Changeset 996
 Timestamp:
 20080528T12:38:21+02:00 (13 years ago)
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 trunk/DOC/TexFiles/Chapters
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trunk/DOC/TexFiles/Chapters/Annex_A.tex
r994 r996 6 6 \label{Apdx_A} 7 7 \minitoc 8 8 9 9 10 In order to establish the set of Primitive Equation in curvilinear $s$coordinates ($i.e.$ 
trunk/DOC/TexFiles/Chapters/Annex_E.tex
r707 r996 14 14 15 15 The UBS advection scheme is an upstream biased third order scheme based on 16 an upstreambiased parabolic interpolation. It is also known as Cell 17 AveragedQUICK scheme (Quadratic Upstream Interpolation for Convective16 an upstreambiased parabolic interpolation. It is also known as Cell Averaged 17 QUICK scheme (Quadratic Upstream Interpolation for Convective 18 18 Kinematics). For example, in the $i$direction : 19 19 \begin{equation} \label{Eq_tra_adv_ubs2} 
trunk/DOC/TexFiles/Chapters/Chap_Conservation.tex
r707 r996 81 81 \end{equation} 82 82 where $dv = e_1\, e_2\, e_3\, di\, dj\, dk$ is the volume element. 83 (II.4.1a) means that $\varsigma $ is conserved. (II.4.1b) is obtained by an integration by part. It means that $\varsigma^2$ is conserved for a horizontally nondivergent flow. 83 (II.4.1a) means that $\varsigma $ is conserved. (II.4.1b) is obtained by an 84 integration by part. It means that $\varsigma^2$ is conserved for a horizontally 85 nondivergent flow. 84 86 (II.4.1c) is even satisfied locally since the vorticity term is orthogonal 85 87 to the horizontal velocity. It means that the vorticity term has no 
trunk/DOC/TexFiles/Chapters/Chap_DOM.tex
r994 r996 16 16 %  domclo: closed sea and lakes.... management of closea sea area : specific to global configuration, both forced and coupled 17 17 18 \gmcomment{STEVEN :maybe a picture of the directory structure in the introduction which could be referred to here, would help ==> to be added} 18 \gmcomment{STEVEN :maybe a picture of the directory structure in the introduction 19 which could be referred to here, would help ==> to be added} 19 20 %%%% 20 21 
trunk/DOC/TexFiles/Chapters/Chap_DYN.tex
r994 r996 56 56 3D terms. 57 57 %%% 58 \gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does MISC correspond to "extracting tendency terms" or "vorticity balance"?} 58 \gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does 59 MISC correspond to "extracting tendency terms" or "vorticity balance"?} 59 60 60 61 % ================================================================ 
trunk/DOC/TexFiles/Chapters/Chap_LBC.tex
r994 r996 72 72 \begin{figure}[!p] \label{Fig_LBC_shlat} \begin{center} 73 73 \includegraphics[width=0.90\textwidth]{./Figures/Fig_LBC_shlat.pdf} 74 \caption {lateral boundary condition (a) freeslip ($shlat=0$) ; (b) noslip ($shlat=2$) ; (c) "partial" freeslip ($0<shlat<2$) and (d) "strong" noslip ($2<shlat$). Implied "ghost" velocity inside land area is display in grey. } 74 \caption {lateral boundary condition (a) freeslip ($shlat=0$) ; (b) noslip ($shlat=2$) 75 ; (c) "partial" freeslip ($0<shlat<2$) and (d) "strong" noslip ($2<shlat$). 76 Implied "ghost" velocity inside land area is display in grey. } 75 77 \end{center} \end{figure} 76 78 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
trunk/DOC/TexFiles/Chapters/Chap_LDF.tex
r994 r996 9 9 $\ $\newline % force a new ligne 10 10 11 The lateral physics on momentum and tracer equations have been given in \S\ref{PE_zdf} and their discrete formulation in \S\ref{TRA_ldf} and \S\ref{DYN_ldf}). In this section we 12 further discuss the choices that underlie each lateral physics option. 13 Choosing one lateral physics means for the user defining, (1) the space and time variations of the eddy coefficients ; (2) the direction along which the lateral diffusive fluxes are evaluated (model level, geopotential or isopycnal surfaces); and (3) the type of operator used (harmonic, or biharmonic operators, and for tracers only, eddy induced advection on tracers). These 14 three aspects of the lateral diffusion are set through namelist parameters and CPP keys (see the nam\_traldf and nam\_dynldf below). 11 The lateral physics on momentum and tracer equations have been given in 12 \S\ref{PE_zdf} and their discrete formulation in \S\ref{TRA_ldf} and \S\ref{DYN_ldf}). 13 In this section we further discuss the choices that underlie each lateral physics option. 14 Choosing one lateral physics means for the user defining, (1) the space and time 15 variations of the eddy coefficients ; (2) the direction along which the lateral diffusive 16 fluxes are evaluated (model level, geopotential or isopycnal surfaces); and (3) the 17 type of operator used (harmonic, or biharmonic operators, and for tracers only, eddy 18 induced advection on tracers). These three aspects of the lateral diffusion are set 19 through namelist parameters and CPP keys (see the nam\_traldf and nam\_dynldf 20 below). 15 21 %nam_traldf  nam_dynldf 16 22 \namdisplay{nam_traldf} 
trunk/DOC/TexFiles/Chapters/Chap_MISC.tex
r994 r996 306 306 \left(C_{i+1,j}^{NS} + C_{i,j+1}^{EW} + C_{i,j}^{NS} + C_{i,j}^{EW} \right) { \left( \frac{\partial \psi}{\partial t } \right) }_{i,j} = B_{i,j} 307 307 \end{multline} 308 \eqref{Eq_solmat} is a linear symmetric system of equations. All the elements of the309 corresponding matrix \textbf{A} vanish except those of five diagonals. With308 \eqref{Eq_solmat} is a linear symmetric system of equations. All the elements of 309 the corresponding matrix \textbf{A} vanish except those of five diagonals. With 310 310 the natural ordering of the grid points (i.e. from west to east and from 311 311 south to north), the structure of \textbf{A} is blocktridiagonal with 
trunk/DOC/TexFiles/Chapters/Chap_Model_Basics.tex
r994 r996 22 22 23 23 24 The ocean is a fluid that can be described to a good approximation by the primitive equations, $i.e.$ the NavierStokes equations along with a nonlinear equation of state which couples the two active tracers (temperature and salinity) to the fluid velocity, plus the following additional assumptions made from scale considerations: 24 The ocean is a fluid that can be described to a good approximation by the primitive 25 equations, $i.e.$ the NavierStokes equations along with a nonlinear equation of 26 state which couples the two active tracers (temperature and salinity) to the fluid 27 velocity, plus the following additional assumptions made from scale considerations: 25 28 26 29 \textit{(1) spherical earth approximation: }the geopotential surfaces are assumed to be spheres so that gravity (local vertical) is parallel to the earth's radius 
trunk/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex
r707 r996 15 15 16 16 In that case, the free surface equation is nonlinear, and the variations of 17 volume are fully taken into account. These coordinates systems is presented in a report18 \citep{Levier2007} available on the \NEMO web site.17 volume are fully taken into account. These coordinates systems is presented in 18 a report \citep{Levier2007} available on the \NEMO web site. 19 19 20 20 \colorbox{yellow}{ end of to be updated} 
trunk/DOC/TexFiles/Chapters/Chap_SBC.tex
r994 r996 408 408 409 409 The presence at the sea surface of an ice covered area modifies all the fluxes 410 transmitted to the ocean. There are several way to handle seaice in the system depending on the value of the \np{nn{\_}ice} namelist parameter. 410 transmitted to the ocean. There are several way to handle seaice in the system 411 depending on the value of the \np{nn{\_}ice} namelist parameter. 411 412 \begin{description} 412 413 \item[nn{\_}ice = 0] there will never be seaice in the computational domain. This is a typical namelist value used for tropical ocean domain. The surface fluxes are simply specified for an icefree ocean. No specific things are done for seaice. 
trunk/DOC/TexFiles/Chapters/Chap_TRA.tex
r994 r996 258 258 where $c_u$ is a flux limiter function taking values between 0 and 1. There 259 259 exist many ways to define $c_u$, each correcponding to a different total 260 variance decreasing scheme. The one chosen in \NEMO is described in \citet{Zalesak1979}. $c_u$ only departs from $1$ when the advective term 260 variance decreasing scheme. The one chosen in \NEMO is described in 261 \citet{Zalesak1979}. $c_u$ only departs from $1$ when the advective term 261 262 produces a local extremum in the tracer field. The resulting scheme is quite 262 263 expensive but \emph{positive}. It can be used on both active and passive tracers. 
trunk/DOC/TexFiles/Chapters/Chap_ZDF.tex
r994 r996 599 599 600 600 This update is done in \mdl{zdfbfr}. The coefficients that control the strength of the 601 nonlinear bottom friction are initialized as namelist parameters: $C_D$= \np{bfri2}, and $e_b$ =\np{bfeb2}. 602 603 % ================================================================ 601 nonlinear bottom friction are initialized as namelist parameters: $C_D$= \np{bfri2}, 602 and $e_b$ =\np{bfeb2}. 603 604 % ================================================================ 
trunk/DOC/TexFiles/Chapters/Introduction.tex
r994 r996 20 20 (www.loceanipsl.upmc.fr/NEMO). 21 21 22 The ocean component of \NEMO has been developed from the OPA model, release 8.2, described in \citet{Madec1998}. This model has been used for a wide range of applications, both regional or global, as a forced ocean model and as a model coupled with the atmosphere. A complete list of references is found on the \NEMO web site. 22 The ocean component of \NEMO has been developed from the OPA model, 23 release 8.2, described in \citet{Madec1998}. This model has been used for a wide 24 range of applications, both regional or global, as a forced ocean model and as a 25 model coupled with the atmosphere. A complete list of references is found on the 26 \NEMO web site. 23 27 24 28 This manual is organised in as follows. Chapter~\ref{PE} presents the model basics, 25 29 $i.e.$ the equations and their assumptions, the vertical coordinates used, and the 26 30 subgrid scale physics. This part deals with the continuous equations of the model 27 (primitive equations, with potential temperature, salinity and an equation of state). The28 equations are written in a curvilinear coordinate system, with a choice of vertical31 (primitive equations, with potential temperature, salinity and an equation of state). 32 The equations are written in a curvilinear coordinate system, with a choice of vertical 29 33 coordinates ($z$ or $s$, with the rescaled height coordinate formulation \textit{z*}, or 30 34 \textit{s*}). Momentum equations are formulated in the vector invariant form or in the … … 118 122 119 123 OPA, like all research tools, is in perpetual evolution. The present document describes 120 the OPA version include in the release 2.3of NEMO. This release differs significantly124 the OPA version include in the release 3.0 of NEMO. This release differs significantly 121 125 from version 8, documented in \citet{Madec1998}. The main modifications are :\\ 122 (1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic reduction of CPP keys; \\ 126 (1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic 127 reduction of CPP keys; \\ 123 128 (2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06}; \\ 124 (3) partial reactivation of a terrainfollowing vertical coordinate ($s$ and hybrid $s$$z$) with the addition of several options for pressure gradient computation \footnote{Partial support of $s$coordinate: there is presently no support for neutral physics in $s$coordinate and for the new options for horizontal pressure gradient computation with a nonlinear equation of state.}; \\ 125 (4) more choices for the treatment of the free surface: full explicit, splitexplicit , filtered and rigidlid; \\ 126 (5) non linear free surface option (associated with the rescaled height coordinate \textit{z*} or \textit{s*}); \\ 129 (3) partial reactivation of a terrainfollowing vertical coordinate ($s$ and hybrid $s$$z$) 130 with the addition of several options for pressure gradient computation \footnote{Partial 131 support of $s$coordinate: there is presently no support for neutral physics in $s$ 132 coordinate and for the new options for horizontal pressure gradient computation with 133 a nonlinear equation of state.}; \\ 134 (4) more choices for the treatment of the free surface: full explicit, splitexplicit , filtered 135 and rigidlid; \\ 136 (5) non linear free surface option (associated with the rescaled height coordinate 137 \textit{z*} or \textit{s*}); \\ 127 138 (6) additional schemes for vector and flux forms of the momentum advection; \\ 128 139 (7) additional advection schemes for tracers; \\ … … 131 142 (10) rewriting of the I/O management; \\ 132 143 (11) OASIS 3 and 4 couplers interfacing with atmospheric global circulation models. 144 (12) surface module (SBC) that simplify the way the ocean is forced and include two 145 bulk formulea (CLIO and CORE) 146 (13) introduction of LIM 3, the new LouvainlaNeuve seaice model (Cgrid rheology and 147 new thermodynamics including bulk ice salinity) 133 148 134 149 In addition, several minor modifications in the coding have been introduced with the constant concern of improving performance on both scalar and vector computers. 135 150 136 At the time of this writing, the current release is NEMO 2.3. The new surface module described in this document is not yet part of the current distribution.137 138 \vspace{1cm}139 \colorbox{red}{Red color}: not in the current reference version (v2.3) but expected soon.140 141 \colorbox{yellow}{Yellow color}: missing references, text to be updated.142
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