# Changeset 10442

Ignore:
Timestamp:
2018-12-21T15:18:38+01:00 (2 years ago)
Message:

Front page edition, cleaning in custom LaTeX commands and add index for single subfile compilation

• Use \thanks storing cmd to refer to the ST members list for 2018 in an footnote on the cover page
• NEMO and Fortran in small capitals
• Removing of unused or underused custom cmds, move local cmds to their respective .tex file
• Addition of new ones (\zstar, \ztilde, \sstar, \stilde, \ie, \eg, \fortran, \fninety)
• Fonts for indexed items: italic font for files (modules and .nc files), preformat for code (CPP keys, routines names and namelists content)
Location:
NEMO/trunk/doc/latex/NEMO
Files:
1 deleted
28 edited

Unmodified
Removed
• ## NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.sty

• ## NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.tex

• ## NEMO/trunk/doc/latex/NEMO/subfiles/annex_A.tex

 r10414 In order to establish the set of Primitive Equation in curvilinear $s$-coordinates ($i.e.$ an orthogonal curvilinear coordinate in the horizontal and (\ie an orthogonal curvilinear coordinate in the horizontal and an Arbitrary Lagrangian Eulerian (ALE) coordinate in the vertical), we start from the set of equations established in \autoref{subsec:PE_zco_Eq} for \] leads to the $s-$coordinate formulation of the total $z-$coordinate time derivative, $i.e.$ the total $s-$coordinate time derivative : \ie the total $s-$coordinate time derivative : \begin{align} \label{apdx:A_sco_Dt_vect} % Introducing the vertical scale factor inside the horizontal derivative of the first two terms ($i.e.$ the horizontal divergence), it becomes : (\ie the horizontal divergence), it becomes : \begin{align*} { \end{align*} which leads to the $s-$coordinate flux formulation of the total $s-$coordinate time derivative, $i.e.$ the total $s-$coordinate time derivative in flux form: \ie the total $s-$coordinate time derivative in flux form: \begin{flalign} \label{apdx:A_sco_Dt_flux} in particular the pressure gradient. By contrast, $\omega$ is not $w$, the third component of the velocity, but the dia-surface velocity component, $i.e.$ the volume flux across the moving $s$-surfaces per unit horizontal area. \ie the volume flux across the moving $s$-surfaces per unit horizontal area. \biblio \pindex \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/annex_B.tex

 r10414 \biblio \pindex \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/annex_C.tex

 r10414 \minitoc %%%  Appendix put in gmcomment as it has not been updated for z* and s coordinate %%%  Appendix put in gmcomment as it has not been updated for \zstar and s coordinate %I'm writting this appendix. It will be available in a forthcoming release of the documentation $dv=e_1\,e_2\,e_3 \,di\,dj\,dk$  is the volume element, with only $e_3$ that depends on time. $D$ and $S$ are the ocean domain volume and surface, respectively. No wetting/drying is allow ($i.e.$ $\frac{\partial S}{\partial t} = 0$). No wetting/drying is allow (\ie $\frac{\partial S}{\partial t} = 0$). Let $k_s$ and $k_b$ be the ocean surface and bottom, resp. ($i.e.$ $s(k_s) = \eta$ and $s(k_b)=-H$, where $H$ is the bottom depth). (\ie $s(k_s) = \eta$ and $s(k_b)=-H$, where $H$ is the bottom depth). \begin{flalign*} z(k) = \eta - \int\limits_{\tilde{k}=k}^{\tilde{k}=k_s}  e_3(\tilde{k}) \;d\tilde{k} \label{sec:C.1} The discretization of pimitive equation in $s$-coordinate ($i.e.$ time and space varying vertical coordinate) The discretization of pimitive equation in $s$-coordinate (\ie time and space varying vertical coordinate) must be chosen so that the discrete equation of the model satisfy integral constrains on energy and enstrophy. Let us first establish those constraint in the continuous world. The total energy ($i.e.$ kinetic plus potential energies) is conserved: The total energy (\ie kinetic plus potential energies) is conserved: \begin{flalign} \label{eq:Tot_Energy} +   \frac{1}{2} \int_D {  \frac{{\textbf{U}_h}^2}{e_3} \partial_t ( e_3) \;dv } \] Indeed, using successively \autoref{eq:DOM_di_adj} ($i.e.$ the skew symmetry property of the $\delta$ operator) Indeed, using successively \autoref{eq:DOM_di_adj} (\ie the skew symmetry property of the $\delta$ operator) and the continuity equation, then \autoref{eq:DOM_di_adj} again, then the commutativity of operators $\overline {\,\cdot \,}$ and $\delta$, and finally \autoref{eq:DOM_mi_adj} ($i.e.$ the symmetry property of the $\overline {\,\cdot \,}$ operator) (\ie the symmetry property of the $\overline {\,\cdot \,}$ operator) applied in the horizontal and vertical directions, it becomes: \begin{flalign*} When the equation of state is linear ($i.e.$ when an advection-diffusion equation for density can be derived from those of temperature and salinity) (\ie when an advection-diffusion equation for density can be derived from those of temperature and salinity) the change of KE due to the work of pressure forces is balanced by the change of potential energy due to buoyancy forces: % \allowdisplaybreaks \intertext{Using successively \autoref{eq:DOM_di_adj}, $i.e.$ the skew symmetry property of \intertext{Using successively \autoref{eq:DOM_di_adj}, \ie the skew symmetry property of the $\delta$ operator, \autoref{eq:wzv}, the continuity equation, \autoref{eq:dynhpg_sco}, the hydrostatic equation in the $s$-coordinate, and $\delta_{k+1/2} \left[ z_t \right] \equiv e_{3w}$, Let us first consider the first term of the scalar product ($i.e.$ just the the terms associated with the i-component of the advection): (\ie just the the terms associated with the i-component of the advection): \begin{flalign*} &  - \int_D u \cdot \nabla \cdot \left(   \textbf{U}\,u   \right) \; dv   \\ When the UBS scheme is used to evaluate the flux form momentum advection, the discrete operator does not contribute to the global budget of linear momentum (flux form). The horizontal kinetic energy is not conserved, but forced to decay ($i.e.$ the scheme is diffusive). The horizontal kinetic energy is not conserved, but forced to decay (\ie the scheme is diffusive). % ================================================================ The scheme does not allow but the conservation of the total kinetic energy but the conservation of $q^2$, the potential enstrophy for a horizontally non-divergent flow ($i.e.$ when $\chi$=$0$). the potential enstrophy for a horizontally non-divergent flow (\ie when $\chi$=$0$). Indeed, using the symmetry or skew symmetry properties of the operators ( \autoref{eq:DOM_mi_adj} and \autoref{eq:DOM_di_adj}), } \end{flalign*} The later equality is obtain only when the flow is horizontally non-divergent, $i.e.$ $\chi$=$0$. The later equality is obtain only when the flow is horizontally non-divergent, \ie $\chi$=$0$. % ------------------------------------------------------------------------------------------------------------- This formulation does conserve the potential enstrophy for a horizontally non-divergent flow ($i.e.$ $\chi=0$). This formulation does conserve the potential enstrophy for a horizontally non-divergent flow (\ie $\chi=0$). Let consider one of the vorticity triad, for example ${^{i}_j}\mathbb{Q}^{+1/2}_{+1/2}$, the internal dynamics and physics (equations in flux form). For advection, only the CEN2 scheme ($i.e.$ $2^{nd}$ order finite different scheme) conserves the global variance of tracer. only the CEN2 scheme (\ie $2^{nd}$ order finite different scheme) conserves the global variance of tracer. Nevertheless the other schemes ensure that the global variance decreases ($i.e.$ they are at least slightly diffusive). (\ie they are at least slightly diffusive). For diffusion, all the schemes ensure the decrease of the total tracer variance, except the iso-neutral operator. There is generally no strict conservation of mass, The conservation of the variance of tracer due to the advection tendency can be achieved only with the CEN2 scheme, $i.e.$ when $\tau_u= \overline T^{\,i+1/2}$, $\tau_v= \overline T^{\,j+1/2}$, and $\tau_w= \overline T^{\,k+1/2}$. \ie when $\tau_u= \overline T^{\,i+1/2}$, $\tau_v= \overline T^{\,j+1/2}$, and $\tau_w= \overline T^{\,k+1/2}$. It can be demonstarted as follows: \begin{flalign*} the conservation of potential vorticity and the horizontal divergence, and the dissipation of the square of these quantities ($i.e.$ enstrophy and the variance of the horizontal divergence) as well as (\ie enstrophy and the variance of the horizontal divergence) as well as the dissipation of the horizontal kinetic energy. In particular, when the eddy coefficients are horizontally uniform, \end{flalign*} If the vertical diffusion coefficient is uniform over the whole domain, the enstrophy is dissipated, $i.e.$ If the vertical diffusion coefficient is uniform over the whole domain, the enstrophy is dissipated, \ie \begin{flalign*} \int\limits_D \zeta \, \textbf{k} \cdot \nabla \times \left( \frac{A^{\,vm}} {e_3 }\; \frac{\partial \textbf{U}_h } {\partial k} \right) \right)\; dv = 0    &&& \end{flalign*} and the square of the horizontal divergence decreases ($i.e.$ the horizontal divergence is dissipated) if and the square of the horizontal divergence decreases (\ie the horizontal divergence is dissipated) if the vertical diffusion coefficient is uniform over the whole domain: the heat and salt contents are conserved (equations in flux form). Since a flux form is used to compute the temperature and salinity, the quadratic form of these quantities ($i.e.$ their variance) globally tends to diminish. the quadratic form of these quantities (\ie their variance) globally tends to diminish. As for the advection term, there is conservation of mass only if the Equation Of Seawater is linear. \biblio \pindex \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/annex_D.tex

 r10414 \label{sec:D_coding} - Use of the universal language \textsc{Fortran} 90, and try to avoid obsolescent features like statement functions, - Use of the universal language \fninety, and try to avoid obsolescent features like statement functions, do not use GO TO and EQUIVALENCE statements. %-------------------------------------------------------------------------------------------------------------- N.B. Parameter here, in not only parameter in the \textsc{Fortran} acceptation, N.B. Parameter here, in not only parameter in the \fortran acceptation, it is also used for code variables that are read in namelist and should never been modified during a simulation. It is the case, for example, for the size of a domain (jpi,jpj,jpk). \biblio \pindex \end{document}

• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

 r10414 \biblio \pindex \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex

 r10414 the 3x3 domain is imposed over the whole domain; \item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}); a call to \rou{lbc\_lnk} is systematically done when reading input data (\ie in \mdl{iom}); \item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which \protect\label{fig:MISC_ORCA_msh} ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN. The departure from an isotropic Mercator grid start poleward of 20\deg{N}. The two "north pole" are the foci of a series of embedded ellipses (blue curves) which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) for ORCA 0.5\deg ~mesh. South of 20\degN a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1. Poleward of 20\degN, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1. Poleward of 20\deg{N}, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island (Canadian Arctic Archipelago). } %>>>>>>>>>>>>>>>>>>>>>>>>>>>> The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward of 20\degN, The method is applied to Mercator grid (\ie same zonal and meridional grid spacing) poleward of 20\deg{N}, so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and variation of the ellipses) For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used. In the other ORCA configurations, 31 levels are used (see \autoref{tab:orca_zgr} \sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}). (see \autoref{tab:orca_zgr} %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}). Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution. and their contribution to the large scale circulation. The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\degN and The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}). The domain is bounded by vertical walls and by a flat bottom. The circulation is forced by analytical profiles of wind and buoyancy fluxes. The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{Levy_al_OM10}. The wind stress is zonal and its curl changes sign at 22\degN and 36\degN. The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}. It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and a small recirculation gyre in the southern corner. \biblio \pindex \end{document}

• ## NEMO/trunk/doc/latex/NEMO/subfiles/foreword.tex

 r10414 \biblio \pindex \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/introduction.tex

 r10414 This manual is organised in as follows. \autoref{chap:PE} presents the model basics, $i.e.$ the equations and their assumptions, \autoref{chap:PE} presents the model basics, \ie 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 temperature, salinity and an equation of seawater). The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates ($z$, $s$, \textit{z*}, \textit{s*}, $\tilde{z}$, $\tilde{s}$, and a mixture of them). ($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mixture of them). Momentum equations are formulated in vector invariant or flux form. Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. linear free surface (level position are then fixed in time). In non-linear free surface, the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used (the level position then vary in time as a function of the sea surface heigh). The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of Interactive coupling to Atmospheric models is possible via the OASIS coupler \citep{OASIS2006}. Two-way nesting is also available through an interface to the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. (Adaptative Grid Refinement in \fortran) \citep{Debreu_al_CG2008}. The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so that it works for both global and regional domains, although AGRIF is still not available. \noindent \index{CPP keys} CPP keys \newline Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. Some CPP keys are implemented in the \fortran code to allow code selection at compiling step. This selection of code at compilation time reduces the reliability of the whole platform since it changes the code from one set of CPP keys to the other. \begin{forlines} #if defined key_option1 ! This part of the FORTRAN code will be active ! This part of the \fortran code will be active ! only if key_option1 is activated at compiling step #endif There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) containing all the FOTRAN namelists needed. The implementation in NEMO uses a two step process. For each FORTRAN namelist, two files are read: The implementation in NEMO uses a two step process. For each \fortran namelist, two files are read: \begin{enumerate} \item (water column model, ORCA and GYRE families of configurations). The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). The model is implemented in \fninety, with preprocessing (C-pre-processor). It runs under UNIX. It is optimized for vector computers and parallelised by domain decomposition with MPI. The model is organized with a high internal modularity based on physics. For example, each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and tracers For example, each trend (\ie, a term in the RHS of the prognostic equation) for momentum and tracers is computed in a dedicated module. To make it easier for the user to find his way around the code, the module names follow a three-letter rule. \begin{enumerate} \item transition to full native \textsc{Fortran} 90, deep code restructuring and drastic reduction of CPP keys; transition to full native \fninety, deep code restructuring and drastic reduction of CPP keys; \item introduction of partial step representation of bottom topography and suppression of the rigid-lid option; \item non linear free surface associated with the rescaled height coordinate \textit{z*} or \textit{s}; non linear free surface associated with the rescaled height coordinate \zstar or \textit{s}; \item additional schemes for vector and flux forms of the momentum advection; additional advection schemes for tracers; \item implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; implementation of the AGRIF package (Adaptative Grid Refinement in \fortran) \citep{Debreu_al_CG2008}; \item online diagnostics : tracers trend in the mixed layer and vorticity balance; \biblio \pindex \end{document}
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