Changeset 11435 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

Timestamp:

2019-08-14T14:45:08+02:00 (5 years ago)

Author:

nicolasmartin

Message:

Various corrections on chapters

Cleaning the indexes by fixing/removing wrong entries (or appending a ? to unknown items) and
improve the classification with new index definitions for CPP keys and namelist blocks:

• from \key{...} cmd, key_ prefix no longer precedes the index entry
• namelist block declaration moves from \ngn{nam...} to \nam{...} (i.e. \ngn{namtra\_ldf} -> \nam{tra\_ldf}) The expected prefix nam is added to the printed word but not the index entry.

Now we have indexes with a better sorting instead of all CPP keys under 'K' and namelists blocks under 'N'.

Fix missing space issues with alias commands by adding a trailing backslash (\NEMO\, \ie\, \eg\, ...).
There is no perfect solution for this, and I prefer not using a particular package to solve it.

Review the initial LaTeX code snippet for the historic changes in chapters

Finally, for readability and future diff visualisations, please avoid writing paragraphs with continuous lines.
Break the lines around 80 to 100 characters long

File:

• NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex (modified) (14 diffs)

NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

@@ -9 +9 @@
 \label{chap:LDF}
 
-\minitoc
+\chaptertoc
 
 \newpage
@@ -22 +22 @@
 (3) the space and time variations of the eddy coefficients.
 These three aspects of the lateral diffusion are set through namelist parameters
-(see the \ngn{nam\_traldf} and \ngn{nam\_dynldf} below).
+(see the \nam{tra\_ldf} and \nam{dyn\_ldf} below).
 Note that this chapter describes the standard implementation of iso-neutral tracer mixing. 
 Griffies's implementation, which is used if \np{ln\_traldf\_triad}\forcode{ = .true.},
@@ -53 +53 @@
 {Laplacian mixing (\protect\np{ln\_traldf\_lap}, \protect\np{ln\_dynldf\_lap})}
 Setting \protect\np{ln\_traldf\_lap}\forcode{ = .true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{ = .true.} enables 
-a second order diffusion on tracers and momentum respectively. Note that in \NEMO 4, one can not combine 
+a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine 
 Laplacian and Bilaplacian operators for the same variable.
 
@@ -60 +60 @@
 Setting \protect\np{ln\_traldf\_blp}\forcode{ = .true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{ = .true.} enables 
 a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice. 
-We stress again that from \NEMO 4, the simultaneous use Laplacian and Bilaplacian operators is not allowed.
+We stress again that from \NEMO\ 4, the simultaneous use Laplacian and Bilaplacian operators is not allowed.
 
 % ================================================================
@@ -90 +90 @@
 \subsection{Slopes for tracer geopotential mixing in the $s$-coordinate}
 
-In $s$-coordinates, geopotential mixing (\ie horizontal mixing) $r_1$ and $r_2$ are the slopes between
+In $s$-coordinates, geopotential mixing (\ie\ horizontal mixing) $r_1$ and $r_2$ are the slopes between
 the geopotential and computational surfaces.
 Their discrete formulation is found by locally solving \autoref{eq:tra_ldf_iso} when
 the diffusive fluxes in the three directions are set to zero and $T$ is assumed to be horizontally uniform,
-\ie a linear function of $z_T$, the depth of a $T$-point. 
+\ie\ a linear function of $z_T$, the depth of a $T$-point. 
 %gm { Steven : My version is obviously wrong since I'm left with an arbitrary constant which is the local vertical temperature gradient}
 
@@ -124 +124 @@
 Their formulation does not depend on the vertical coordinate used.
 Their discrete formulation is found using the fact that the diffusive fluxes of
-locally referenced potential density (\ie $in situ$ density) vanish.
+locally referenced potential density (\ie\ $in situ$ density) vanish.
 So, substituting $T$ by $\rho$ in \autoref{eq:tra_ldf_iso} and setting the diffusive fluxes in
 the three directions to zero leads to the following definition for the neutral slopes:
@@ -230 +230 @@
 To overcome this problem, several techniques have been proposed in which the numerical schemes of
 the ocean model are modified \citep{weaver.eby_JPO97, griffies.gnanadesikan.ea_JPO98}.
-Griffies's scheme is now available in \NEMO if \np{ln\_traldf\_triad}=\forcode{= .true.}; see \autoref{apdx:triad}.
+Griffies's scheme is now available in \NEMO\ if \np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:triad}.
 Here, another strategy is presented \citep{lazar_phd97}:
 a local filtering of the iso-neutral slopes (made on 9 grid-points) prevents the development of
@@ -284 +284 @@
       \textit{(a)} in the real ocean the slope is the iso-neutral slope in the ocean interior,
       which has to be adjusted at the surface boundary
-      \ie it must tend to zero at the surface since there is no mixing across the air-sea interface:
+      \ie\ it must tend to zero at the surface since there is no mixing across the air-sea interface:
       wall boundary condition).
       Nevertheless, the profile between the surface zero value and the interior iso-neutral one is unknown,
@@ -309 +309 @@
 \textit{vw}- points for the $v$-component.
 They are computed from the slopes used for tracer diffusion,
-\ie \autoref{eq:ldfslp_geo} and \autoref{eq:ldfslp_iso}:
+\ie\ \autoref{eq:ldfslp_geo} and \autoref{eq:ldfslp_iso}:
 
 \[
@@ -323 +323 @@
 The major issue remaining is in the specification of the boundary conditions.
 The same boundary conditions are chosen as those used for lateral diffusion along model level surfaces,
-\ie using the shear computed along the model levels and with no additional friction at the ocean bottom
+\ie\ using the shear computed along the model levels and with no additional friction at the ocean bottom
 (see \autoref{sec:LBC_coast}).
 
@@ -420 +420 @@
 
 The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases above,
-\ie a hyperbolic tangent variation with depth associated with a grid size dependence of
+\ie\ a hyperbolic tangent variation with depth associated with a grid size dependence of
 the magnitude of the coefficient. 
 
@@ -527 +527 @@
 the formulation of which depends on the slopes of iso-neutral surfaces.
 Contrary to the case of iso-neutral mixing, the slopes used here are referenced to the geopotential surfaces,
-\ie \autoref{eq:ldfslp_geo} is used in $z$-coordinates,
+\ie\ \autoref{eq:ldfslp_geo} is used in $z$-coordinates,
 and the sum \autoref{eq:ldfslp_geo} + \autoref{eq:ldfslp_iso} in $s$-coordinates.
 
-If isopycnal mixing is used in the standard way, \ie \np{ln\_traldf\_triad}\forcode{ = .false.}, the eddy induced velocity is given by: 
+If isopycnal mixing is used in the standard way, \ie\ \np{ln\_traldf\_triad}\forcode{ = .false.}, the eddy induced velocity is given by: 
 \begin{equation}
   \label{eq:ldfeiv}
@@ -539 +539 @@
   \end{split}
 \end{equation}
-where $A^{eiv}$ is the eddy induced velocity coefficient whose value is set through \np{nn\_aei\_ijk\_t} \ngn{namtra\_eiv} namelist parameter. 
+where $A^{eiv}$ is the eddy induced velocity coefficient whose value is set through \np{nn\_aei\_ijk\_t} \nam{tra\_eiv} namelist parameter. 
 The three components of the eddy induced velocity are computed in \rou{ldf\_eiv\_trp} and
 added to the eulerian velocity in \rou{tra\_adv} where tracer advection is performed.
@@ -570 +570 @@
 %--------------------------------------------------------------------------------------------------------------
 
-If  \np{ln\_mle}\forcode{ = .true.} in \ngn{namtra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection.
+If  \np{ln\_mle}\forcode{ = .true.} in \nam{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection.
 
 \colorbox{yellow}{TBC}