Changeset 11179 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex
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- 2019-06-25T15:46:19+02:00 (5 years ago)
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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.
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