcav}\forcode{ = .true.}) are computed in the same way as 
     1382The partial cell properties at the top (\np{ln\_isfcav}\forcode{=.true.}) are computed in the same way as 
    13831383for the bottom. 
    13841384So, only the bottom interpolation is explained below. 
     
    13961396      \protect\label{fig:Partial_step_scheme} 
    13971397      Discretisation of the horizontal difference and average of tracers in the $z$-partial step coordinate 
    1398       (\protect\np{ln\_zps}\forcode{ = .true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$. 
     1398      (\protect\np{ln\_zps}\forcode{=.true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$. 
    13991399      A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$, 
    14001400      the tracer value at the depth of the shallower tracer point of the two adjacent bottom $T$-points. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r11435 r11537  
    3939are computed and added to the general trend in the \mdl{dynzdf} and \mdl{trazdf} modules, respectively. 
    4040%These trends can be computed using either a forward time stepping scheme 
    41 %(namelist parameter \np{ln\_zdfexp}\forcode{ = .true.}) or a backward time stepping scheme 
    42 %(\np{ln\_zdfexp}\forcode{ = .false.}) depending on the magnitude of the mixing coefficients, 
     41%(namelist parameter \np{ln\_zdfexp}\forcode{=.true.}) or a backward time stepping scheme 
     42%(\np{ln\_zdfexp}\forcode{=.false.}) depending on the magnitude of the mixing coefficients, 
    4343%and thus of the formulation used (see \autoref{chap:STP}). 
    4444 
     
    5151%        Constant 
    5252% ------------------------------------------------------------------------------------------------------------- 
    53 \subsection[Constant (\forcode{ln_zdfcst = .true.})] 
    54 {Constant (\protect\np{ln\_zdfcst}\forcode{ = .true.})} 
     53\subsection[Constant (\forcode{ln_zdfcst=.true.})] 
     54{Constant (\protect\np{ln\_zdfcst}\forcode{=.true.})} 
    5555\label{subsec:ZDF_cst} 
    5656 
     
    7474%        Richardson Number Dependent 
    7575% ------------------------------------------------------------------------------------------------------------- 
    76 \subsection[Richardson number dependent (\forcode{ln_zdfric = .true.})] 
    77 {Richardson number dependent (\protect\np{ln\_zdfric}\forcode{ = .true.})} 
     76\subsection[Richardson number dependent (\forcode{ln_zdfric=.true.})] 
     77{Richardson number dependent (\protect\np{ln\_zdfric}\forcode{=.true.})} 
    7878\label{subsec:ZDF_ric} 
    7979 
     
    8383%-------------------------------------------------------------------------------------------------------------- 
    8484 
    85 When \np{ln\_zdfric}\forcode{ = .true.}, a local Richardson number dependent formulation for the vertical momentum and 
     85When \np{ln\_zdfric}\forcode{=.true.}, a local Richardson number dependent formulation for the vertical momentum and 
    8686tracer eddy coefficients is set through the \nam{zdf\_ric} namelist variables. 
    8787The vertical mixing coefficients are diagnosed from the large scale variables computed by the model. 
     
    109109 
    110110A simple mixing-layer model to transfer and dissipate the atmospheric forcings 
    111 (wind-stress and buoyancy fluxes) can be activated setting the \np{ln\_mldw}\forcode{ = .true.} in the namelist. 
     111(wind-stress and buoyancy fluxes) can be activated setting the \np{ln\_mldw}\forcode{=.true.} in the namelist. 
    112112 
    113113In this case, the local depth of turbulent wind-mixing or "Ekman depth" $h_{e}(x,y,t)$ is evaluated and 
     
    132132%        TKE Turbulent Closure Scheme 
    133133% ------------------------------------------------------------------------------------------------------------- 
    134 \subsection[TKE turbulent closure scheme (\forcode{ln_zdftke = .true.})] 
    135 {TKE turbulent closure scheme (\protect\np{ln\_zdftke}\forcode{ = .true.})} 
     134\subsection[TKE turbulent closure scheme (\forcode{ln_zdftke=.true.})] 
     135{TKE turbulent closure scheme (\protect\np{ln\_zdftke}\forcode{=.true.})} 
    136136\label{subsec:ZDF_tke} 
    137137%--------------------------------------------namzdf_tke-------------------------------------------------- 
     
    213213which is valid in a stable stratified region with constant values of the Brunt-Vais\"{a}l\"{a} frequency. 
    214214The resulting length scale is bounded by the distance to the surface or to the bottom 
    215 (\np{nn\_mxl}\forcode{ = 0}) or by the local vertical scale factor (\np{nn\_mxl}\forcode{ = 1}). 
     215(\np{nn\_mxl}\forcode{=0}) or by the local vertical scale factor (\np{nn\_mxl}\forcode{=1}). 
    216216\citet{blanke.delecluse_JPO93} notice that this simplification has two major drawbacks: 
    217217it makes no sense for locally unstable stratification and the computation no longer uses all 
    218218the information contained in the vertical density profile. 
    219 To overcome these drawbacks, \citet{madec.delecluse.ea_NPM98} introduces the \np{nn\_mxl}\forcode{ = 2, 3} cases, 
     219To overcome these drawbacks, \citet{madec.delecluse.ea_NPM98} introduces the \np{nn\_mxl}\forcode{=2, 3} cases, 
    220220which add an extra assumption concerning the vertical gradient of the computed length scale. 
    221221So, the length scales are first evaluated as in \autoref{eq:tke_mxl0_1} and then bounded such that: 
     
    258258where $l^{(k)}$ is computed using \autoref{eq:tke_mxl0_1}, \ie\ $l^{(k)} = \sqrt {2 {\bar e}^{(k)} / {N^2}^{(k)} }$. 
    259259 
    260 In the \np{nn\_mxl}\forcode{ = 2} case, the dissipation and mixing length scales take the same value: 
    261 $ l_k=  l_\epsilon = \min \left(\ l_{up} \;,\;  l_{dwn}\ \right)$, while in the \np{nn\_mxl}\forcode{ = 3} case, 
     260In the \np{nn\_mxl}\forcode{=2} case, the dissipation and mixing length scales take the same value: 
     261$ l_k=  l_\epsilon = \min \left(\ l_{up} \;,\;  l_{dwn}\ \right)$, while in the \np{nn\_mxl}\forcode{=3} case, 
    262262the dissipation and mixing turbulent length scales are give as in \citet{gaspar.gregoris.ea_JGR90}: 
    263263\[ 
     
    376376(\ie\ near-inertial oscillations and ocean swells and waves). 
    377377 
    378 When using this parameterization (\ie\ when \np{nn\_etau}\forcode{ = 1}), 
     378When using this parameterization (\ie\ when \np{nn\_etau}\forcode{=1}), 
    379379the TKE input to the ocean ($S$) imposed by the winds in the form of near-inertial oscillations, 
    380380swell and waves is parameterized by \autoref{eq:ZDF_Esbc} the standard TKE surface boundary condition, 
     
    389389(no penetration if $f_i=1$, \ie\ if the ocean is entirely covered by sea-ice). 
    390390The value of $f_r$, usually a few percents, is specified through \np{rn\_efr} namelist parameter. 
    391 The vertical mixing length scale, $h_\tau$, can be set as a 10~m uniform value (\np{nn\_etau}\forcode{ = 0}) or 
     391The vertical mixing length scale, $h_\tau$, can be set as a 10~m uniform value (\np{nn\_etau}\forcode{=0}) or 
    392392a latitude dependent value (varying from 0.5~m at the Equator to a maximum value of 30~m at high latitudes 
    393 (\np{nn\_etau}\forcode{ = 1}). 
    394  
    395 Note that two other option exist, \np{nn\_etau}\forcode{ = 2, 3}. 
     393(\np{nn\_etau}\forcode{=1}). 
     394 
     395Note that two other option exist, \np{nn\_etau}\forcode{=2, 3}. 
    396396They correspond to applying \autoref{eq:ZDF_Ehtau} only at the base of the mixed layer, 
    397397or to using the high frequency part of the stress to evaluate the fraction of TKE that penetrates the ocean. 
     
    415415%        GLS Generic Length Scale Scheme 
    416416% ------------------------------------------------------------------------------------------------------------- 
    417 \subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls = .true.})] 
    418 {GLS: Generic Length Scale (\protect\np{ln\_zdfgls}\forcode{ = .true.})} 
     417\subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls=.true.})] 
     418{GLS: Generic Length Scale (\protect\np{ln\_zdfgls}\forcode{=.true.})} 
    419419\label{subsec:ZDF_gls} 
    420420 
     
    497497      \protect\label{tab:GLS} 
    498498      Set of predefined GLS parameters, or equivalently predefined turbulence models available with 
    499       \protect\np{ln\_zdfgls}\forcode{ = .true.} and controlled by the \protect\np{nn\_clos} namelist variable in \protect\nam{zdf\_gls}. 
     499      \protect\np{ln\_zdfgls}\forcode{=.true.} and controlled by the \protect\np{nn\_clos} namelist variable in \protect\nam{zdf\_gls}. 
    500500    } 
    501501  \end{center} 
     
    508508$C_{\mu}$ and $C_{\mu'}$ are calculated from stability function proposed by \citet{galperin.kantha.ea_JAS88}, 
    509509or by \citet{kantha.clayson_JGR94} or one of the two functions suggested by \citet{canuto.howard.ea_JPO01} 
    510 (\np{nn\_stab\_func}\forcode{ = 0, 3}, resp.). 
     510(\np{nn\_stab\_func}\forcode{=0, 3}, resp.). 
    511511The value of $C_{0\mu}$ depends on the choice of the stability function. 
    512512 
     
    525525the entrainment depth predicted in stably stratified situations, 
    526526and that its value has to be chosen in accordance with the algebraic model for the turbulent fluxes. 
    527 The clipping is only activated if \np{ln\_length\_lim}\forcode{ = .true.}, 
     527The clipping is only activated if \np{ln\_length\_lim}\forcode{=.true.}, 
    528528and the $c_{lim}$ is set to the \np{rn\_clim\_galp} value. 
    529529 
     
    537537%        OSM OSMOSIS BL Scheme 
    538538% ------------------------------------------------------------------------------------------------------------- 
    539 \subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm = .true.})] 
    540 {OSM: OSMosis boundary layer scheme (\protect\np{ln\_zdfosm}\forcode{ = .true.})} 
     539\subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm=.true.})] 
     540{OSM: OSMosis boundary layer scheme (\protect\np{ln\_zdfosm}\forcode{=.true.})} 
    541541\label{subsec:ZDF_osm} 
    542542%--------------------------------------------namzdf_osm--------------------------------------------------------- 
     
    670670%       Non-Penetrative Convective Adjustment 
    671671% ------------------------------------------------------------------------------------------------------------- 
    672 \subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc = .true.})] 
    673 {Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{ = .true.})} 
     672\subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc=.true.})] 
     673{Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{=.true.})} 
    674674\label{subsec:ZDF_npc} 
    675675 
     
    697697 
    698698Options are defined through the \nam{zdf} namelist variables. 
    699 The non-penetrative convective adjustment is used when \np{ln\_zdfnpc}\forcode{ = .true.}. 
     699The non-penetrative convective adjustment is used when \np{ln\_zdfnpc}\forcode{=.true.}. 
    700700It is applied at each \np{nn\_npc} time step and mixes downwards instantaneously the statically unstable portion of 
    701701the water column, but only until the density structure becomes neutrally stable 
     
    737737%       Enhanced Vertical Diffusion 
    738738% ------------------------------------------------------------------------------------------------------------- 
    739 \subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd = .true.})] 
    740 {Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{ = .true.})} 
     739\subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd=.true.})] 
     740{Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{=.true.})} 
    741741\label{subsec:ZDF_evd} 
    742742 
    743743Options are defined through the  \nam{zdf} namelist variables. 
    744 The enhanced vertical diffusion parameterisation is used when \np{ln\_zdfevd}\forcode{ = .true.}. 
     744The enhanced vertical diffusion parameterisation is used when \np{ln\_zdfevd}\forcode{=.true.}. 
    745745In this case, the vertical eddy mixing coefficients are assigned very large values 
    746746in regions where the stratification is unstable 
    747747(\ie\ when $N^2$ the Brunt-Vais\"{a}l\"{a} frequency is negative) \citep{lazar_phd97, lazar.madec.ea_JPO99}. 
    748 This is done either on tracers only (\np{nn\_evdm}\forcode{ = 0}) or 
    749 on both momentum and tracers (\np{nn\_evdm}\forcode{ = 1}). 
    750  
    751 In practice, where $N^2\leq 10^{-12}$, $A_T^{vT}$ and $A_T^{vS}$, and if \np{nn\_evdm}\forcode{ = 1}, 
     748This is done either on tracers only (\np{nn\_evdm}\forcode{=0}) or 
     749on both momentum and tracers (\np{nn\_evdm}\forcode{=1}). 
     750 
     751In practice, where $N^2\leq 10^{-12}$, $A_T^{vT}$ and $A_T^{vS}$, and if \np{nn\_evdm}\forcode{=1}, 
    752752the four neighbouring $A_u^{vm} \;\mbox{and}\;A_v^{vm}$ values also, are set equal to 
    753753the namelist parameter \np{rn\_avevd}. 
     
    764764%       Turbulent Closure Scheme 
    765765% ------------------------------------------------------------------------------------------------------------- 
    766 \subsection{Handling convection with turbulent closure schemes (\forcode{ln_zdf\{tke,gls,osm\} = .true.})} 
     766\subsection{Handling convection with turbulent closure schemes (\forcode{ln_zdf{tke,gls,osm}=.true.})} 
    767767\label{subsec:ZDF_tcs} 
    768768 
     
    786786The OSMOSIS turbulent closure scheme already includes enhanced vertical diffusion in the case of convection, 
    787787%as governed by the variables $bvsqcon$ and $difcon$ found in \mdl{zdfkpp}, 
    788 therefore \np{ln\_zdfevd}\forcode{ = .false.} should be used with the OSMOSIS scheme. 
     788therefore \np{ln\_zdfevd}\forcode{=.false.} should be used with the OSMOSIS scheme. 
    789789% gm%  + one word on non local flux with KPP scheme trakpp.F90 module... 
    790790 
     
    792792% Double Diffusion Mixing 
    793793% ================================================================ 
    794 \section[Double diffusion mixing (\forcode{ln_zdfddm = .true.})] 
    795 {Double diffusion mixing (\protect\np{ln\_zdfddm}\forcode{ = .true.})} 
     794\section[Double diffusion mixing (\forcode{ln_zdfddm=.true.})] 
     795{Double diffusion mixing (\protect\np{ln\_zdfddm}\forcode{=.true.})} 
    796796\label{subsec:ZDF_ddm} 
    797797 
     
    956956%       Linear Bottom Friction 
    957957% ------------------------------------------------------------------------------------------------------------- 
    958  \subsection[Linear top/bottom friction (\forcode{ln_lin = .true.})] 
    959  {Linear top/bottom friction (\protect\np{ln\_lin}\forcode{ = .true.)}} 
     958 \subsection[Linear top/bottom friction (\forcode{ln_lin=.true.})] 
     959 {Linear top/bottom friction (\protect\np{ln\_lin}\forcode{=.true.)}} 
    960960 \label{subsec:ZDF_drg_linear} 
    961961 
     
    984984\] 
    985985When \np{ln\_lin} \forcode{= .true.}, the value of $r$ used is \np{rn\_Uc0}*\np{rn\_Cd0}. 
    986 Setting \np{ln\_OFF} \forcode{= .true.} (and \forcode{ln_lin = .true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition. 
     986Setting \np{ln\_OFF} \forcode{= .true.} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition. 
    987987 
    988988These values are assigned in \mdl{zdfdrg}. 
    989989Note that there is support for local enhancement of these values via an externally defined 2D mask array 
    990 (\np{ln\_boost}\forcode{ = .true.}) given in the \ifile{bfr\_coef} input NetCDF file. 
     990(\np{ln\_boost}\forcode{=.true.}) given in the \ifile{bfr\_coef} input NetCDF file. 
    991991The mask values should vary from 0 to 1. 
    992992Locations with a non-zero mask value will have the friction coefficient increased by 
     
    996996%       Non-Linear Bottom Friction 
    997997% ------------------------------------------------------------------------------------------------------------- 
    998  \subsection[Non-linear top/bottom friction (\forcode{ln_non_lin = .true.})] 
    999  {Non-linear top/bottom friction (\protect\np{ln\_non\_lin}\forcode{ = .true.})} 
     998 \subsection[Non-linear top/bottom friction (\forcode{ln_non_lin=.true.})] 
     999 {Non-linear top/bottom friction (\protect\np{ln\_non\_lin}\forcode{=.true.})} 
    10001000 \label{subsec:ZDF_drg_nonlinear} 
    10011001 
     
    10251025$C_D$= \np{rn\_Cd0}, and $e_b$ =\np{rn\_bfeb2}. 
    10261026Note that for applications which consider tides explicitly, a low or even zero value of \np{rn\_bfeb2} is recommended. A local enhancement of $C_D$ is again possible via an externally defined 2D mask array 
    1027 (\np{ln\_boost}\forcode{ = .true.}). 
     1027(\np{ln\_boost}\forcode{=.true.}). 
    10281028This works in the same way as for the linear friction case with non-zero masked locations increased by 
    10291029$mask\_value$ * \np{rn\_boost} * \np{rn\_Cd0}. 
     
    10321032%       Bottom Friction Log-layer 
    10331033% ------------------------------------------------------------------------------------------------------------- 
    1034  \subsection[Log-layer top/bottom friction (\forcode{ln_loglayer = .true.})] 
    1035  {Log-layer top/bottom friction (\protect\np{ln\_loglayer}\forcode{ = .true.})} 
     1034 \subsection[Log-layer top/bottom friction (\forcode{ln_loglayer=.true.})] 
     1035 {Log-layer top/bottom friction (\protect\np{ln\_loglayer}\forcode{=.true.})} 
    10361036 \label{subsec:ZDF_drg_loglayer} 
    10371037 
     
    10531053 
    10541054\noindent The log-layer enhancement can also be applied to the top boundary friction if 
    1055 under ice-shelf cavities are activated (\np{ln\_isfcav}\forcode{ = .true.}). 
     1055under ice-shelf cavities are activated (\np{ln\_isfcav}\forcode{=.true.}). 
    10561056%In this case, the relevant namelist parameters are \np{rn\_tfrz0}, \np{rn\_tfri2} and \np{rn\_tfri2\_max}. 
    10571057 
     
    10591059%       Explicit bottom Friction 
    10601060% ------------------------------------------------------------------------------------------------------------- 
    1061  \subsection{Explicit top/bottom friction (\forcode{ln_drgimp = .false.})} 
     1061 \subsection{Explicit top/bottom friction (\forcode{ln_drgimp=.false.})} 
    10621062 \label{subsec:ZDF_drg_stability} 
    10631063 
     
    11201120%       Implicit Bottom Friction 
    11211121% ------------------------------------------------------------------------------------------------------------- 
    1122  \subsection[Implicit top/bottom friction (\forcode{ln_drgimp = .true.})] 
    1123  {Implicit top/bottom friction (\protect\np{ln\_drgimp}\forcode{ = .true.})} 
     1122 \subsection[Implicit top/bottom friction (\forcode{ln_drgimp=.true.})] 
     1123 {Implicit top/bottom friction (\protect\np{ln\_drgimp}\forcode{=.true.})} 
    11241124 \label{subsec:ZDF_drg_imp} 
    11251125 
     
    11551155 \label{subsec:ZDF_drg_ts} 
    11561156 
    1157 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}\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. 
     1157With 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}\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. 
    11581158 
    11591159The strategy to handle top/bottom stresses with split-explicit free surface in \NEMO\ is as follows: 
     
    11691169% Internal wave-driven mixing 
    11701170% ================================================================ 
    1171 \section[Internal wave-driven mixing (\forcode{ln_zdfiwm = .true.})] 
    1172 {Internal wave-driven mixing (\protect\np{ln\_zdfiwm}\forcode{ = .true.})} 
     1171\section[Internal wave-driven mixing (\forcode{ln_zdfiwm=.true.})] 
     1172{Internal wave-driven mixing (\protect\np{ln\_zdfiwm}\forcode{=.true.})} 
    11731173\label{subsec:ZDF_tmx_new} 
    11741174 
     
    12301230% surface wave-induced mixing 
    12311231% ================================================================ 
    1232 \section[Surface wave-induced mixing (\forcode{ln_zdfswm = .true.})] 
    1233 {Surface wave-induced mixing (\protect\np{ln\_zdfswm}\forcode{ = .true.})} 
     1232\section[Surface wave-induced mixing (\forcode{ln_zdfswm=.true.})] 
     1233{Surface wave-induced mixing (\protect\np{ln\_zdfswm}\forcode{=.true.})} 
    12341234\label{subsec:ZDF_swm} 
    12351235 
     
    12541254and diffusivity coefficients. 
    12551255 
    1256 In order to account for this contribution set: \forcode{ln_zdfswm = .true.}, 
    1257 then wave interaction has to be activated through \forcode{ln_wave = .true.}, 
    1258 the Stokes Drift can be evaluated by setting \forcode{ln_sdw = .true.} 
     1256In order to account for this contribution set: \forcode{ln_zdfswm=.true.}, 
     1257then wave interaction has to be activated through \forcode{ln_wave=.true.}, 
     1258the Stokes Drift can be evaluated by setting \forcode{ln_sdw=.true.} 
    12591259(see \autoref{subsec:SBC_wave_sdw}) 
    12601260and the needed wave fields can be provided either in forcing or coupled mode 
     
    12641264% Adaptive-implicit vertical advection 
    12651265% ================================================================ 
    1266 \section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp = .true.})] 
    1267 {Adaptive-implicit vertical advection(\protect\np{ln\_zad\_Aimp}\forcode{ = .true.})} 
     1266\section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp=.true.})] 
     1267{Adaptive-implicit vertical advection(\protect\np{ln\_zad\_Aimp}\forcode{=.true.})} 
    12681268\label{subsec:ZDF_aimp} 
    12691269 
     
    12831283interest or due to short-lived conditions such that the extra numerical diffusion or 
    12841284viscosity does not greatly affect the overall solution. With such applications, setting: 
    1285 \forcode{ln_zad_Aimp = .true.} should allow much longer model timesteps to be used whilst 
     1285\forcode{ln_zad_Aimp=.true.} should allow much longer model timesteps to be used whilst 
    12861286retaining the accuracy of the high order explicit schemes over most of the domain. 
    12871287 
     
    14071407 
    14081408\noindent which were chosen to provide a slightly more stable and less noisy solution. The 
    1409 result when using the default value of \forcode{nn_rdt = 10.} without adaptive-implicit 
     1409result when using the default value of \forcode{nn_rdt=10.} without adaptive-implicit 
    14101410vertical velocity is illustrated in \autoref{fig:zad_Aimp_overflow_frames}. The mass of 
    14111411cold water, initially sitting on the shelf, moves down the slope and forms a 
    14121412bottom-trapped, dense plume. Even with these extra physics choices the model is close to 
    1413 stability limits and attempts with \forcode{nn_rdt = 30.} will fail after about 5.5 hours 
     1413stability limits and attempts with \forcode{nn_rdt=30.} will fail after about 5.5 hours 
    14141414with excessively high horizontal velocities. This time-scale corresponds with the time the 
    14151415plume reaches the steepest part of the topography and, although detected as a horizontal 
     
    14231423significantly altering the solution (although at this extreme the plume is more diffuse 
    14241424and has not travelled so far).  Notably, the solution with and without the scheme is 
    1425 slightly different even with \forcode{nn_rdt = 10.}; suggesting that the base run was 
     1425slightly different even with \forcode{nn_rdt=10.}; suggesting that the base run was 
    14261426close enough to instability to trigger the scheme despite completing successfully. 
    14271427To assist in diagnosing how active the scheme is, in both location and time, the 3D 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11435 r11537  
    304304The default value is 1, as recommended by \citet{Roullet2000?} 
    305305 
    306 \colorbox{red}{\np{rnu}\forcode{ = 1} to be suppressed from namelist !} 
     306\colorbox{red}{\np{rnu}\forcode{=1} to be suppressed from namelist !} 
    307307 
    308308%------------------------------------------------------------- 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11435 r11537  
    8686where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient. 
    8787$\gamma$ is initialized as \np{rn\_atfp} (namelist parameter). 
    88 Its default value is \np{rn\_atfp}\forcode{ = 10.e-3} (see \autoref{sec:STP_mLF}), 
     88Its default value is \np{rn\_atfp}\forcode{=10.e-3} (see \autoref{sec:STP_mLF}), 
    8989causing only a weak dissipation of high frequency motions (\citep{farge-coulombier_phd87}). 
    9090The addition of a time filter degrades the accuracy of the calculation from second to first order. 
     
    172172 
    173173The leapfrog environment supports a centred in time computation of the surface pressure, \ie\ evaluated 
    174 at \textit{now} time step. This refers to as the explicit free surface case in the code (\np{ln\_dynspg\_exp}\forcode{ = .true.}). 
     174at \textit{now} time step. This refers to as the explicit free surface case in the code (\np{ln\_dynspg\_exp}\forcode{=.true.}). 
    175175This choice however imposes a strong constraint on the time step which should be small enough to resolve the propagation 
    176176of external gravity waves. As a matter of fact, one rather use in a realistic setup, a split-explicit free surface 
    177 (\np{ln\_dynspg\_ts}\forcode{ = .true.}) in which barotropic and baroclinic dynamical equations are solved separately with ad-hoc 
     177(\np{ln\_dynspg\_ts}\forcode{=.true.}) in which barotropic and baroclinic dynamical equations are solved separately with ad-hoc 
    178178time steps. The use of the time-splitting (in combination with non-linear free surface) imposes some constraints on the design of 
    179179the overall flowchart, in particular to ensure exact tracer conservation (see \autoref{fig:TimeStep_flowchart}). 
  • NEMO/trunk/doc/latex/SI3/main/chapters.tex

    r11171 r11537  
    11\subfile{../subfiles/todolist} 
    2  
    3 \subfile{../subfiles/introduction}               % Introduction 
    42 
    53\subfile{../subfiles/chap_model_basics} 
  • NEMO/trunk/doc/latex/SI3/main/definitions.tex

    r11433 r11537  
    1212 
    1313%% Color for document (frontpage banner, links and chapter boxes) 
    14 \def \setcolor{ \definecolor{manualcolor}{cmyk}{0, 0, 0, 0.4} } 
     14\def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{0, 0, 0, 0.4} } 
    1515 
    1616%% IPSL publication number 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_bdy_agrif.tex

    r11015 r11537  
    99\chapter{BDY and AGRIF with SI$^3$} 
    1010\label{chap:REG} 
    11 \minitoc 
     11\chaptertoc 
    1212 
    1313\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_domain.tex

    r11031 r11537  
    1010\chapter{Time, space and thickness space domain} 
    1111\label{chap:DOM} 
    12 \minitoc 
     12\chaptertoc 
    1313 
    1414\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_dynamics.tex

    r11015 r11537  
    1010\chapter{Ice dynamics} 
    1111\label{chap:DYN} 
    12 \minitoc 
     12\chaptertoc 
    1313 
    1414\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_interfaces.tex

    r11015 r11537  
    99\chapter{Ice-atmosphere and ice-ocean interfaces} 
    1010\label{chap:INT} 
    11 \minitoc 
     11\chaptertoc 
    1212 
    1313\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_miscellaneous.tex

    r11015 r11537  
    99\chapter{Miscellaneous topics} 
    1010\label{chap:MIS} 
    11 \minitoc 
     11\chaptertoc 
    1212 
    1313\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_model_basics.tex

    r11043 r11537  
    99\chapter{Model Basics} 
    1010\label{chap:MB} 
    11 \minitoc 
     11\chaptertoc 
    1212 
    1313\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_output_diagnostics.tex

    r11031 r11537  
    99\chapter{Output and diagnostics} 
    1010\label{chap:DIA} 
    11 \minitoc 
     11\chaptertoc 
    1212 
    1313\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_radiative_transfer.tex

    r11031 r11537  
    1313\chapter{Radiative transfer} 
    1414\label{chap:RAD} 
    15 \minitoc 
     15\chaptertoc 
    1616 
    1717\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_ridging_rafting.tex

    r11043 r11537  
    1010\chapter{Ridging and rafting} 
    1111\label{chap:RDG} 
    12 \minitoc 
     12\chaptertoc 
    1313 
    1414\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_single_category_use.tex

    r11015 r11537  
    1111 
    1212\label{chap:INT} 
    13 \minitoc 
     13\chaptertoc 
    1414 
    1515\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_thermo.tex

    r11031 r11537  
    99\chapter{Ice thermodynamics} 
    1010\label{chap:THD} 
    11 \minitoc 
     11\chaptertoc 
    1212 
    1313\newpage 
  • NEMO/trunk/doc/latex/SI3/subfiles/chap_transport.tex

    r11031 r11537  
    1010\chapter{Ice transport} 
    1111\label{chap:TRP} 
    12 \minitoc 
     12\chaptertoc 
    1313 
    1414\newpage 
Note: See TracChangeset for help on using the changeset viewer.