Changeset 11512 for NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/subfiles/introduction.tex

Timestamp:

2019-09-09T12:05:20+02:00 (5 years ago)

Author:

smasson

Message:

dev_r10984_HPC-13 : merge with trunk@11511, see #2285

File:

• NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/subfiles/introduction.tex (modified) (17 diffs)

NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/subfiles/introduction.tex

@@ -1 +1 @@
 \documentclass[../main/NEMO_manual]{subfiles}
+
+%% Remove section heading (no section here)
+\rehead{}
 
 \begin{document}
@@ -12 +15 @@
 namely OPA \footnote{OPA: Oc\'{e}an PArall\'{e}lis\'{e} (french)} for the ocean dynamics and thermodynamics,
 SI$^3$ \footnote{SI$^3$: Sea-Ice modelling Integrated Initiative} for the sea-ice dynamics and thermodynamics,
-TOP \footnote{TOP: Tracer in the Ocean Paradigm} for the biogeochemistry 
-(both transport (TRP) and sources minus sinks 
+TOP \footnote{TOP: Tracer in the Ocean Paradigm} for the biogeochemistry
+(both transport (TRP) and sources minus sinks
 (PISCES \footnote{PISCES: Pelagic Interactions Scheme for Carbon and Ecosystem Studies})).
 It is intended to be a flexible tool for studying the ocean and its interactions with the other components of
 the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over
 a wide range of space and time scales.
-This manual provides information about the physics represented by the ocean component of \NEMO and
+This manual provides information about the physics represented by the ocean component of \NEMO\ and
 the rationale for the choice of numerical schemes and the model design.
-For the use of framework, 
-a guide which gathers the \texttt{README} files spread out in the source code can be build and 
+For the use of framework,
+a guide which gathers the \texttt{README} files spread out in the source code can be build and
 exported in web or printable format (see \path{./doc/rst}).
-An online version of the guide is also available on the 
-\href{http://forge.ipsl.jussieu.fr/nemo}{\NEMO forge platform}.
-
-The ocean component of \NEMO has been developed from the legacy of the OPA model, release 8.2, 
+An online version of the guide is also available on the
+\href{http://forge.ipsl.jussieu.fr/nemo}{\NEMO\ forge platform}.
+
+The ocean component of \NEMO\ has been developed from the legacy of the OPA model, release 8.2,
 described in \citet{madec.delecluse.ea_NPM98}.
-This model has been used for a wide range of applications, both regional or global, as a forced ocean model and 
+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 sea-ice and/or the atmosphere.
 
 This manual is organised in as follows.
-\autoref{chap:PE} presents the model basics, \ie 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
@@ -43 +46 @@
 The following chapters deal with the discrete equations.
 \autoref{chap:STP} presents the time domain.
-The model time stepping environment is a three level scheme in which 
-the tendency terms of the equations are evaluated either centered in time, or forward, or backward depending of 
+The model time stepping environment is a three level scheme in which
+the tendency terms of the equations are evaluated either centered in time, or forward, or backward depending of
 the nature of the term.
 \autoref{chap:DOM} presents the space domain.
 The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas.
-Vertical discretisation used depends on both how the bottom topography is represented and whether 
+Vertical discretisation used depends on both how the bottom topography is represented and whether
 the free surface is linear or not.
-Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with linear free surface 
+Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with linear free surface
 (level position are then fixed in time).
 In non-linear free surface, the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used
@@ -57 +60 @@
 the prognostic equations for the active tracers and the momentum.
 Explicit, split-explicit and filtered free surface formulations are implemented.
-A number of numerical schemes are available for momentum advection, 
-for the computation of the pressure gradients, as well as for the advection of tracers 
+A number of numerical schemes are available for momentum advection,
+for the computation of the pressure gradients, as well as for the advection of tracers
 (second or higher order advection schemes, including positive ones).
 
-Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, or bulk formulations for 
+Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, or bulk formulations for
 the surface fluxes (wind stress, heat, freshwater).
 The model allows penetration of solar radiation.
 There is an optional geothermal heating at the ocean bottom.
-Within the \NEMO system the ocean model is interactively coupled with a sea ice model (SI$^3$) and
+Within the \NEMO\ system the ocean model is interactively coupled with a sea ice model (SI$^3$) and
 a biogeochemistry model (PISCES).
 Interactive coupling to Atmospheric models is possible via the \href{https://portal.enes.org/oasis}{OASIS coupler}.
@@ -86 +89 @@
 \citet{treguier.held.ea_JPO97}.
 The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient,
-with options to compute the coefficients with \citet{blanke.delecluse_JPO93}, \citet{pacanowski.philander_JPO81}, or 
+with options to compute the coefficients with \citet{blanke.delecluse_JPO93}, \citet{pacanowski.philander_JPO81}, or
 \citet{umlauf.burchard_JMR03} mixing schemes.
- 
+
 %%gm    To be put somewhere else ....
 %%nm    We should consider creating a glossary for all this kind of stuff (terms, acronyms and symbols)
@@ -100 +103 @@
 it changes the code from one set of CPP keys to the other.
 It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time.
-Usual coding looks like: 
+Usual coding looks like:
 
 \begin{forlines}
@@ -112 +115 @@
 
 The namelist allows to input variables (character, logical, real and integer) into the code.
-There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...)
+There is one namelist file for each component of \NEMO\ (dynamics, sea-ice, biogeochemistry...)
 containing all the \fortran namelists needed.
-The implementation in NEMO uses a 2-step process. 
+The implementation in \NEMO\ uses a 2-step process.
 For each \fortran namelist, two files are read:
 
@@ -136 +139 @@
 the computation of on-line floats trajectories...
 \autoref{chap:OBS} describes a tool which reads in observation files
-(profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration) 
+(profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration)
 and calculates an interpolated model equivalent value at the observation location and nearest model timestep.
 Originally developed of data assimilation, it is a fantastic tool for model and data comparison.
@@ -143 +146 @@
 (water column model, ORCA and GYRE families of configurations).
 
-%%nm: Add some words on the NEMO dependencies
+%%nm: Add some words on the \NEMO\ dependencies
 The model is implemented in \fninety, with preprocessing (C pre-processor).
 It runs under UNIX.
@@ -164 +167 @@
 The manual mirrors the organization of the model.
 After the presentation of the continuous equations (\autoref{chap:PE}),
-the following chapters refer to specific terms of the equations each associated with a group of modules 
+the following chapters refer to specific terms of the equations each associated with a group of modules
 (\autoref{tab:chapters}).
 
 %--------------------------------------------------TABLE--------------------------------------------------
-\begin{table}[!t] 
+\begin{table}[!t]
   \caption{
     \protect\label{tab:chapters}
@@ -207 +210 @@
 %--------------------------------------------------------------------------------------------------------------
 
-%% nm: the following section has to vastly remodeled to focus only on well-identified versions of NEMO
+%% nm: the following section has to vastly remodeled to focus only on well-identified versions of \NEMO
 %% (3.4, 3.6, 4.0 and further releases). Then its formatting must be improved too.
 \subsubsection{Changes between releases}
 
-NEMO/OPA, like all research tools, is in perpetual evolution.
-The present document describes the OPA version include in the release 3.4 of NEMO.
+\NEMO/OPA, like all research tools, is in perpetual evolution.
+The present document describes the OPA version include in the release 3.4 of \NEMO.
 This release differs significantly from version 8, documented in \citet{madec.delecluse.ea_NPM98}. \\
 
-The main modifications from OPA v8 and NEMO/OPA v3.2 are :
-
-\begin{itemize}
-\item
-  transition to full native \fninety, deep code restructuring and drastic reduction of CPP keys; 
+The main modifications from OPA v8 and \NEMO/OPA v3.2 are :
+
+\begin{itemize}
+\item
+  transition to full native \fninety, deep code restructuring and drastic reduction of CPP keys;
 \item
   introduction of partial step representation of bottom topography
@@ -253 +256 @@
   which includes an on-the-fly interpolation of input forcing fields;
 \item
-  RGB light penetration and optional use of ocean color 
+  RGB light penetration and optional use of ocean color
 \item
   major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{axell_JGR02},
@@ -267 +270 @@
 \end{itemize}
 
-The main modifications from NEMO/OPA v3.2 and v3.3 are:
+The main modifications from \NEMO/OPA v3.2 and v3.3 are:
 
 \begin{itemize}
 \item
   introduction of a modified leapfrog-Asselin filter time stepping scheme
-  \citep{leclair.madec_OM09}; 
+  \citep{leclair.madec_OM09};
 \item
   additional scheme for iso-neutral mixing \citep{griffies.gnanadesikan.ea_JPO98}, although it is still a "work in progress";
@@ -315 +318 @@
 improving the model performance.
 
-The main modifications from NEMO/OPA v3.3 and v3.4 are:
+The main modifications from \NEMO/OPA v3.3 and v3.4 are:
 
 \begin{itemize}
@@ -329 +332 @@
 \end{itemize}
 
-The main modifications from NEMO/OPA v3.4 and v3.6 are:
+The main modifications from \NEMO/OPA v3.4 and v3.6 are:
 
 \begin{itemize}
@@ -335 +338 @@
 \end{itemize}
 
-The main modifications from NEMO/OPA v3.6 and v4.0 are:
+The main modifications from \NEMO/OPA v3.6 and v4.0 are:
 
 \begin{itemize}
 \item new definition of configurations;
 \item bulk formulation;
-\item NEMO-wave large scale interactions;
+\item \NEMO-wave large scale interactions;
 \item ...;
 \end{itemize}
@@ -348 +351 @@
 \pindex
 
+%% Restore section heading
+\rehead{Sect.\ \thesection\ \rightmark}
+
 \end{document}