- Timestamp:
- 2019-06-25T15:46:19+02:00 (5 years ago)
- Location:
- NEMO/trunk/doc/latex/NEMO
- Files:
-
- 1 added
- 1 deleted
- 12 edited
Legend:
- Unmodified
- Added
- Removed
-
NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex
r11151 r11179 34 34 % 1D model configuration 35 35 % ================================================================ 36 \section{C1D: 1D Water column model (\protect\key{c1d}) } 36 \section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})] 37 {C1D: 1D Water column model (\protect\key{c1d})} 37 38 \label{sec:CFG_c1d} 38 39 … … 227 228 % GYRE family: double gyre basin 228 229 % ------------------------------------------------------------------------------------------------------------- 229 \section{GYRE family: double gyre basin 230 \section{GYRE family: double gyre basin} 230 231 \label{sec:CFG_gyre} 231 232 -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex
r11151 r11179 1332 1332 % NetCDF4 support 1333 1333 % ================================================================ 1334 \section{NetCDF4 support (\protect\key{netcdf4})} 1334 \section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})] 1335 {NetCDF4 support (\protect\key{netcdf4})} 1335 1336 \label{sec:DIA_nc4} 1336 1337 … … 1450 1451 % Tracer/Dynamics Trends 1451 1452 % ------------------------------------------------------------------------------------------------------------- 1452 \section{Tracer/Dynamics trends (\protect\ngn{namtrd})} 1453 \section[Tracer/Dynamics trends (\texttt{namtrd})] 1454 {Tracer/Dynamics trends (\protect\ngn{namtrd})} 1453 1455 \label{sec:DIA_trd} 1454 1456 … … 1497 1499 % On-line Floats trajectories 1498 1500 % ------------------------------------------------------------------------------------------------------------- 1499 \section{FLO: On-Line Floats trajectories (\protect\key{floats})} 1501 \section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})] 1502 {FLO: On-Line Floats trajectories (\protect\key{floats})} 1500 1503 \label{sec:FLO} 1501 1504 %--------------------------------------------namflo------------------------------------------------------- … … 1605 1608 % Harmonic analysis of tidal constituents 1606 1609 % ------------------------------------------------------------------------------------------------------------- 1607 \section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) } 1610 \section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})] 1611 {Harmonic analysis of tidal constituents (\protect\key{diaharm})} 1608 1612 \label{sec:DIA_diag_harm} 1609 1613 … … 1652 1656 % Sections transports 1653 1657 % ------------------------------------------------------------------------------------------------------------- 1654 \section{Transports across sections (\protect\key{diadct}) } 1658 \section[Transports across sections (\texttt{\textbf{key\_diadct}})] 1659 {Transports across sections (\protect\key{diadct})} 1655 1660 \label{sec:DIA_diag_dct} 1656 1661 … … 1976 1981 % Other Diagnostics 1977 1982 % ------------------------------------------------------------------------------------------------------------- 1978 \section{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})} 1983 \section[Other diagnostics (\texttt{\textbf{key\_diahth}}, \texttt{\textbf{key\_diaar5}})] 1984 {Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})} 1979 1985 \label{sec:DIA_diag_others} 1980 1986 … … 1982 1988 The available ready-to-add diagnostics modules can be found in directory DIA. 1983 1989 1984 \subsection{Depth of various quantities (\protect\mdl{diahth})} 1990 \subsection[Depth of various quantities (\textit{diahth.F90})] 1991 {Depth of various quantities (\protect\mdl{diahth})} 1985 1992 1986 1993 Among the available diagnostics the following ones are obtained when defining the \key{diahth} CPP key: … … 1998 2005 % ----------------------------------------------------------- 1999 2006 2000 \subsection{Poleward heat and salt transports (\protect\mdl{diaptr})} 2007 \subsection[Poleward heat and salt transports (\textit{diaptr.F90})] 2008 {Poleward heat and salt transports (\protect\mdl{diaptr})} 2001 2009 2002 2010 %------------------------------------------namptr----------------------------------------- … … 2032 2040 % CMIP specific diagnostics 2033 2041 % ----------------------------------------------------------- 2034 \subsection{CMIP specific diagnostics (\protect\mdl{diaar5})} 2042 \subsection[CMIP specific diagnostics (\textit{diaar5.F90})] 2043 {CMIP specific diagnostics (\protect\mdl{diaar5})} 2035 2044 2036 2045 A series of diagnostics has been added in the \mdl{diaar5}. -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex
r11151 r11179 345 345 % Domain: Horizontal Grid (mesh) 346 346 % ================================================================ 347 \section{Horizontal grid mesh (\protect\mdl{domhgr})} 347 \section[Horizontal grid mesh (\textit{domhgr.F90})] 348 {Horizontal grid mesh (\protect\mdl{domhgr})} 348 349 \label{sec:DOM_hgr} 349 350 … … 451 452 % Domain: Vertical Grid (domzgr) 452 453 % ================================================================ 453 \section{Vertical grid (\protect\mdl{domzgr})} 454 \section[Vertical grid (\textit{domzgr.F90})] 455 {Vertical grid (\protect\mdl{domzgr})} 454 456 \label{sec:DOM_zgr} 455 457 %-----------------------------------------nam_zgr & namdom------------------------------------------- … … 480 482 (d) hybrid $s-z$ coordinate, 481 483 (e) hybrid $s-z$ coordinate with partial step, and 482 (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh} ~\forcode{= .false.}).484 (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}\forcode{ = .false.}). 483 485 Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e). 484 486 } … … 491 493 It is not intended as an option which can be enabled or disabled in the middle of an experiment. 492 494 Three main choices are offered (\autoref{fig:z_zps_s_sps}): 493 $z$-coordinate with full step bathymetry (\np{ln\_zco} ~\forcode{= .true.}),494 $z$-coordinate with partial step bathymetry (\np{ln\_zps} ~\forcode{= .true.}),495 or generalized, $s$-coordinate (\np{ln\_sco} ~\forcode{= .true.}).495 $z$-coordinate with full step bathymetry (\np{ln\_zco}\forcode{ = .true.}), 496 $z$-coordinate with partial step bathymetry (\np{ln\_zps}\forcode{ = .true.}), 497 or generalized, $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}). 496 498 Hybridation of the three main coordinates are available: 497 499 $s-z$ or $s-zps$ coordinate (\autoref{fig:z_zps_s_sps} and \autoref{fig:z_zps_s_sps}). 498 500 By default a non-linear free surface is used: the coordinate follow the time-variation of the free surface so that 499 501 the transformation is time dependent: $z(i,j,k,t)$ (\autoref{fig:z_zps_s_sps}). 500 When a linear free surface is assumed (\np{ln\_linssh} ~\forcode{= .true.}),502 When a linear free surface is assumed (\np{ln\_linssh}\forcode{ = .true.}), 501 503 the vertical coordinate are fixed in time, but the seawater can move up and down across the $z_0$ surface 502 504 (in other words, the top of the ocean in not a rigid-lid). … … 513 515 N.B. in full step $z$-coordinate, a \ifile{bathy\_level} file can replace the \ifile{bathy\_meter} file, 514 516 so that the computation of the number of wet ocean point in each water column is by-passed}. 515 If \np{ln\_isfcav} ~\forcode{= .true.}, an extra file input file (\ifile{isf\_draft\_meter}) describing517 If \np{ln\_isfcav}\forcode{ = .true.}, an extra file input file (\ifile{isf\_draft\_meter}) describing 516 518 the ice shelf draft (in meters) is needed. 517 519 … … 535 537 %%% 536 538 537 Unless a linear free surface is used (\np{ln\_linssh} ~\forcode{= .false.}),539 Unless a linear free surface is used (\np{ln\_linssh}\forcode{ = .false.}), 538 540 the arrays describing the grid point depths and vertical scale factors are three set of 539 541 three dimensional arrays $(i,j,k)$ defined at \textit{before}, \textit{now} and \textit{after} time step. … … 541 543 They are updated at each model time step using a fixed reference coordinate system which 542 544 computer names have a $\_0$ suffix. 543 When the linear free surface option is used (\np{ln\_linssh} ~\forcode{= .true.}), \textit{before},545 When the linear free surface option is used (\np{ln\_linssh}\forcode{ = .true.}), \textit{before}, 544 546 \textit{now} and \textit{after} arrays are simply set one for all to their reference counterpart. 545 547 … … 553 555 (found in \ngn{namdom} namelist): 554 556 \begin{description} 555 \item[\np{nn\_bathy} ~\forcode{= 0}]:557 \item[\np{nn\_bathy}\forcode{ = 0}]: 556 558 a flat-bottom domain is defined. 557 559 The total depth $z_w (jpk)$ is given by the coordinate transformation. 558 560 The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}. 559 \item[\np{nn\_bathy} ~\forcode{= -1}]:561 \item[\np{nn\_bathy}\forcode{ = -1}]: 560 562 a domain with a bump of topography one third of the domain width at the central latitude. 561 563 This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 562 \item[\np{nn\_bathy} ~\forcode{= 1}]:564 \item[\np{nn\_bathy}\forcode{ = 1}]: 563 565 read a bathymetry and ice shelf draft (if needed). 564 566 The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at … … 571 573 The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 572 574 each grid point of the model grid. 573 This file is only needed if \np{ln\_isfcav} ~\forcode{= .true.}.575 This file is only needed if \np{ln\_isfcav}\forcode{ = .true.}. 574 576 Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. 575 577 \end{description} … … 586 588 % z-coordinate and reference coordinate transformation 587 589 % ------------------------------------------------------------------------------------------------------------- 588 \subsection[$Z$-coordinate (\ protect\np{ln\_zco}~\forcode{= .true.}) and ref. coordinate]589 {$Z$-coordinate (\protect\np{ln\_zco}~\forcode{= .true.}) and reference coordinate}590 \subsection[$Z$-coordinate (\forcode{ln_zco = .true.}) and ref. coordinate] 591 {$Z$-coordinate (\protect\np{ln\_zco}\forcode{ = .true.}) and reference coordinate} 590 592 \label{subsec:DOM_zco} 591 593 … … 616 618 using parameters provided in the \ngn{namcfg} namelist. 617 619 618 It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr} ~\forcode{= 0}).620 It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr}\forcode{ = 0}). 619 621 In that case, the parameters \jp{jpk} (number of $w$-levels) and 620 622 \np{pphmax} (total ocean depth in meters) fully define the grid. … … 631 633 a smooth hyperbolic tangent transition in between (\autoref{fig:zgr}). 632 634 633 If the ice shelf cavities are opened (\np{ln\_isfcav} ~\forcode{= .true.}), the definition of $z_0$ is the same.635 If the ice shelf cavities are opened (\np{ln\_isfcav}\forcode{ = .true.}), the definition of $z_0$ is the same. 634 636 However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to: 635 637 \begin{equation} … … 765 767 % z-coordinate with partial step 766 768 % ------------------------------------------------------------------------------------------------------------- 767 \subsection{$Z$-coordinate with partial step (\protect\np{ln\_zps}~\forcode{= .true.})} 769 \subsection[$Z$-coordinate with partial step (\forcode{ln_zps = .true.})] 770 {$Z$-coordinate with partial step (\protect\np{ln\_zps}\forcode{ = .true.})} 768 771 \label{subsec:DOM_zps} 769 772 %--------------------------------------------namdom------------------------------------------------------- … … 796 799 % s-coordinate 797 800 % ------------------------------------------------------------------------------------------------------------- 798 \subsection{$S$-coordinate (\protect\np{ln\_sco}~\forcode{= .true.})} 801 \subsection[$S$-coordinate (\forcode{ln_sco = .true.})] 802 {$S$-coordinate (\protect\np{ln\_sco}\forcode{ = .true.})} 799 803 \label{subsec:DOM_sco} 800 804 %------------------------------------------nam_zgr_sco--------------------------------------------------- … … 803 807 %-------------------------------------------------------------------------------------------------------------- 804 808 Options are defined in \ngn{namzgr\_sco}. 805 In $s$-coordinate (\np{ln\_sco} ~\forcode{= .true.}), the depth and thickness of the model levels are defined from809 In $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}), the depth and thickness of the model levels are defined from 806 810 the product of a depth field and either a stretching function or its derivative, respectively: 807 811 … … 826 830 827 831 The original default NEMO s-coordinate stretching is available if neither of the other options are specified as true 828 (\np{ln\_s\_SH94} ~\forcode{= .false.} and \np{ln\_s\_SF12}~\forcode{= .false.}).832 (\np{ln\_s\_SH94}\forcode{ = .false.} and \np{ln\_s\_SF12}\forcode{ = .false.}). 829 833 This uses a depth independent $\tanh$ function for the stretching \citep{madec.delecluse.ea_JPO96}: 830 834 … … 846 850 847 851 A stretching function, 848 modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln\_s\_SH94} ~\forcode{= .true.}),852 modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln\_s\_SH94}\forcode{ = .true.}), 849 853 is also available and is more commonly used for shelf seas modelling: 850 854 … … 946 950 % z*- or s*-coordinate 947 951 % ------------------------------------------------------------------------------------------------------------- 948 \subsection{\zstar- or \sstar-coordinate (\protect\np{ln\_linssh}~\forcode{= .false.})} 952 \subsection[\zstar- or \sstar-coordinate (\forcode{ln_linssh = .false.})] 953 {\zstar- or \sstar-coordinate (\protect\np{ln\_linssh}\forcode{ = .false.})} 949 954 \label{subsec:DOM_zgr_star} 950 955 … … 1014 1019 % Domain: Initial State (dtatsd & istate) 1015 1020 % ================================================================ 1016 \section{Initial state (\protect\mdl{istate} and \protect\mdl{dtatsd})} 1021 \section[Initial state (\textit{istate.F90} and \textit{dtatsd.F90})] 1022 {Initial state (\protect\mdl{istate} and \protect\mdl{dtatsd})} 1017 1023 \label{sec:DTA_tsd} 1018 1024 %-----------------------------------------namtsd------------------------------------------- … … 1025 1031 salinity fields is controlled through the \np{ln\_tsd\_ini} namelist parameter. 1026 1032 \begin{description} 1027 \item[\np{ln\_tsd\_init} ~\forcode{= .true.}]1033 \item[\np{ln\_tsd\_init}\forcode{ = .true.}] 1028 1034 use a T and S input files that can be given on the model grid itself or on their native input data grid. 1029 1035 In the latter case, … … 1032 1038 The information relative to the input files are given in the \np{sn\_tem} and \np{sn\_sal} structures. 1033 1039 The computation is done in the \mdl{dtatsd} module. 1034 \item[\np{ln\_tsd\_init} ~\forcode{= .false.}]1040 \item[\np{ln\_tsd\_init}\forcode{ = .false.}] 1035 1041 use constant salinity value of $35.5~psu$ and an analytical profile of temperature 1036 1042 (typical of the tropical ocean), see \rou{istate\_t\_s} subroutine called from \mdl{istate} module. -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex
r11151 r11179 65 65 % Horizontal divergence and relative vorticity 66 66 %-------------------------------------------------------------------------------------------------------------- 67 \subsection{Horizontal divergence and relative vorticity (\protect\mdl{divcur})} 67 \subsection[Horizontal divergence and relative vorticity (\textit{divcur.F90})] 68 {Horizontal divergence and relative vorticity (\protect\mdl{divcur})} 68 69 \label{subsec:DYN_divcur} 69 70 … … 101 102 % Sea Surface Height evolution 102 103 %-------------------------------------------------------------------------------------------------------------- 103 \subsection{Horizontal divergence and relative vorticity (\protect\mdl{sshwzv})} 104 \subsection[Horizontal divergence and relative vorticity (\textit{sshwzv.F90})] 105 {Horizontal divergence and relative vorticity (\protect\mdl{sshwzv})} 104 106 \label{subsec:DYN_sshwzv} 105 107 … … 181 183 % Vorticity term 182 184 % ------------------------------------------------------------------------------------------------------------- 183 \subsection{Vorticity term (\protect\mdl{dynvor})} 185 \subsection[Vorticity term (\textit{dynvor.F90})] 186 {Vorticity term (\protect\mdl{dynvor})} 184 187 \label{subsec:DYN_vor} 185 188 %------------------------------------------nam_dynvor---------------------------------------------------- … … 203 206 % enstrophy conserving scheme 204 207 %------------------------------------------------------------- 205 \subsubsection{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.})} 206 210 \label{subsec:DYN_vor_ens} 207 211 … … 226 230 % energy conserving scheme 227 231 %------------------------------------------------------------- 228 \subsubsection{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.})} 229 234 \label{subsec:DYN_vor_ene} 230 235 … … 246 251 % mix energy/enstrophy conserving scheme 247 252 %------------------------------------------------------------- 248 \subsubsection{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.})} 249 255 \label{subsec:DYN_vor_mix} 250 256 … … 271 277 % energy and enstrophy conserving scheme 272 278 %------------------------------------------------------------- 273 \subsubsection{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.})} 274 281 \label{subsec:DYN_vor_een} 275 282 … … 364 371 % Kinetic Energy Gradient term 365 372 %-------------------------------------------------------------------------------------------------------------- 366 \subsection{Kinetic energy gradient term (\protect\mdl{dynkeg})} 373 \subsection[Kinetic energy gradient term (\textit{dynkeg.F90})] 374 {Kinetic energy gradient term (\protect\mdl{dynkeg})} 367 375 \label{subsec:DYN_keg} 368 376 … … 384 392 % Vertical advection term 385 393 %-------------------------------------------------------------------------------------------------------------- 386 \subsection{Vertical advection term (\protect\mdl{dynzad}) } 394 \subsection[Vertical advection term (\textit{dynzad.F90})] 395 {Vertical advection term (\protect\mdl{dynzad})} 387 396 \label{subsec:DYN_zad} 388 397 … … 430 439 % Coriolis plus curvature metric terms 431 440 %-------------------------------------------------------------------------------------------------------------- 432 \subsection{Coriolis plus curvature metric terms (\protect\mdl{dynvor}) } 441 \subsection[Coriolis plus curvature metric terms (\textit{dynvor.F90})] 442 {Coriolis plus curvature metric terms (\protect\mdl{dynvor})} 433 443 \label{subsec:DYN_cor_flux} 434 444 … … 451 461 % Flux form Advection term 452 462 %-------------------------------------------------------------------------------------------------------------- 453 \subsection{Flux form advection term (\protect\mdl{dynadv}) } 463 \subsection[Flux form advection term (\textit{dynadv.F90})] 464 {Flux form advection term (\protect\mdl{dynadv})} 454 465 \label{subsec:DYN_adv_flux} 455 466 … … 484 495 % 2nd order centred scheme 485 496 %------------------------------------------------------------- 486 \subsubsection{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.})} 487 499 \label{subsec:DYN_adv_cen2} 488 500 … … 507 519 % UBS scheme 508 520 %------------------------------------------------------------- 509 \subsubsection{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.})} 510 523 \label{subsec:DYN_adv_ubs} 511 524 … … 560 573 % Hydrostatic pressure gradient term 561 574 % ================================================================ 562 \section{Hydrostatic pressure gradient (\protect\mdl{dynhpg})} 575 \section[Hydrostatic pressure gradient (\textit{dynhpg.F90})] 576 {Hydrostatic pressure gradient (\protect\mdl{dynhpg})} 563 577 \label{sec:DYN_hpg} 564 578 %------------------------------------------nam_dynhpg--------------------------------------------------- … … 582 596 % z-coordinate with full step 583 597 %-------------------------------------------------------------------------------------------------------------- 584 \subsection{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.})} 585 600 \label{subsec:DYN_hpg_zco} 586 601 … … 627 642 % z-coordinate with partial step 628 643 %-------------------------------------------------------------------------------------------------------------- 629 \subsection{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.})} 630 646 \label{subsec:DYN_hpg_zps} 631 647 … … 712 728 % Time-scheme 713 729 %-------------------------------------------------------------------------------------------------------------- 714 \subsection{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\}}.)} 715 732 \label{subsec:DYN_hpg_imp} 716 733 … … 773 790 % Surface Pressure Gradient 774 791 % ================================================================ 775 \section{Surface pressure gradient (\protect\mdl{dynspg})} 792 \section[Surface pressure gradient (\textit{dynspg.F90})] 793 {Surface pressure gradient (\protect\mdl{dynspg})} 776 794 \label{sec:DYN_spg} 777 795 %-----------------------------------------nam_dynspg---------------------------------------------------- … … 811 829 % Explicit free surface formulation 812 830 %-------------------------------------------------------------------------------------------------------------- 813 \subsection{Explicit free surface (\protect\key{dynspg\_exp})} 831 \subsection[Explicit free surface (texttt{\textbf{key\_dynspg\_exp}})] 832 {Explicit free surface (\protect\key{dynspg\_exp})} 814 833 \label{subsec:DYN_spg_exp} 815 834 … … 837 856 % Split-explict free surface formulation 838 857 %-------------------------------------------------------------------------------------------------------------- 839 \subsection{Split-explicit free surface (\protect\key{dynspg\_ts})} 858 \subsection[Split-explicit free surface (texttt{\textbf{key\_dynspg\_ts}})] 859 {Split-explicit free surface (\protect\key{dynspg\_ts})} 840 860 \label{subsec:DYN_spg_ts} 841 861 %------------------------------------------namsplit----------------------------------------------------------- … … 1081 1101 % Filtered free surface formulation 1082 1102 %-------------------------------------------------------------------------------------------------------------- 1083 \subsection{Filtered free surface (\protect\key{dynspg\_flt})} 1103 \subsection[Filtered free surface (\texttt{\textbf{key\_dynspg\_flt}})] 1104 {Filtered free surface (\protect\key{dynspg\_flt})} 1084 1105 \label{subsec:DYN_spg_fltp} 1085 1106 … … 1109 1130 % Lateral diffusion term 1110 1131 % ================================================================ 1111 \section{Lateral diffusion term and operators (\protect\mdl{dynldf})} 1132 \section[Lateral diffusion term and operators (\textit{dynldf.F90})] 1133 {Lateral diffusion term and operators (\protect\mdl{dynldf})} 1112 1134 \label{sec:DYN_ldf} 1113 1135 %------------------------------------------nam_dynldf---------------------------------------------------- … … 1143 1165 1144 1166 % ================================================================ 1145 \subsection[Iso-level laplacian (\ protect\np{ln\_dynldf\_lap}\forcode{= .true.})]1146 1167 \subsection[Iso-level laplacian (\forcode{ln_dynldf_lap = .true.})] 1168 {Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})} 1147 1169 \label{subsec:DYN_ldf_lap} 1148 1170 … … 1169 1191 % Rotated laplacian operator 1170 1192 %-------------------------------------------------------------------------------------------------------------- 1171 \subsection[Rotated laplacian (\ protect\np{ln\_dynldf\_iso}\forcode{= .true.})]1172 1193 \subsection[Rotated laplacian (\forcode{ln_dynldf_iso = .true.})] 1194 {Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})} 1173 1195 \label{subsec:DYN_ldf_iso} 1174 1196 … … 1228 1250 % Iso-level bilaplacian operator 1229 1251 %-------------------------------------------------------------------------------------------------------------- 1230 \subsection[Iso-level bilaplacian (\ protect\np{ln\_dynldf\_bilap}\forcode{= .true.})]1231 1252 \subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap = .true.})] 1253 {Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})} 1232 1254 \label{subsec:DYN_ldf_bilap} 1233 1255 … … 1243 1265 % Vertical diffusion term 1244 1266 % ================================================================ 1245 \section{Vertical diffusion term (\protect\mdl{dynzdf})} 1267 \section[Vertical diffusion term (\textit{dynzdf.F90})] 1268 {Vertical diffusion term (\protect\mdl{dynzdf})} 1246 1269 \label{sec:DYN_zdf} 1247 1270 %----------------------------------------------namzdf------------------------------------------------------ … … 1372 1395 % Iterative limiters 1373 1396 %----------------------------------------------------------------------------------------- 1374 \subsection [Directional limiter (\textit{wet\_dry})]1375 1397 \subsection[Directional limiter (\textit{wet\_dry.F90})] 1398 {Directional limiter (\mdl{wet\_dry})} 1376 1399 \label{subsec:DYN_wd_directional_limiter} 1377 1400 The principal idea of the directional limiter is that … … 1412 1435 %----------------------------------------------------------------------------------------- 1413 1436 1414 \subsection [Iterative limiter (\textit{wet\_dry})]1415 1437 \subsection[Iterative limiter (\textit{wet\_dry.F90})] 1438 {Iterative limiter (\mdl{wet\_dry})} 1416 1439 \label{subsec:DYN_wd_iterative_limiter} 1417 1440 1418 \subsubsection [Iterative flux limiter (\textit{wet\_dry})]1419 1441 \subsubsection[Iterative flux limiter (\textit{wet\_dry.F90})] 1442 {Iterative flux limiter (\mdl{wet\_dry})} 1420 1443 \label{subsubsec:DYN_wd_il_spg_limiter} 1421 1444 … … 1522 1545 % Surface pressure gradients 1523 1546 %---------------------------------------------------------------------------------------- 1524 \subsubsection [Modification of surface pressure gradients (\textit{dynhpg})]1525 1547 \subsubsection[Modification of surface pressure gradients (\textit{dynhpg.F90})] 1548 {Modification of surface pressure gradients (\mdl{dynhpg})} 1526 1549 \label{subsubsec:DYN_wd_il_spg} 1527 1550 … … 1588 1611 conditions. 1589 1612 1590 \subsubsection [Additional considerations (\textit{usrdef\_zgr})]1591 1613 \subsubsection[Additional considerations (\textit{usrdef\_zgr.F90})] 1614 {Additional considerations (\mdl{usrdef\_zgr})} 1592 1615 \label{subsubsec:WAD_additional} 1593 1616 … … 1603 1626 % The WAD test cases 1604 1627 %---------------------------------------------------------------------------------------- 1605 \subsection [The WAD test cases (\textit{usrdef\_zgr})]1606 1628 \subsection[The WAD test cases (\textit{usrdef\_zgr.F90})] 1629 {The WAD test cases (\mdl{usrdef\_zgr})} 1607 1630 \label{WAD_test_cases} 1608 1631 … … 1614 1637 % Time evolution term 1615 1638 % ================================================================ 1616 \section{Time evolution term (\protect\mdl{dynnxt})} 1639 \section[Time evolution term (\textit{dynnxt.F90})] 1640 {Time evolution term (\protect\mdl{dynnxt})} 1617 1641 \label{sec:DYN_nxt} 1618 1642 -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex
r11151 r11179 17 17 % Boundary Condition at the Coast 18 18 % ================================================================ 19 \section{Boundary condition at the coast (\protect\np{rn\_shlat})} 19 \section[Boundary condition at the coast (\texttt{rn\_shlat})] 20 {Boundary condition at the coast (\protect\np{rn\_shlat})} 20 21 \label{sec:LBC_coast} 21 22 %--------------------------------------------nam_lbc------------------------------------------------------- … … 147 148 % Boundary Condition around the Model Domain 148 149 % ================================================================ 149 \section{Model domain boundary condition (\protect\np{jperio})} 150 \section[Model domain boundary condition (\texttt{jperio})] 151 {Model domain boundary condition (\protect\np{jperio})} 150 152 \label{sec:LBC_jperio} 151 153 … … 158 160 % Closed, cyclic (\np{jperio}\forcode{ = 0..2}) 159 161 % ------------------------------------------------------------------------------------------------------------- 160 \subsection{Closed, cyclic (\protect\np{jperio}\forcode{= [0127]})} 162 \subsection[Closed, cyclic (\forcode{jperio = [0127]})] 163 {Closed, cyclic (\protect\np{jperio}\forcode{ = [0127]})} 161 164 \label{subsec:LBC_jperio012} 162 165 … … 206 209 % North fold (\textit{jperio = 3 }to $6)$ 207 210 % ------------------------------------------------------------------------------------------------------------- 208 \subsection{North-fold (\protect\np{jperio}\forcode{ = 3..6})} 211 \subsection[North-fold (\forcode{jperio = [3-6]})] 212 {North-fold (\protect\np{jperio}\forcode{ = [3-6]})} 209 213 \label{subsec:LBC_north_fold} 210 214 … … 232 236 % Exchange with neighbouring processors 233 237 % ==================================================================== 234 \section{Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})} 238 \section[Exchange with neighbouring processors (\textit{lbclnk.F90}, \textit{lib\_mpp.F90})] 239 {Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})} 235 240 \label{sec:LBC_mpp} 236 241 -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex
r11151 r11179 38 38 % Direction of lateral Mixing 39 39 % ================================================================ 40 \section{Direction of lateral mixing (\protect\mdl{ldfslp})} 40 \section[Direction of lateral mixing (\textit{ldfslp.F90})] 41 {Direction of lateral mixing (\protect\mdl{ldfslp})} 41 42 \label{sec:LDF_slp} 42 43 … … 301 302 % Lateral Mixing Operator 302 303 % ================================================================ 303 \section{Lateral mixing operators (\protect\mdl{traldf}, \protect\mdl{traldf}) } 304 \section[Lateral mixing operators (\textit{traldf.F90})] 305 {Lateral mixing operators (\protect\mdl{traldf}, \protect\mdl{traldf})} 304 306 \label{sec:LDF_op} 305 307 … … 309 311 % Lateral Mixing Coefficients 310 312 % ================================================================ 311 \section{Lateral mixing coefficient (\protect\mdl{ldftra}, \protect\mdl{ldfdyn}) } 313 \section[Lateral mixing coefficient (\textit{ldftra.F90}, \textit{ldfdyn.F90})] 314 {Lateral mixing coefficient (\protect\mdl{ldftra}, \protect\mdl{ldfdyn})} 312 315 \label{sec:LDF_coef} 313 316 … … 339 342 which is specified through the \np{rn\_ahm0} and \np{rn\_aht0} namelist parameters. 340 343 341 \subsubsection{Vertically varying mixing coefficients (\protect\key{traldf\_c1d} and \key{dynldf\_c1d})} 344 \subsubsection[Vertically varying mixing coefficients (\texttt{\textbf{key\_traldf\_c1d}} and \texttt{\textbf{key\_dynldf\_c1d}})] 345 {Vertically varying mixing coefficients (\protect\key{traldf\_c1d} and \key{dynldf\_c1d})} 342 346 The 1D option is only available when using the $z$-coordinate with full step. 343 347 Indeed in all the other types of vertical coordinate, … … 350 354 This profile is hard coded in file \textit{traldf\_c1d.h90}, but can be easily modified by users. 351 355 352 \subsubsection{Horizontally varying mixing coefficients (\protect\key{traldf\_c2d} and \protect\key{dynldf\_c2d})} 356 \subsubsection[Horizontally varying mixing coefficients (\texttt{\textbf{key\_traldf\_c2d}} and \texttt{\textbf{key\_dynldf\_c2d}})] 357 {Horizontally varying mixing coefficients (\protect\key{traldf\_c2d} and \protect\key{dynldf\_c2d})} 353 358 By default the horizontal variation of the eddy coefficient depends on the local mesh size and 354 359 the type of operator used: … … 381 386 ORCA2 and ORCA05 (see \&namcfg namelist). 382 387 383 \subsubsection{Space varying mixing coefficients (\protect\key{traldf\_c3d} and \key{dynldf\_c3d})} 388 \subsubsection[Space varying mixing coefficients (\texttt{\textbf{key\_traldf\_c3d}} and \texttt{\textbf{key\_dynldf\_c3d}})] 389 {Space varying mixing coefficients (\protect\key{traldf\_c3d} and \key{dynldf\_c3d})} 384 390 385 391 The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases, … … 430 436 % Eddy Induced Mixing 431 437 % ================================================================ 432 \section{Eddy induced velocity (\protect\mdl{traadv\_eiv}, \protect\mdl{ldfeiv})} 438 \section[Eddy induced velocity (\textit{traadv\_eiv.F90}, \textit{ldfeiv.F90})] 439 {Eddy induced velocity (\protect\mdl{traadv\_eiv}, \protect\mdl{ldfeiv})} 433 440 \label{sec:LDF_eiv} 434 441 -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex
r11151 r11179 5 5 % Chapter —— Surface Boundary Condition (SBC, ISF, ICB) 6 6 % ================================================================ 7 \chapter{Surface Boundary Condition (SBC, ISF, ICB) 7 \chapter{Surface Boundary Condition (SBC, ISF, ICB)} 8 8 \label{chap:SBC} 9 9 \minitoc … … 226 226 % Input Data specification (\mdl{fldread}) 227 227 % ------------------------------------------------------------------------------------------------------------- 228 \subsection{Input data specification (\protect\mdl{fldread})} 228 \subsection[Input data specification (\textit{fldread.F90})] 229 {Input data specification (\protect\mdl{fldread})} 229 230 \label{subsec:SBC_fldread} 230 231 … … 559 560 % Analytical formulation (sbcana module) 560 561 % ================================================================ 561 \section{Analytical formulation (\protect\mdl{sbcana})} 562 \section[Analytical formulation (\textit{sbcana.F90})] 563 {Analytical formulation (\protect\mdl{sbcana})} 562 564 \label{sec:SBC_ana} 563 565 … … 584 586 % Flux formulation 585 587 % ================================================================ 586 \section{Flux formulation (\protect\mdl{sbcflx})} 588 \section[Flux formulation (\textit{sbcflx.F90})] 589 {Flux formulation (\protect\mdl{sbcflx})} 587 590 \label{sec:SBC_flx} 588 591 %------------------------------------------namsbc_flx---------------------------------------------------- … … 606 609 % ================================================================ 607 610 \section[Bulk formulation {(\textit{sbcblk\{\_core,\_clio\}.F90})}] 608 611 {Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}} 609 612 \label{sec:SBC_blk} 610 613 … … 625 628 % CORE Bulk formulea 626 629 % ------------------------------------------------------------------------------------------------------------- 627 \subsection{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})} 630 \subsection[CORE formulea (\textit{sbcblk\_core.F90}, \forcode{ln_core = .true.})] 631 {CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})} 628 632 \label{subsec:SBC_blk_core} 629 633 %------------------------------------------namsbc_core---------------------------------------------------- … … 688 692 % CLIO Bulk formulea 689 693 % ------------------------------------------------------------------------------------------------------------- 690 \subsection{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})} 694 \subsection[CLIO formulea (\textit{sbcblk\_clio.F90}, \forcode{ln_clio = .true.})] 695 {CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})} 691 696 \label{subsec:SBC_blk_clio} 692 697 %------------------------------------------namsbc_clio---------------------------------------------------- … … 729 734 % Coupled formulation 730 735 % ================================================================ 731 \section{Coupled formulation (\protect\mdl{sbccpl})} 736 \section[Coupled formulation (\textit{sbccpl.F90})] 737 {Coupled formulation (\protect\mdl{sbccpl})} 732 738 \label{sec:SBC_cpl} 733 739 %------------------------------------------namsbc_cpl---------------------------------------------------- … … 770 776 % Atmospheric pressure 771 777 % ================================================================ 772 \section{Atmospheric pressure (\protect\mdl{sbcapr})} 778 \section[Atmospheric pressure (\textit{sbcapr.F90})] 779 {Atmospheric pressure (\protect\mdl{sbcapr})} 773 780 \label{sec:SBC_apr} 774 781 %------------------------------------------namsbc_apr---------------------------------------------------- … … 806 813 % Surface Tides Forcing 807 814 % ================================================================ 808 \section{Surface tides (\protect\mdl{sbctide})} 815 \section[Surface tides (\textit{sbctide.F90})] 816 {Surface tides (\protect\mdl{sbctide})} 809 817 \label{sec:SBC_tide} 810 818 … … 857 865 % River runoffs 858 866 % ================================================================ 859 \section{River runoffs (\protect\mdl{sbcrnf})} 867 \section[River runoffs (\textit{sbcrnf.F90})] 868 {River runoffs (\protect\mdl{sbcrnf})} 860 869 \label{sec:SBC_rnf} 861 870 %------------------------------------------namsbc_rnf---------------------------------------------------- … … 982 991 % Ice shelf melting 983 992 % ================================================================ 984 \section{Ice shelf melting (\protect\mdl{sbcisf})} 993 \section[Ice shelf melting (\textit{sbcisf.F90})] 994 {Ice shelf melting (\protect\mdl{sbcisf})} 985 995 \label{sec:SBC_isf} 986 996 %------------------------------------------namsbc_isf---------------------------------------------------- … … 1227 1237 % Interactions with waves (sbcwave.F90, ln_wave) 1228 1238 % ------------------------------------------------------------------------------------------------------------- 1229 \section{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})} 1239 \section[Interactions with waves (\textit{sbcwave.F90}, \texttt{ln\_wave})] 1240 {Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})} 1230 1241 \label{sec:SBC_wave} 1231 1242 %------------------------------------------namsbc_wave-------------------------------------------------------- … … 1258 1269 1259 1270 % ================================================================ 1260 \subsection{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})} 1271 \subsection[Neutral drag coefficient from wave model (\texttt{ln\_cdgw})] 1272 {Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})} 1261 1273 \label{subsec:SBC_wave_cdgw} 1262 1274 … … 1271 1283 % 3D Stokes Drift (ln_sdw, nn_sdrift) 1272 1284 % ================================================================ 1273 \subsection{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})} 1285 \subsection[3D Stokes Drift (\texttt{ln\_sdw}, \texttt{nn\_sdrift})] 1286 {3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})} 1274 1287 \label{subsec:SBC_wave_sdw} 1275 1288 … … 1367 1380 % Stokes-Coriolis term (ln_stcor) 1368 1381 % ================================================================ 1369 \subsection{Stokes-Coriolis term (\protect\np{ln\_stcor})} 1382 \subsection[Stokes-Coriolis term (\texttt{ln\_stcor})] 1383 {Stokes-Coriolis term (\protect\np{ln\_stcor})} 1370 1384 \label{subsec:SBC_wave_stcor} 1371 1385 … … 1381 1395 % Waves modified stress (ln_tauwoc, ln_tauw) 1382 1396 % ================================================================ 1383 \subsection{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})} 1397 \subsection[Wave modified sress (\texttt{ln\_tauwoc}, \texttt{ln\_tauw})] 1398 {Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})} 1384 1399 \label{subsec:SBC_wave_tauw} 1385 1400 … … 1428 1443 % Diurnal cycle 1429 1444 % ------------------------------------------------------------------------------------------------------------- 1430 \subsection{Diurnal cycle (\protect\mdl{sbcdcy})} 1445 \subsection[Diurnal cycle (\textit{sbcdcy.F90})] 1446 {Diurnal cycle (\protect\mdl{sbcdcy})} 1431 1447 \label{subsec:SBC_dcy} 1432 1448 %------------------------------------------namsbc_rnf---------------------------------------------------- … … 1514 1530 % Surface restoring to observed SST and/or SSS 1515 1531 % ------------------------------------------------------------------------------------------------------------- 1516 \subsection{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})} 1532 \subsection[Surface restoring to observed SST and/or SSS (\textit{sbcssr.F90})] 1533 {Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})} 1517 1534 \label{subsec:SBC_ssr} 1518 1535 %------------------------------------------namsbc_ssr---------------------------------------------------- … … 1593 1610 % {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?} 1594 1611 1595 \subsection{Interface to CICE (\protect\mdl{sbcice\_cice})} 1612 \subsection[Interface to CICE (\textit{sbcice\_cice.F90})] 1613 {Interface to CICE (\protect\mdl{sbcice\_cice})} 1596 1614 \label{subsec:SBC_cice} 1597 1615 … … 1626 1644 % Freshwater budget control 1627 1645 % ------------------------------------------------------------------------------------------------------------- 1628 \subsection{Freshwater budget control (\protect\mdl{sbcfwb})} 1646 \subsection[Freshwater budget control (\textit{sbcfwb.F90})] 1647 {Freshwater budget control (\protect\mdl{sbcfwb})} 1629 1648 \label{subsec:SBC_fwb} 1630 1649 -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex
r11151 r11179 55 55 56 56 The 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}. 58 58 59 59 % ================================================================ 60 60 % Tracer Advection 61 61 % ================================================================ 62 \section{Tracer advection (\protect\mdl{traadv})} 62 \section[Tracer advection (\textit{traadv.F90})] 63 {Tracer advection (\protect\mdl{traadv})} 63 64 \label{sec:TRA_adv} 64 65 %------------------------------------------namtra_adv----------------------------------------------------- … … 81 82 Indeed, it is obtained by using the following equality: $\nabla \cdot (\vect U \, T) = \vect U \cdot \nabla T$ which 82 83 results from the use of the continuity equation, $\partial_t e_3 + e_3 \; \nabla \cdot \vect U = 0$ 83 (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.}). 84 85 Therefore it is of paramount importance to design the discrete analogue of the advection tendency so that 85 86 it is consistent with the continuity equation in order to enforce the conservation properties of … … 119 120 \begin{description} 120 121 \item[linear free surface:] 121 (\np{ln\_linssh} ~\forcode{= .true.})122 (\np{ln\_linssh}\forcode{ = .true.}) 122 123 the first level thickness is constant in time: 123 124 the vertical boundary condition is applied at the fixed surface $z = 0$ rather than on … … 127 128 the first level tracer value. 128 129 \item[non-linear free surface:] 129 (\np{ln\_linssh} ~\forcode{= .false.})130 (\np{ln\_linssh}\forcode{ = .false.}) 130 131 convergence/divergence in the first ocean level moves the free surface up/down. 131 132 There is no tracer advection through it so that the advective fluxes through the surface are also zero. … … 183 184 % 2nd and 4th order centred schemes 184 185 % ------------------------------------------------------------------------------------------------------------- 185 \subsection{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.})} 186 188 \label{subsec:TRA_adv_cen} 187 189 188 190 % 2nd order centred scheme 189 191 190 The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen} ~\forcode{= .true.}.192 The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen}\forcode{ = .true.}. 191 193 Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by 192 194 setting \np{nn\_cen\_h} and \np{nn\_cen\_v} to $2$ or $4$. … … 220 222 \tau_u^{cen4} = \overline{T - \frac{1}{6} \, \delta_i \Big[ \delta_{i + 1/2}[T] \, \Big]}^{\,i + 1/2} 221 223 \end{equation} 222 In the vertical direction (\np{nn\_cen\_v} ~\forcode{= 4}),224 In the vertical direction (\np{nn\_cen\_v}\forcode{ = 4}), 223 225 a $4^{th}$ COMPACT interpolation has been prefered \citep{demange_phd14}. 224 226 In the COMPACT scheme, both the field and its derivative are interpolated, which leads, after a matrix inversion, … … 250 252 % FCT scheme 251 253 % ------------------------------------------------------------------------------------------------------------- 252 \subsection{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.})} 253 256 \label{subsec:TRA_adv_tvd} 254 257 255 The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct} ~\forcode{= .true.}.258 The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct}\forcode{ = .true.}. 256 259 Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by 257 260 setting \np{nn\_fct\_h} and \np{nn\_fct\_v} to $2$ or $4$. … … 300 303 % MUSCL scheme 301 304 % ------------------------------------------------------------------------------------------------------------- 302 \subsection{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}~\forcode{= .true.})} 305 \subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus = .true.})] 306 {MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}\forcode{ = .true.})} 303 307 \label{subsec:TRA_adv_mus} 304 308 305 The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus} ~\forcode{= .true.}.309 The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus}\forcode{ = .true.}. 306 310 MUSCL implementation can be found in the \mdl{traadv\_mus} module. 307 311 … … 331 335 This choice ensure the \textit{positive} character of the scheme. 332 336 In addition, fluxes round a grid-point where a runoff is applied can optionally be computed using upstream fluxes 333 (\np{ln\_mus\_ups} ~\forcode{= .true.}).337 (\np{ln\_mus\_ups}\forcode{ = .true.}). 334 338 335 339 % ------------------------------------------------------------------------------------------------------------- 336 340 % UBS scheme 337 341 % ------------------------------------------------------------------------------------------------------------- 338 \subsection{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}~\forcode{= .true.})} 342 \subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs = .true.})] 343 {UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}\forcode{ = .true.})} 339 344 \label{subsec:TRA_adv_ubs} 340 345 341 The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs} ~\forcode{= .true.}.346 The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs}\forcode{ = .true.}. 342 347 UBS implementation can be found in the \mdl{traadv\_mus} module. 343 348 … … 369 374 \citep{shchepetkin.mcwilliams_OM05, demange_phd14}. 370 375 Therefore the vertical flux is evaluated using either a $2^nd$ order FCT scheme or a $4^th$ order COMPACT scheme 371 (\np{nn\_cen\_v} ~\forcode{= 2 or 4}).376 (\np{nn\_cen\_v}\forcode{ = 2 or 4}). 372 377 373 378 For stability reasons (see \autoref{chap:STP}), the first term in \autoref{eq:tra_adv_ubs} … … 408 413 % QCK scheme 409 414 % ------------------------------------------------------------------------------------------------------------- 410 \subsection{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}~\forcode{= .true.})} 415 \subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck = .true.})] 416 {QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}\forcode{ = .true.})} 411 417 \label{subsec:TRA_adv_qck} 412 418 413 419 The Quadratic Upstream Interpolation for Convective Kinematics with Estimated Streaming Terms (QUICKEST) scheme 414 proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck} ~\forcode{= .true.}.420 proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck}\forcode{ = .true.}. 415 421 QUICKEST implementation can be found in the \mdl{traadv\_qck} module. 416 422 … … 431 437 % Tracer Lateral Diffusion 432 438 % ================================================================ 433 \section{Tracer lateral diffusion (\protect\mdl{traldf})} 439 \section[Tracer lateral diffusion (\textit{traldf.F90})] 440 {Tracer lateral diffusion (\protect\mdl{traldf})} 434 441 \label{sec:TRA_ldf} 435 442 %-----------------------------------------nam_traldf------------------------------------------------------ … … 453 460 except for the pure vertical component that appears when a rotation tensor is used. 454 461 This 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 which462 When \np{ln\_traldf\_msc}\forcode{ = .true.}, a Method of Stabilizing Correction is used in which 456 463 the pure vertical component is split into an explicit and an implicit part \citep{lemarie.debreu.ea_OM12}. 457 464 … … 459 466 % Type of operator 460 467 % ------------------------------------------------------------------------------------------------------------- 461 \subsection[Type of operator (\protect\np{ln\_traldf}\{\_NONE,\_lap,\_blp\}\})]{Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 468 \subsection[Type of operator (\texttt{ln\_traldf}\{\texttt{\_NONE,\_lap,\_blp}\})] 469 {Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 462 470 \label{subsec:TRA_ldf_op} 463 471 … … 465 473 466 474 \begin{description} 467 \item[\np{ln\_traldf\_NONE} ~\forcode{= .true.}:]475 \item[\np{ln\_traldf\_NONE}\forcode{ = .true.}:] 468 476 no operator selected, the lateral diffusive tendency will not be applied to the tracer equation. 469 477 This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example). 470 \item[\np{ln\_traldf\_lap} ~\forcode{= .true.}:]478 \item[\np{ln\_traldf\_lap}\forcode{ = .true.}:] 471 479 a laplacian operator is selected. 472 480 This harmonic operator takes the following expression: $\mathpzc{L}(T) = \nabla \cdot A_{ht} \; \nabla T $, 473 481 where the gradient operates along the selected direction (see \autoref{subsec:TRA_ldf_dir}), 474 482 and $A_{ht}$ is the eddy diffusivity coefficient expressed in $m^2/s$ (see \autoref{chap:LDF}). 475 \item[\np{ln\_traldf\_blp} ~\forcode{= .true.}]:483 \item[\np{ln\_traldf\_blp}\forcode{ = .true.}]: 476 484 a bilaplacian operator is selected. 477 485 This biharmonic operator takes the following expression: … … 493 501 % Direction of action 494 502 % ------------------------------------------------------------------------------------------------------------- 495 \subsection[Action direction (\protect\np{ln\_traldf}\{\_lev,\_hor,\_iso,\_triad\})]{Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad}) } 503 \subsection[Action direction (\texttt{ln\_traldf}\{\texttt{\_lev,\_hor,\_iso,\_triad}\})] 504 {Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad}) } 496 505 \label{subsec:TRA_ldf_dir} 497 506 498 507 The choice of a direction of action determines the form of operator used. 499 508 The operator is a simple (re-entrant) laplacian acting in the (\textbf{i},\textbf{j}) plane when 500 iso-level option is used (\np{ln\_traldf\_lev} ~\forcode{= .true.}) or509 iso-level option is used (\np{ln\_traldf\_lev}\forcode{ = .true.}) or 501 510 when a horizontal (\ie geopotential) operator is demanded in \textit{z}-coordinate 502 511 (\np{ln\_traldf\_hor} and \np{ln\_zco} equal \forcode{.true.}). … … 519 528 % iso-level operator 520 529 % ------------------------------------------------------------------------------------------------------------- 521 \subsection{Iso-level (bi -)laplacian operator ( \protect\np{ln\_traldf\_iso}) } 530 \subsection[Iso-level (bi-)laplacian operator (\texttt{ln\_traldf\_iso})] 531 {Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})} 522 532 \label{subsec:TRA_ldf_lev} 523 533 … … 537 547 It is a \textit{horizontal} operator (\ie acting along geopotential surfaces) in 538 548 the $z$-coordinate with or without partial steps, but is simply an iso-level operator in the $s$-coordinate. 539 It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp} ~\forcode{= .true.},540 we have \np{ln\_traldf\_lev} ~\forcode{= .true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}~\forcode{= .true.}.549 It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}\forcode{ = .true.}, 550 we have \np{ln\_traldf\_lev}\forcode{ = .true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}\forcode{ = .true.}. 541 551 In both cases, it significantly contributes to diapycnal mixing. 542 552 It is therefore never recommended, even when using it in the bilaplacian case. 543 553 544 Note that in the partial step $z$-coordinate (\np{ln\_zps} ~\forcode{= .true.}),554 Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{ = .true.}), 545 555 tracers in horizontally adjacent cells are located at different depths in the vicinity of the bottom. 546 556 In this case, horizontal derivatives in (\autoref{eq:tra_ldf_lap}) at the bottom level require a specific treatment. … … 550 560 % Rotated laplacian operator 551 561 % ------------------------------------------------------------------------------------------------------------- 552 \subsection{Standard and triad (bi 562 \subsection{Standard and triad (bi-)laplacian operator} 553 563 \label{subsec:TRA_ldf_iso_triad} 554 564 555 %&& Standard rotated (bi 565 %&& Standard rotated (bi-)laplacian operator 556 566 %&& ---------------------------------------------- 557 \subsubsection{Standard rotated (bi -)laplacian operator (\protect\mdl{traldf\_iso})} 567 \subsubsection[Standard rotated (bi-)laplacian operator (\textit{traldf\_iso.F90})] 568 {Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})} 558 569 \label{subsec:TRA_ldf_iso} 559 570 The general form of the second order lateral tracer subgrid scale physics (\autoref{eq:PE_zdf}) … … 574 585 $r_1$ and $r_2$ are the slopes between the surface of computation ($z$- or $s$-surfaces) and 575 586 the surface along which the diffusion operator acts (\ie horizontal or iso-neutral surfaces). 576 It is thus used when, in addition to \np{ln\_traldf\_lap} ~\forcode{= .true.},577 we have \np{ln\_traldf\_iso} ~\forcode{= .true.},578 or both \np{ln\_traldf\_hor} ~\forcode{= .true.} and \np{ln\_zco}~\forcode{= .true.}.587 It is thus used when, in addition to \np{ln\_traldf\_lap}\forcode{ = .true.}, 588 we have \np{ln\_traldf\_iso}\forcode{ = .true.}, 589 or both \np{ln\_traldf\_hor}\forcode{ = .true.} and \np{ln\_zco}\forcode{ = .true.}. 579 590 The way these slopes are evaluated is given in \autoref{sec:LDF_slp}. 580 591 At the surface, bottom and lateral boundaries, the turbulent fluxes of heat and salt are set to zero using … … 592 603 any additional background horizontal diffusion \citep{guilyardi.madec.ea_CD01}. 593 604 594 Note that in the partial step $z$-coordinate (\np{ln\_zps} ~\forcode{= .true.}),605 Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{ = .true.}), 595 606 the horizontal derivatives at the bottom level in \autoref{eq:tra_ldf_iso} require a specific treatment. 596 607 They are calculated in module zpshde, described in \autoref{sec:TRA_zpshde}. 597 608 598 %&& Triad rotated (bi 609 %&& Triad rotated (bi-)laplacian operator 599 610 %&& ------------------------------------------- 600 \subsubsection{Triad rotated (bi -)laplacian operator (\protect\np{ln\_traldf\_triad})} 611 \subsubsection[Triad rotated (bi-)laplacian operator (\textit{ln\_traldf\_triad})] 612 {Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})} 601 613 \label{subsec:TRA_ldf_triad} 602 614 603 If the Griffies triad scheme is employed (\np{ln\_traldf\_triad} ~\forcode{= .true.}; see \autoref{apdx:triad})615 If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:triad}) 604 616 605 617 An alternative scheme developed by \cite{griffies.gnanadesikan.ea_JPO98} which ensures tracer variance decreases 606 is also available in \NEMO (\np{ln\_traldf\_grif} ~\forcode{= .true.}).618 is also available in \NEMO (\np{ln\_traldf\_grif}\forcode{ = .true.}). 607 619 A complete description of the algorithm is given in \autoref{apdx:triad}. 608 620 … … 632 644 % Tracer Vertical Diffusion 633 645 % ================================================================ 634 \section{Tracer vertical diffusion (\protect\mdl{trazdf})} 646 \section[Tracer vertical diffusion (\textit{trazdf.F90})] 647 {Tracer vertical diffusion (\protect\mdl{trazdf})} 635 648 \label{sec:TRA_zdf} 636 649 %--------------------------------------------namzdf--------------------------------------------------------- … … 663 676 664 677 The large eddy coefficient found in the mixed layer together with high vertical resolution implies that 665 in the case of explicit time stepping (\np{ln\_zdfexp} ~\forcode{= .true.})678 in the case of explicit time stepping (\np{ln\_zdfexp}\forcode{ = .true.}) 666 679 there would be too restrictive a constraint on the time step. 667 680 Therefore, the default implicit time stepping is preferred for the vertical diffusion since 668 681 it overcomes the stability constraint. 669 A forward time differencing scheme (\np{ln\_zdfexp} ~\forcode{= .true.}) using682 A forward time differencing scheme (\np{ln\_zdfexp}\forcode{ = .true.}) using 670 683 a time splitting technique (\np{nn\_zdfexp} $> 1$) is provided as an alternative. 671 684 Namelist variables \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics. … … 680 693 % surface boundary condition 681 694 % ------------------------------------------------------------------------------------------------------------- 682 \subsection{Surface boundary condition (\protect\mdl{trasbc})} 695 \subsection[Surface boundary condition (\textit{trasbc.F90})] 696 {Surface boundary condition (\protect\mdl{trasbc})} 683 697 \label{subsec:TRA_sbc} 684 698 … … 730 744 Such time averaging prevents the divergence of odd and even time step (see \autoref{chap:STP}). 731 745 732 In the linear free surface case (\np{ln\_linssh} ~\forcode{= .true.}), an additional term has to be added on746 In the linear free surface case (\np{ln\_linssh}\forcode{ = .true.}), an additional term has to be added on 733 747 both temperature and salinity. 734 748 On temperature, this term remove the heat content associated with mass exchange that has been added to $Q_{ns}$. … … 753 767 % Solar Radiation Penetration 754 768 % ------------------------------------------------------------------------------------------------------------- 755 \subsection{Solar radiation penetration (\protect\mdl{traqsr})} 769 \subsection[Solar radiation penetration (\textit{traqsr.F90})] 770 {Solar radiation penetration (\protect\mdl{traqsr})} 756 771 \label{subsec:TRA_qsr} 757 772 %--------------------------------------------namqsr-------------------------------------------------------- … … 761 776 762 777 Options are defined through the \ngn{namtra\_qsr} namelist variables. 763 When the penetrative solar radiation option is used (\np{ln\_flxqsr} ~\forcode{= .true.}),778 When the penetrative solar radiation option is used (\np{ln\_flxqsr}\forcode{ = .true.}), 764 779 the solar radiation penetrates the top few tens of meters of the ocean. 765 If it is not used (\np{ln\_flxqsr} ~\forcode{= .false.}) all the heat flux is absorbed in the first ocean level.780 If it is not used (\np{ln\_flxqsr}\forcode{ = .false.}) all the heat flux is absorbed in the first ocean level. 766 781 Thus, in the former case a term is added to the time evolution equation of temperature \autoref{eq:PE_tra_T} and 767 782 the surface boundary condition is modified to take into account only the non-penetrative part of the surface … … 792 807 larger depths where it contributes to local heating. 793 808 The way this second part of the solar energy penetrates into the ocean depends on which formulation is chosen. 794 In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd} ~\forcode{= .true.})809 In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd}\forcode{ = .true.}) 795 810 a chlorophyll-independent monochromatic formulation is chosen for the shorter wavelengths, 796 811 leading to the following expression \citep{paulson.simpson_JPO77}: … … 820 835 The 2-bands formulation does not reproduce the full model very well. 821 836 822 The RGB formulation is used when \np{ln\_qsr\_rgb} ~\forcode{= .true.}.837 The RGB formulation is used when \np{ln\_qsr\_rgb}\forcode{ = .true.}. 823 838 The RGB attenuation coefficients (\ie the inverses of the extinction length scales) are tabulated over 824 839 61 nonuniform chlorophyll classes ranging from 0.01 to 10 g.Chl/L … … 827 842 828 843 \begin{description} 829 \item[\np{nn\_chdta} ~\forcode{= 0}]844 \item[\np{nn\_chdta}\forcode{ = 0}] 830 845 a constant 0.05 g.Chl/L value everywhere ; 831 \item[\np{nn\_chdta} ~\forcode{= 1}]846 \item[\np{nn\_chdta}\forcode{ = 1}] 832 847 an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in 833 848 the vertical direction; 834 \item[\np{nn\_chdta} ~\forcode{= 2}]849 \item[\np{nn\_chdta}\forcode{ = 2}] 835 850 same as previous case except that a vertical profile of chlorophyl is used. 836 851 Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value; 837 \item[\np{ln\_qsr\_bio} ~\forcode{= .true.}]852 \item[\np{ln\_qsr\_bio}\forcode{ = .true.}] 838 853 simulated time varying chlorophyll by TOP biogeochemical model. 839 854 In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in … … 874 889 % Bottom Boundary Condition 875 890 % ------------------------------------------------------------------------------------------------------------- 876 \subsection{Bottom boundary condition (\protect\mdl{trabbc})} 891 \subsection[Bottom boundary condition (\textit{trabbc.F90})] 892 {Bottom boundary condition (\protect\mdl{trabbc})} 877 893 \label{subsec:TRA_bbc} 878 894 %--------------------------------------------nambbc-------------------------------------------------------- … … 912 928 % Bottom Boundary Layer 913 929 % ================================================================ 914 \section{Bottom boundary layer (\protect\mdl{trabbl} - \protect\key{trabbl})} 930 \section[Bottom boundary layer (\textit{trabbl.F90} - \texttt{\textbf{key\_trabbl}})] 931 {Bottom boundary layer (\protect\mdl{trabbl} - \protect\key{trabbl})} 915 932 \label{sec:TRA_bbl} 916 933 %--------------------------------------------nambbl--------------------------------------------------------- … … 944 961 % Diffusive BBL 945 962 % ------------------------------------------------------------------------------------------------------------- 946 \subsection{Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}~\forcode{= 1})} 963 \subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf = 1})] 964 {Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}\forcode{ = 1})} 947 965 \label{subsec:TRA_bbl_diff} 948 966 … … 983 1001 % Advective BBL 984 1002 % ------------------------------------------------------------------------------------------------------------- 985 \subsection{Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}~\forcode{= 1..2})} 1003 \subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv = [12]})] 1004 {Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{ = [12]})} 986 1005 \label{subsec:TRA_bbl_adv} 987 1006 … … 1014 1033 %%%gmcomment : this section has to be really written 1015 1034 1016 When applying an advective BBL (\np{nn\_bbl\_adv} ~\forcode{= 1..2}), an overturning circulation is added which1035 When applying an advective BBL (\np{nn\_bbl\_adv}\forcode{ = 1..2}), an overturning circulation is added which 1017 1036 connects two adjacent bottom grid-points only if dense water overlies less dense water on the slope. 1018 1037 The density difference causes dense water to move down the slope. 1019 1038 1020 \np{nn\_bbl\_adv} ~\forcode{= 1}:1039 \np{nn\_bbl\_adv}\forcode{ = 1}: 1021 1040 the downslope velocity is chosen to be the Eulerian ocean velocity just above the topographic step 1022 1041 (see black arrow in \autoref{fig:bbl}) \citep{beckmann.doscher_JPO97}. … … 1025 1044 if the velocity is directed towards greater depth (\ie $\vect U \cdot \nabla H > 0$). 1026 1045 1027 \np{nn\_bbl\_adv} ~\forcode{= 2}:1046 \np{nn\_bbl\_adv}\forcode{ = 2}: 1028 1047 the downslope velocity is chosen to be proportional to $\Delta \rho$, 1029 1048 the density difference between the higher cell and lower cell densities \citep{campin.goosse_T99}. … … 1074 1093 % Tracer damping 1075 1094 % ================================================================ 1076 \section{Tracer damping (\protect\mdl{tradmp})} 1095 \section[Tracer damping (\textit{tradmp.F90})] 1096 {Tracer damping (\protect\mdl{tradmp})} 1077 1097 \label{sec:TRA_dmp} 1078 1098 %--------------------------------------------namtra_dmp------------------------------------------------- … … 1129 1149 % Tracer time evolution 1130 1150 % ================================================================ 1131 \section{Tracer time evolution (\protect\mdl{tranxt})} 1151 \section[Tracer time evolution (\textit{tranxt.F90})] 1152 {Tracer time evolution (\protect\mdl{tranxt})} 1132 1153 \label{sec:TRA_nxt} 1133 1154 %--------------------------------------------namdom----------------------------------------------------- … … 1151 1172 (\ie fluxes plus content in mass exchanges). 1152 1173 $\gamma$ is initialized as \np{rn\_atfp} (\textbf{namelist} parameter). 1153 Its default value is \np{rn\_atfp} ~\forcode{= 10.e-3}.1174 Its default value is \np{rn\_atfp}\forcode{ = 10.e-3}. 1154 1175 Note that the forcing correction term in the filter is not applied in linear free surface 1155 (\jp{lk\_vvl} ~\forcode{= .false.}) (see \autoref{subsec:TRA_sbc}).1176 (\jp{lk\_vvl}\forcode{ = .false.}) (see \autoref{subsec:TRA_sbc}). 1156 1177 Not also that in constant volume case, the time stepping is performed on $T$, not on its content, $e_{3t}T$. 1157 1178 … … 1166 1187 % Equation of State (eosbn2) 1167 1188 % ================================================================ 1168 \section{Equation of state (\protect\mdl{eosbn2}) } 1189 \section[Equation of state (\textit{eosbn2.F90})] 1190 {Equation of state (\protect\mdl{eosbn2})} 1169 1191 \label{sec:TRA_eosbn2} 1170 1192 %--------------------------------------------nameos----------------------------------------------------- … … 1176 1198 % Equation of State 1177 1199 % ------------------------------------------------------------------------------------------------------------- 1178 \subsection{Equation of seawater (\protect\np{nn\_eos}~\forcode{= -1..1})} 1200 \subsection[Equation of seawater (\forcode{nn_eos = {-1,1}})] 1201 {Equation of seawater (\protect\np{nn\_eos}\forcode{ = {-1,1}})} 1179 1202 \label{subsec:TRA_eos} 1180 1203 … … 1210 1233 1211 1234 \begin{description} 1212 \item[\np{nn\_eos} ~\forcode{= -1}]1235 \item[\np{nn\_eos}\forcode{ = -1}] 1213 1236 the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used. 1214 1237 The accuracy of this approximation is comparable to the TEOS-10 rational function approximation, … … 1229 1252 either computing the air-sea and ice-sea fluxes (forced mode) or 1230 1253 sending the SST field to the atmosphere (coupled mode). 1231 \item[\np{nn\_eos} ~\forcode{= 0}]1254 \item[\np{nn\_eos}\forcode{ = 0}] 1232 1255 the polyEOS80-bsq equation of seawater is used. 1233 1256 It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to … … 1241 1264 Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which 1242 1265 is conserved by the model: $C_p$ is set to a constant value, the TEOS10 value. 1243 \item[\np{nn\_eos} ~\forcode{= 1}]1266 \item[\np{nn\_eos}\forcode{ = 1}] 1244 1267 a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen, 1245 1268 the coefficients of which has been optimized to fit the behavior of TEOS10 … … 1303 1326 % Brunt-V\"{a}is\"{a}l\"{a} Frequency 1304 1327 % ------------------------------------------------------------------------------------------------------------- 1305 \subsection{Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}~\forcode{= 0..2})} 1328 \subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency (\forcode{nn_eos = [0-2]})] 1329 {Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}\forcode{ = [0-2]})} 1306 1330 \label{subsec:TRA_bn2} 1307 1331 … … 1357 1381 % Horizontal Derivative in zps-coordinate 1358 1382 % ================================================================ 1359 \section{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})} 1383 \section[Horizontal derivative in \textit{zps}-coordinate (\textit{zpshde.F90})] 1384 {Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})} 1360 1385 \label{sec:TRA_zpshde} 1361 1386 … … 1363 1388 I've changed "derivative" to "difference" and "mean" to "average"} 1364 1389 1365 With partial cells (\np{ln\_zps} ~\forcode{= .true.}) at bottom and top (\np{ln\_isfcav}~\forcode{= .true.}),1390 With partial cells (\np{ln\_zps}\forcode{ = .true.}) at bottom and top (\np{ln\_isfcav}\forcode{ = .true.}), 1366 1391 in general, tracers in horizontally adjacent cells live at different depths. 1367 1392 Horizontal gradients of tracers are needed for horizontal diffusion (\mdl{traldf} module) and 1368 1393 the hydrostatic pressure gradient calculations (\mdl{dynhpg} module). 1369 The partial cell properties at the top (\np{ln\_isfcav} ~\forcode{= .true.}) are computed in the same way as1394 The partial cell properties at the top (\np{ln\_isfcav}\forcode{ = .true.}) are computed in the same way as 1370 1395 for the bottom. 1371 1396 So, only the bottom interpolation is explained below. … … 1383 1408 \protect\label{fig:Partial_step_scheme} 1384 1409 Discretisation of the horizontal difference and average of tracers in the $z$-partial step coordinate 1385 (\protect\np{ln\_zps} ~\forcode{= .true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$.1410 (\protect\np{ln\_zps}\forcode{ = .true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$. 1386 1411 A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$, 1387 1412 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
r11151 r11179 46 46 % Constant 47 47 % ------------------------------------------------------------------------------------------------------------- 48 \subsection{Constant (\protect\key{zdfcst})} 48 \subsection[Constant (\texttt{\textbf{key\_zdfcst}})] 49 {Constant (\protect\key{zdfcst})} 49 50 \label{subsec:ZDF_cst} 50 51 %--------------------------------------------namzdf--------------------------------------------------------- … … 72 73 % Richardson Number Dependent 73 74 % ------------------------------------------------------------------------------------------------------------- 74 \subsection{Richardson number dependent (\protect\key{zdfric})} 75 \subsection[Richardson number dependent (\texttt{\textbf{key\_zdfric}})] 76 {Richardson number dependent (\protect\key{zdfric})} 75 77 \label{subsec:ZDF_ric} 76 78 … … 129 131 % TKE Turbulent Closure Scheme 130 132 % ------------------------------------------------------------------------------------------------------------- 131 \subsection{TKE turbulent closure scheme (\protect\key{zdftke})} 133 \subsection[TKE turbulent closure scheme (\texttt{\textbf{key\_zdftke}})] 134 {TKE turbulent closure scheme (\protect\key{zdftke})} 132 135 \label{subsec:ZDF_tke} 133 136 … … 408 411 % TKE discretization considerations 409 412 % ------------------------------------------------------------------------------------------------------------- 410 \subsection{TKE discretization considerations (\protect\key{zdftke})} 413 \subsection[TKE discretization considerations (\texttt{\textbf{key\_zdftke}})] 414 {TKE discretization considerations (\protect\key{zdftke})} 411 415 \label{subsec:ZDF_tke_ene} 412 416 … … 514 518 % GLS Generic Length Scale Scheme 515 519 % ------------------------------------------------------------------------------------------------------------- 516 \subsection{GLS: Generic Length Scale (\protect\key{zdfgls})} 520 \subsection[GLS: Generic Length Scale (\texttt{\textbf{key\_zdfgls}})] 521 {GLS: Generic Length Scale (\protect\key{zdfgls})} 517 522 \label{subsec:ZDF_gls} 518 523 … … 633 638 % OSM OSMOSIS BL Scheme 634 639 % ------------------------------------------------------------------------------------------------------------- 635 \subsection{OSM: OSMOSIS boundary layer scheme (\protect\key{zdfosm})} 640 \subsection[OSM: OSMosis boundary layer scheme (\texttt{\textbf{key\_zdfosm}})] 641 {OSM: OSMosis boundary layer scheme (\protect\key{zdfosm})} 636 642 \label{subsec:ZDF_osm} 637 643 … … 664 670 % Non-Penetrative Convective Adjustment 665 671 % ------------------------------------------------------------------------------------------------------------- 666 \subsection[Non-penetrative convective adj mt (\protect\np{ln\_tranpc}\forcode{= .true.})]667 672 \subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc = .true.})] 673 {Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{ = .true.})} 668 674 \label{subsec:ZDF_npc} 669 675 … … 736 742 % Enhanced Vertical Diffusion 737 743 % ------------------------------------------------------------------------------------------------------------- 738 \subsection{Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{ = .true.})} 744 \subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd = .true.})] 745 {Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{ = .true.})} 739 746 \label{subsec:ZDF_evd} 740 747 … … 769 776 % Turbulent Closure Scheme 770 777 % ------------------------------------------------------------------------------------------------------------- 771 \subsection[Turbulent closure scheme (\protect\key{zdf}\{tke,gls,osm\})]{Turbulent Closure Scheme (\protect\key{zdftke}, \protect\key{zdfgls} or \protect\key{zdfosm})} 778 \subsection[Turbulent closure scheme (\texttt{\textbf{key\_zdf}}\texttt{\textbf{\{tke,gls,osm\}}})] 779 {Turbulent Closure Scheme (\protect\key{zdftke}, \protect\key{zdfgls} or \protect\key{zdfosm})} 772 780 \label{subsec:ZDF_tcs} 773 781 … … 795 803 % Double Diffusion Mixing 796 804 % ================================================================ 797 \section{Double diffusion mixing (\protect\key{zdfddm})} 805 \section[Double diffusion mixing (\texttt{\textbf{key\_zdfddm}})] 806 {Double diffusion mixing (\protect\key{zdfddm})} 798 807 \label{sec:ZDF_ddm} 799 808 … … 887 896 % Bottom Friction 888 897 % ================================================================ 889 \section{Bottom and top friction (\protect\mdl{zdfbfr})} 898 \section[Bottom and top friction (\textit{zdfbfr.F90})] 899 {Bottom and top friction (\protect\mdl{zdfbfr})} 890 900 \label{sec:ZDF_bfr} 891 901 … … 951 961 % Linear Bottom Friction 952 962 % ------------------------------------------------------------------------------------------------------------- 953 \subsection{Linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 0..1})} 963 \subsection[Linear bottom friction (\forcode{nn_botfr = [01]})] 964 {Linear bottom friction (\protect\np{nn\_botfr}\forcode{ = [01])}} 954 965 \label{subsec:ZDF_bfr_linear} 955 966 … … 993 1004 % Non-Linear Bottom Friction 994 1005 % ------------------------------------------------------------------------------------------------------------- 995 \subsection{Non-linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 2})} 1006 \subsection[Non-linear bottom friction (\forcode{nn_botfr = 2})] 1007 {Non-linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 2})} 996 1008 \label{subsec:ZDF_bfr_nonlinear} 997 1009 … … 1032 1044 % Bottom Friction Log-layer 1033 1045 % ------------------------------------------------------------------------------------------------------------- 1034 \subsection[Log-layer b tm frict enhncmnt (\protect\np{nn\_botfr}\forcode{ = 2}, \protect\np{ln\_loglayer}\forcode{= .true.})]1035 1046 \subsection[Log-layer bottom friction enhancement (\forcode{nn_botfr = 2}, \forcode{ln_loglayer = .true.})] 1047 {Log-layer bottom friction enhancement (\protect\np{nn\_botfr}\forcode{ = 2}, \protect\np{ln\_loglayer}\forcode{ = .true.})} 1036 1048 \label{subsec:ZDF_bfr_loglayer} 1037 1049 … … 1109 1121 % Implicit Bottom Friction 1110 1122 % ------------------------------------------------------------------------------------------------------------- 1111 \subsection{Implicit bottom friction (\protect\np{ln\_bfrimp}\forcode{ = .true.})} 1123 \subsection[Implicit bottom friction (\forcode{ln_bfrimp = .true.})] 1124 {Implicit bottom friction (\protect\np{ln\_bfrimp}\forcode{ = .true.})} 1112 1125 \label{subsec:ZDF_bfr_imp} 1113 1126 … … 1162 1175 % Bottom Friction with split-explicit time splitting 1163 1176 % ------------------------------------------------------------------------------------------------------------- 1164 \subsection[Bottom friction w / split-explicit time splitting (\protect\np{ln\_bfrimp})]1165 1177 \subsection[Bottom friction with split-explicit time splitting (\texttt{ln\_bfrimp})] 1178 {Bottom friction with split-explicit time splitting (\protect\np{ln\_bfrimp})} 1166 1179 \label{subsec:ZDF_bfr_ts} 1167 1180 … … 1218 1231 % Tidal Mixing 1219 1232 % ================================================================ 1220 \section{Tidal mixing (\protect\key{zdftmx})} 1233 \section[Tidal mixing (\texttt{\textbf{key\_zdftmx}})] 1234 {Tidal mixing (\protect\key{zdftmx})} 1221 1235 \label{sec:ZDF_tmx} 1222 1236 … … 1297 1311 % Indonesian area specific treatment 1298 1312 % ------------------------------------------------------------------------------------------------------------- 1299 \subsection{Indonesian area specific treatment (\protect\np{ln\_zdftmx\_itf})} 1313 \subsection[Indonesian area specific treatment (\texttt{ln\_zdftmx\_itf})] 1314 {Indonesian area specific treatment (\protect\np{ln\_zdftmx\_itf})} 1300 1315 \label{subsec:ZDF_tmx_itf} 1301 1316 … … 1342 1357 % Internal wave-driven mixing 1343 1358 % ================================================================ 1344 \section{Internal wave-driven mixing (\protect\key{zdftmx\_new})} 1359 \section[Internal wave-driven mixing (\texttt{\textbf{key\_zdftmx\_new}})] 1360 {Internal wave-driven mixing (\protect\key{zdftmx\_new})} 1345 1361 \label{sec:ZDF_tmx_new} 1346 1362 -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex
r11151 r11179 102 102 % Closed seas 103 103 % ================================================================ 104 \section{Closed seas (\protect\mdl{closea})} 104 \section[Closed seas (\textit{closea.F90})] 105 {Closed seas (\protect\mdl{closea})} 105 106 \label{sec:MISC_closea} 106 107 … … 236 237 % Accuracy and Reproducibility 237 238 % ================================================================ 238 \section{Accuracy and reproducibility (\protect\mdl{lib\_fortran})} 239 \section[Accuracy and reproducibility (\textit{lib\_fortran.F90})] 240 {Accuracy and reproducibility (\protect\mdl{lib\_fortran})} 239 241 \label{sec:MISC_fortran} 240 242 241 \subsection{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})} 243 \subsection[Issues with intrinsinc SIGN function (\texttt{\textbf{key\_nosignedzero}})] 244 {Issues with intrinsinc SIGN function (\protect\key{nosignedzero})} 242 245 \label{subsec:MISC_sign} 243 246 -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex
r11151 r11179 73 73 % Surface Pressure Gradient and Sea Surface Height 74 74 % ================================================================ 75 \section{Surface pressure gradient and sea surface heigth (\protect\mdl{dynspg})} 75 \section[Surface pressure gradient and sea surface heigth (\textit{dynspg.F90})] 76 {Surface pressure gradient and sea surface heigth (\protect\mdl{dynspg})} 76 77 \label{sec:DYN_hpg_spg} 77 78 %-----------------------------------------nam_dynspg---------------------------------------------------- … … 97 98 % Explicit 98 99 %------------------------------------------------------------- 99 \subsubsection{Explicit (\protect\key{dynspg\_exp})} 100 \subsubsection[Explicit (\texttt{\textbf{key\_dynspg\_exp}})] 101 {Explicit (\protect\key{dynspg\_exp})} 100 102 \label{subsec:DYN_spg_exp} 101 103 … … 133 135 % Split-explicit time-stepping 134 136 %------------------------------------------------------------- 135 \subsubsection{Split-explicit time-stepping (\protect\key{dynspg\_ts})} 137 \subsubsection[Split-explicit time-stepping (\texttt{\textbf{key\_dynspg\_ts}})] 138 {Split-explicit time-stepping (\protect\key{dynspg\_ts})} 136 139 \label{subsec:DYN_spg_ts} 137 140 %--------------------------------------------namdom---------------------------------------------------- … … 291 294 % Filtered formulation 292 295 %------------------------------------------------------------- 293 \subsubsection{Filtered formulation (\protect\key{dynspg\_flt})} 296 \subsubsection[Filtered formulation (\texttt{\textbf{key\_dynspg\_flt}})] 297 {Filtered formulation (\protect\key{dynspg\_flt})} 294 298 \label{subsec:DYN_spg_flt} 295 299 … … 305 309 % Non-linear free surface formulation 306 310 %------------------------------------------------------------- 307 \subsection{Non-linear free surface formulation (\protect\key{vvl})} 311 \subsection[Non-linear free surface formulation (\texttt{\textbf{key\_vvl}})] 312 {Non-linear free surface formulation (\protect\key{vvl})} 308 313 \label{subsec:DYN_spg_vvl} 309 314 -
NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex
r11151 r11179 88 88 where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient. 89 89 $\gamma$ is initialized as \np{rn\_atfp} (namelist parameter). 90 Its default value is \np{rn\_atfp} ~\forcode{= 10.e-3} (see \autoref{sec:STP_mLF}),90 Its default value is \np{rn\_atfp}\forcode{ = 10.e-3} (see \autoref{sec:STP_mLF}), 91 91 causing only a weak dissipation of high frequency motions (\citep{farge-coulombier_phd87}). 92 92 The addition of a time filter degrades the accuracy of the calculation from second to first order. … … 132 132 but usually the numerical stability condition imposes a strong constraint on the time step. 133 133 Two solutions are available in \NEMO to overcome the stability constraint: 134 $(a)$ a forward time differencing scheme using a time splitting technique (\np{ln\_zdfexp} ~\forcode{= .true.}) or135 $(b)$ a backward (or implicit) time differencing scheme (\np{ln\_zdfexp} ~\forcode{= .false.}).134 $(a)$ a forward time differencing scheme using a time splitting technique (\np{ln\_zdfexp}\forcode{ = .true.}) or 135 $(b)$ a backward (or implicit) time differencing scheme (\np{ln\_zdfexp}\forcode{ = .false.}). 136 136 In $(a)$, the master time step $\Delta$t is cut into $N$ fractional time steps so that 137 137 the stability criterion is reduced by a factor of $N$.
Note: See TracChangeset
for help on using the changeset viewer.