Changeset 996 for trunk/DOC

Timestamp:

2008-05-28T12:38:21+02:00 (16 years ago)

Author:

gm

Message:

trunk - DOC update to correct error in previous update

Location:

trunk/DOC/TexFiles/Chapters

Files:

• 0_page_de_garde_old.tex (deleted)
• Annex_A.tex (modified) (1 diff)
• Annex_E.tex (modified) (1 diff)
• Chap_Conservation.tex (modified) (1 diff)
• Chap_DOM.tex (modified) (1 diff)
• Chap_DYN.tex (modified) (1 diff)
• Chap_LBC.tex (modified) (1 diff)
• Chap_LDF.tex (modified) (1 diff)
• Chap_MISC.tex (modified) (1 diff)
• Chap_Model_Basics.tex (modified) (1 diff)
• Chap_Model_Basics_zstar.tex (modified) (1 diff)
• Chap_SBC.tex (modified) (1 diff)
• Chap_TRA.tex (modified) (1 diff)
• Chap_ZDF.tex (modified) (1 diff)
• Introduction.tex (modified) (3 diffs)

trunk/DOC/TexFiles/Chapters/Annex_A.tex

@@ -6 +6 @@
 \label{Apdx_A}
 \minitoc
+
 
 In order to establish the set of Primitive Equation in curvilinear $s$-coordinates ($i.e.$ 

trunk/DOC/TexFiles/Chapters/Annex_E.tex

@@ -14 +14 @@
 
 The UBS advection scheme is an upstream biased third order scheme based on 
-an upstream-biased parabolic interpolation. It is also known as Cell 
-Averaged QUICK scheme (Quadratic Upstream Interpolation for Convective 
+an upstream-biased parabolic interpolation. It is also known as Cell Averaged 
+QUICK scheme (Quadratic Upstream Interpolation for Convective 
 Kinematics). For example, in the $i$-direction :
 \begin{equation} \label{Eq_tra_adv_ubs2}

trunk/DOC/TexFiles/Chapters/Chap_Conservation.tex

@@ -81 +81 @@
 \end{equation}
 where $dv = e_1\, e_2\, e_3\, di\, dj\, dk$ is the volume element. 
-(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 non-divergent flow. 
+(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 
+non-divergent flow. 
 (II.4.1c) is even satisfied locally since the vorticity term is orthogonal 
 to the horizontal velocity. It means that the vorticity term has no 

trunk/DOC/TexFiles/Chapters/Chap_DOM.tex

@@ -16 +16 @@
 %  - domclo:  closed sea and lakes.... management of closea sea area : specific to global configuration, both forced and coupled
 
-\gmcomment{STEVEN :maybe a picture of the directory structure in the introduction which could be referred to here, would help  ==> to be added}
+\gmcomment{STEVEN :maybe a picture of the directory structure in the introduction 
+which could be referred to here, would help  ==> to be added}
 %%%%
 

trunk/DOC/TexFiles/Chapters/Chap_DYN.tex

@@ -56 +56 @@
 3D terms.
 %%%
-\gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does MISC correspond to "extracting tendency terms" or "vorticity balance"?}
+\gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does 
+MISC correspond to "extracting tendency terms" or "vorticity balance"?}
 
 % ================================================================

trunk/DOC/TexFiles/Chapters/Chap_LBC.tex

@@ -72 +72 @@
 \begin{figure}[!p] \label{Fig_LBC_shlat}  \begin{center}
 \includegraphics[width=0.90\textwidth]{./Figures/Fig_LBC_shlat.pdf}
-\caption {lateral boundary condition (a) free-slip ($shlat=0$) ; (b) no-slip ($shlat=2$) ; (c) "partial" free-slip ($0<shlat<2$) and (d) "strong" no-slip ($2<shlat$). Implied "ghost" velocity inside land area is display in grey. }
+\caption {lateral boundary condition (a) free-slip ($shlat=0$) ; (b) no-slip ($shlat=2$) 
+; (c) "partial" free-slip ($0<shlat<2$) and (d) "strong" no-slip ($2<shlat$). 
+Implied "ghost" velocity inside land area is display in grey. }
 \end{center}   \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>

trunk/DOC/TexFiles/Chapters/Chap_LDF.tex

@@ -9 +9 @@
 $\ $\newline    % force a new ligne
 
-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 
-further discuss the choices that underlie each lateral physics option. 
-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 
-three aspects of the lateral diffusion are set through namelist parameters and CPP keys (see the nam\_traldf and nam\_dynldf below).
+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 further discuss the choices that underlie each lateral physics option. 
+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 three aspects of the lateral diffusion are set 
+through namelist parameters and CPP keys (see the nam\_traldf and nam\_dynldf 
+below).
 %-----------------------------------nam_traldf - nam_dynldf--------------------------------------------
 \namdisplay{nam_traldf} 

trunk/DOC/TexFiles/Chapters/Chap_MISC.tex

@@ -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}
 \end{multline}
-\eqref{Eq_solmat} is a linear symmetric system of equations. All the elements of the 
-corresponding matrix \textbf{A} vanish except those of five diagonals. With 
+\eqref{Eq_solmat} is a linear symmetric system of equations. All the elements of 
+the corresponding matrix \textbf{A} vanish except those of five diagonals. With 
 the natural ordering of the grid points (i.e. from west to east and from 
 south to north), the structure of \textbf{A} is block-tridiagonal with 

trunk/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

@@ -22 +22 @@
 
 
-The ocean is a fluid that can be described to a good approximation by the primitive equations, $i.e.$ the Navier-Stokes 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:
+The ocean is a fluid that can be described to a good approximation by the primitive 
+equations, $i.e.$ the Navier-Stokes 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:
 
 \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

@@ -15 +15 @@
 
 In that case, the free surface equation is nonlinear, and the variations of 
-volume are fully taken into account. These coordinates systems is presented in a report 
-\citep{Levier2007} available on the \NEMO web site. 
+volume are fully taken into account. These coordinates systems is presented in 
+a report \citep{Levier2007} available on the \NEMO web site. 
 
 \colorbox{yellow}{  end of to be updated}

trunk/DOC/TexFiles/Chapters/Chap_SBC.tex

@@ -408 +408 @@
 
 The presence at the sea surface of an ice covered area modifies all the fluxes 
-transmitted to the ocean. There are several way to handle sea-ice in the system depending on the value of the \np{nn{\_}ice} namelist parameter.  
+transmitted to the ocean. There are several way to handle sea-ice in the system 
+depending on the value of the \np{nn{\_}ice} namelist parameter.  
 \begin{description}
 \item[nn{\_}ice = 0]  there will never be sea-ice in the computational domain. This is a typical namelist value used for tropical ocean domain. The surface fluxes are simply specified for an ice-free ocean. No specific things are done for sea-ice.

trunk/DOC/TexFiles/Chapters/Chap_TRA.tex

@@ -258 +258 @@
 where $c_u$ is a flux limiter function taking values between 0 and 1. There 
 exist many ways to define $c_u$, each correcponding to a different total 
-variance decreasing scheme. The one chosen in \NEMO is described in \citet{Zalesak1979}. $c_u$ only departs from $1$ when the advective term 
+variance decreasing scheme. The one chosen in \NEMO is described in 
+\citet{Zalesak1979}. $c_u$ only departs from $1$ when the advective term 
 produces a local extremum in the tracer field. The resulting scheme is quite 
 expensive but \emph{positive}. It can be used on both active and passive tracers. 

trunk/DOC/TexFiles/Chapters/Chap_ZDF.tex

@@ -599 +599 @@
 
 This update is done in \mdl{zdfbfr}. The coefficients that control the strength of the 
-non-linear bottom friction are initialized as namelist parameters: $C_D$= \np{bfri2}, and $e_b$ =\np{bfeb2}.
-
-% ================================================================
+non-linear bottom friction are initialized as namelist parameters: $C_D$= \np{bfri2}, 
+and $e_b$ =\np{bfeb2}.
+
+% ================================================================

trunk/DOC/TexFiles/Chapters/Introduction.tex

@@ -20 +20 @@
 (www.locean-ipsl.upmc.fr/NEMO). 
 
-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. 
+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. 
 
 This manual is organised in as follows. Chapter~\ref{PE} presents the model basics, 
 $i.e.$ the equations and their assumptions, the vertical coordinates used, and the 
 subgrid scale physics. This part deals with the continuous equations of the model 
-(primitive equations, with potential temperature, salinity and an equation of state). The 
-equations are written in a curvilinear coordinate system, with a choice of vertical 
+(primitive equations, with potential temperature, salinity and an equation of state). 
+The equations are written in a curvilinear coordinate system, with a choice of vertical 
 coordinates ($z$ or $s$, with the rescaled height coordinate formulation \textit{z*}, or  
 \textit{s*}). Momentum equations are formulated in the vector invariant form or in the 
@@ -118 +122 @@
 
 OPA, like all research tools, is in perpetual evolution. The present document describes 
-the OPA version include in the release 2.3 of NEMO. This release differs significantly
+the OPA version include in the release 3.0 of NEMO. This release differs significantly
 from version 8, documented in \citet{Madec1998}. The main modifications are :\\
-(1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic reduction of CPP keys; \\
+(1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic 
+reduction of CPP keys; \\
 (2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06}; \\
-(3) partial reactivation of a terrain-following 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 non-linear equation of state.}; \\ 
-(4) more choices for the treatment of the free surface: full explicit, split-explicit , filtered and rigid-lid; \\
-(5) non linear free surface option (associated with the rescaled height coordinate  \textit{z*} or  \textit{s*}); \\
+(3) partial reactivation of a terrain-following 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 non-linear equation of state.}; \\ 
+(4) more choices for the treatment of the free surface: full explicit, split-explicit , filtered 
+and rigid-lid; \\
+(5) non linear free surface option (associated with the rescaled height coordinate  
+\textit{z*} or  \textit{s*}); \\
 (6) additional schemes for vector and flux forms of the momentum  advection; \\
 (7) additional advection schemes for tracers; \\
@@ -131 +142 @@
 (10) rewriting of the I/O management; \\
 (11) OASIS 3 and 4 couplers interfacing with atmospheric global circulation models. 
+(12) surface module (SBC) that simplify the way the ocean is forced and include two
+bulk formulea (CLIO and CORE)
+(13) introduction of LIM 3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and
+new thermodynamics including bulk ice salinity)
 
 In addition, several minor modifications in the coding have been introduced with the constant concern of improving performance on both scalar and vector computers. 
 
-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.
-
-\vspace{1cm}  
-\colorbox{red}{Red color}: not in the current reference version (v2.3) but expected soon.
- 
-\colorbox{yellow}{Yellow color}: missing references, text to be updated.
-