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Changeset 9407 for branches/2017/dev_merge_2017/DOC/tex_sub/annex_E.tex – NEMO

Ignore:
Timestamp:
2018-03-15T17:40:35+01:00 (6 years ago)
Author:
nicolasmartin
Message:

Complete refactoring of cross-referencing

  • Use of \autoref instead of simple \ref for contextual text depending on target type
  • creation of few prefixes for marker to identify the type reference: apdx|chap|eq|fig|sec|subsec|tab
File:
1 edited

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  • branches/2017/dev_merge_2017/DOC/tex_sub/annex_E.tex

    r9393 r9407  
    55% ================================================================ 
    66\chapter{Note on some algorithms} 
    7 \label{Apdx_E} 
     7\label{apdx:E} 
    88\minitoc 
    99 
     
    2020% ------------------------------------------------------------------------------------------------------------- 
    2121\section{Upstream Biased Scheme (UBS) (\protect\np{ln\_traadv\_ubs}\forcode{ = .true.})} 
    22 \label{TRA_adv_ubs} 
     22\label{sec:TRA_adv_ubs} 
    2323 
    2424The UBS advection scheme is an upstream biased third order scheme based on  
     
    2626QUICK scheme (Quadratic Upstream Interpolation for Convective  
    2727Kinematics). For example, in the $i$-direction : 
    28 \begin{equation} \label{Eq_tra_adv_ubs2} 
     28\begin{equation} \label{eq:tra_adv_ubs2} 
    2929\tau _u^{ubs} = \left\{  \begin{aligned} 
    3030  & \tau _u^{cen4} + \frac{1}{12} \,\tau"_i     & \quad \text{if }\ u_{i+1/2} \geqslant 0 \\ 
     
    3333\end{equation} 
    3434or equivalently, the advective flux is 
    35 \begin{equation} \label{Eq_tra_adv_ubs2} 
     35\begin{equation} \label{eq:tra_adv_ubs2} 
    3636U_{i+1/2} \ \tau _u^{ubs}  
    3737=U_{i+1/2} \ \overline{ T_i - \frac{1}{6}\,\tau"_i }^{\,i+1/2} 
     
    6161scheme when \np{ln\_traadv\_ubs}\forcode{ = .true.}. 
    6262 
    63 For stability reasons, in \eqref{Eq_tra_adv_ubs}, the first term which corresponds  
     63For stability reasons, in \autoref{eq:tra_adv_ubs}, the first term which corresponds  
    6464to a second order centred scheme is evaluated using the \textit{now} velocity  
    6565(centred in time) while the second term which is the diffusive part of the scheme,  
     
    6767by \citet{Webb_al_JAOT98} in the context of the Quick advection scheme. UBS and QUICK  
    6868schemes only differ by one coefficient. Substituting 1/6 with 1/8 in  
    69 (\ref{Eq_tra_adv_ubs}) leads to the QUICK advection scheme \citep{Webb_al_JAOT98}.  
     69(\autoref{eq:tra_adv_ubs}) leads to the QUICK advection scheme \citep{Webb_al_JAOT98}.  
    7070This option is not available through a namelist parameter, since the 1/6  
    7171coefficient is hard coded. Nevertheless it is quite easy to make the  
     
    8787eight-order accurate conventional scheme. 
    8888 
    89 NB 3 : It is straight forward to rewrite \eqref{Eq_tra_adv_ubs} as follows: 
    90 \begin{equation} \label{Eq_tra_adv_ubs2} 
     89NB 3 : It is straight forward to rewrite \autoref{eq:tra_adv_ubs} as follows: 
     90\begin{equation} \label{eq:tra_adv_ubs2} 
    9191\tau _u^{ubs} = \left\{  \begin{aligned} 
    9292   & \tau _u^{cen4} + \frac{1}{12} \tau"_i      & \quad \text{if }\ u_{i+1/2} \geqslant 0 \\ 
     
    9595\end{equation} 
    9696or equivalently  
    97 \begin{equation} \label{Eq_tra_adv_ubs2} 
     97\begin{equation} \label{eq:tra_adv_ubs2} 
    9898\begin{split} 
    9999e_{2u} e_{3u}\,u_{i+1/2} \ \tau _u^{ubs}  
     
    102102\end{split} 
    103103\end{equation} 
    104 \eqref{Eq_tra_adv_ubs2} has several advantages. First it clearly evidence that  
     104\autoref{eq:tra_adv_ubs2} has several advantages. First it clearly evidence that  
    105105the UBS scheme is based on the fourth order scheme to which is added an  
    106106upstream biased diffusive term. Second, this emphasises that the $4^{th}$ order  
    107107part have to be evaluated at \emph{now} time step, not only the $2^{th}$ order  
    108 part as stated above using \eqref{Eq_tra_adv_ubs}. Third, the diffusive term is  
     108part as stated above using \autoref{eq:tra_adv_ubs}. Third, the diffusive term is  
    109109in fact a biharmonic operator with a eddy coefficient with is simply proportional  
    110110to the velocity. 
    111111 
    112112laplacian diffusion: 
    113 \begin{equation} \label{Eq_tra_ldf_lap} 
     113\begin{equation} \label{eq:tra_ldf_lap} 
    114114\begin{split} 
    115115D_T^{lT} =\frac{1}{e_{1T} \; e_{2T}\;  e_{3T} } &\left[ {\quad \delta _i  
     
    124124 
    125125bilaplacian: 
    126 \begin{equation} \label{Eq_tra_ldf_lap} 
     126\begin{equation} \label{eq:tra_ldf_lap} 
    127127\begin{split} 
    128128D_T^{lT} =&-\frac{1}{e_{1T} \; e_{2T}\;  e_{3T}} \\ 
     
    136136$i.e.$ $A_u^{lT} = \frac{1}{\sqrt{12}} \,e_{1u}\ \sqrt{ e_{1u}\,|u|\,}$ 
    137137it comes : 
    138 \begin{equation} \label{Eq_tra_ldf_lap} 
     138\begin{equation} \label{eq:tra_ldf_lap} 
    139139\begin{split} 
    140140D_T^{lT} =&-\frac{1}{12}\,\frac{1}{e_{1T} \; e_{2T}\;  e_{3T}} \\ 
     
    146146\end{equation} 
    147147if the velocity is uniform ($i.e.$ $|u|=cst$) then the diffusive flux is 
    148 \begin{equation} \label{Eq_tra_ldf_lap} 
     148\begin{equation} \label{eq:tra_ldf_lap} 
    149149\begin{split} 
    150150F_u^{lT} = - \frac{1}{12} 
     
    157157beurk....  reverte the logic: starting from the diffusive part of the advective flux it comes: 
    158158 
    159 \begin{equation} \label{Eq_tra_adv_ubs2} 
     159\begin{equation} \label{eq:tra_adv_ubs2} 
    160160\begin{split} 
    161161F_u^{lT} 
     
    166166 
    167167sol 1 coefficient at T-point ( add $e_{1u}$ and $e_{1T}$ on both side of first $\delta$): 
    168 \begin{equation} \label{Eq_tra_adv_ubs2} 
     168\begin{equation} \label{eq:tra_adv_ubs2} 
    169169\begin{split} 
    170170F_u^{lT} 
     
    175175 
    176176sol 2 coefficient at u-point: split $|u|$ into $\sqrt{|u|}$ and $e_{1T}$ into $\sqrt{e_{1u}}$ 
    177 \begin{equation} \label{Eq_tra_adv_ubs2} 
     177\begin{equation} \label{eq:tra_adv_ubs2} 
    178178\begin{split} 
    179179F_u^{lT} 
     
    189189% ------------------------------------------------------------------------------------------------------------- 
    190190\section{Leapfrog energetic} 
    191 \label{LF} 
     191\label{sec:LF} 
    192192 
    193193We adopt the following semi-discrete notation for time derivative. Given the values of a variable $q$ at successive time step, the time derivation and averaging operators at the mid time step are: 
    194 \begin{subequations} \label{dt_mt} 
     194\begin{subequations} \label{eq:dt_mt} 
    195195\begin{align} 
    196196 \delta _{t+\rdt/2} [q]     &=  \  \ \,   q^{t+\rdt}  - q^{t}     \\ 
     
    202202, respectively.  
    203203 
    204 The Leap-frog time stepping given by \eqref{Eq_DOM_nxt} can be defined as: 
    205 \begin{equation} \label{LF} 
     204The Leap-frog time stepping given by \autoref{eq:DOM_nxt} can be defined as: 
     205\begin{equation} \label{eq:LF} 
    206206   \frac{\partial q}{\partial t}  
    207207         \equiv \frac{1}{\rdt} \overline{ \delta _{t+\rdt/2}[q]}^{\,t}  
    208208      =         \frac{q^{t+\rdt}-q^{t-\rdt}}{2\rdt} 
    209209\end{equation}  
    210 Note that \eqref{LF} shows that the leapfrog time step is $\rdt$, not $2\rdt$  
     210Note that \autoref{chap:LF} shows that the leapfrog time step is $\rdt$, not $2\rdt$  
    211211as it can be found sometime in literature.  
    212212The leap-Frog time stepping is a second order centered scheme. As such it respects  
    213213the quadratic invariant in integral forms, $i.e.$ the following continuous property, 
    214 \begin{equation} \label{Energy} 
     214\begin{equation} \label{eq:Energy} 
    215215\int_{t_0}^{t_1} {q\, \frac{\partial q}{\partial t} \;dt}  
    216216   =\int_{t_0}^{t_1} {\frac{1}{2}\, \frac{\partial q^2}{\partial t} \;dt}  
     
    252252scheme, but is formulated within the \NEMO framework ($i.e.$ using scale  
    253253factors rather than grid-size and having a position of $T$-points that is not  
    254 necessary in the middle of vertical velocity points, see Fig.~\ref{Fig_zgr_e3}). 
    255  
    256 In the formulation \eqref{Eq_tra_ldf_iso} introduced in 1995 in OPA, the ancestor of \NEMO,  
     254necessary in the middle of vertical velocity points, see \autoref{fig:zgr_e3}). 
     255 
     256In the formulation \autoref{eq:tra_ldf_iso} introduced in 1995 in OPA, the ancestor of \NEMO,  
    257257the off-diagonal terms of the small angle diffusion tensor contain several double  
    258258spatial averages of a gradient, for example $\overline{\overline{\delta_k \cdot}}^{\,i,k}$.  
     
    263263In other word, the operator applied to a tracer does not warranties the decrease of  
    264264its global average variance. To circumvent this, we have introduced a smoothing of  
    265 the slopes of the iso-neutral surfaces (see \S\ref{LDF}). Nevertheless, this technique  
     265the slopes of the iso-neutral surfaces (see \autoref{chap:LDF}). Nevertheless, this technique  
    266266works fine for $T$ and $S$ as they are active tracers ($i.e.$ they enter the computation  
    267267of density), but it does not work for a passive tracer.   \citep{Griffies_al_JPO98} introduce  
     
    270270with a derivative in the same direction by considering triads. For example in the  
    271271(\textbf{i},\textbf{k}) plane, the four triads are defined at the $(i,k)$ $T$-point as follows: 
    272 \begin{equation} \label{Gf_triads} 
     272\begin{equation} \label{eq:Gf_triads} 
    273273_i^k \mathbb{T}_{i_p}^{k_p} (T) 
    274274= \frac{1}{4} \ {b_u}_{\,i+i_p}^{\,k}  \  A_i^k    \left(   
     
    282282$A_i^k$ is the lateral eddy diffusivity coefficient defined at $T$-point, 
    283283and $_i^k \mathbb{R}_{i_p}^{k_p}$ is the slope associated with each triad : 
    284 \begin{equation} \label{Gf_slopes} 
     284\begin{equation} \label{eq:Gf_slopes} 
    285285_i^k \mathbb{R}_{i_p}^{k_p}  
    286286=\frac{ {e_{3w}}_{\,i}^{\,k+k_p}} { {e_{1u}}_{\,i+i_p}^{\,k}} \ \frac  
     
    288288{\left(\alpha / \beta \right)_i^k  \ \delta_{k+k_p}[T^i ] - \delta_{k+k_p}[S^i ] } 
    289289\end{equation} 
    290 Note that in \eqref{Gf_slopes} we use the ratio $\alpha / \beta$ instead of  
     290Note that in \autoref{eq:Gf_slopes} we use the ratio $\alpha / \beta$ instead of  
    291291multiplying the temperature derivative by $\alpha$ and the salinity derivative  
    292292by $\beta$. This is more efficient as the ratio $\alpha / \beta$ can to be  
    293293evaluated directly. 
    294294 
    295 Note that in \eqref{Gf_triads}, we chose to use ${b_u}_{\,i+i_p}^{\,k}$ instead of  
     295Note that in \autoref{eq:Gf_triads}, we chose to use ${b_u}_{\,i+i_p}^{\,k}$ instead of  
    296296${b_{uw}}_{\,i+i_p}^{\,k+k_p}$. This choice has been motivated by the decrease  
    297297of tracer variance and the presence of partial cell at the ocean bottom  
    298 (see Appendix~\ref{Apdx_Gf_operator}). 
     298(see \autoref{apdx:Gf_operator}). 
    299299 
    300300%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    301 \begin{figure}[!ht] \label{Fig_ISO_triad} 
    302 \begin{center} 
     301\begin{figure}[!ht] \begin{center} 
    303302\includegraphics[width=0.70\textwidth]{Fig_ISO_triad} 
    304 \caption{  \protect\label{Fig_ISO_triad}    
     303\caption{  \protect\label{fig:ISO_triad}    
    305304Triads used in the Griffies's like iso-neutral diffision scheme for  
    306305$u$-component (upper panel) and $w$-component (lower panel).} 
     
    311310The four iso-neutral fluxes associated with the triads are defined at $T$-point.  
    312311They take the following expression : 
    313 \begin{flalign} \label{Gf_fluxes} 
     312\begin{flalign} \label{eq:Gf_fluxes} 
    314313\begin{split} 
    315314{_i^k {\mathbb{F}_u}_{i_p}^{k_p} } (T)  
     
    322321 
    323322The resulting iso-neutral fluxes at $u$- and $w$-points are then given by the  
    324 sum of the fluxes that cross the $u$- and $w$-face (Fig.~\ref{Fig_ISO_triad}): 
    325 \begin{flalign} \label{Eq_iso_flux}  
     323sum of the fluxes that cross the $u$- and $w$-face (\autoref{fig:ISO_triad}): 
     324\begin{flalign} \label{eq:iso_flux}  
    326325\textbf{F}_{iso}(T)  
    327326&\equiv  \sum_{\substack{i_p,\,k_p}}  
     
    353352resulting in a iso-neutral diffusion tendency on temperature given by the divergence  
    354353of the sum of all the four triad fluxes : 
    355 \begin{equation} \label{Gf_operator} 
     354\begin{equation} \label{eq:Gf_operator} 
    356355D_l^T = \frac{1}{b_T}  \sum_{\substack{i_p,\,k_p}} \left\{   
    357356       \delta_{i} \left[{_{i+1/2-i_p}^k {\mathbb{F}_u }_{i_p}^{k_p}} \right]  
     
    365364\item[$\bullet$ horizontal diffusion] The discretization of the diffusion operator  
    366365recovers the traditional five-point Laplacian in the limit of flat iso-neutral direction : 
    367 \begin{equation} \label{Gf_property1a} 
     366\begin{equation} \label{eq:Gf_property1a} 
    368367D_l^T = \frac{1}{b_T}  \ \delta_{i}  
    369368   \left[ \frac{e_{2u}\,e_{3u}}{e_{1u}} \; \overline{A}^{\,i} \; \delta_{i+1/2}[T] \right]  
     
    388387\item[$\bullet$ pure iso-neutral operator]  The iso-neutral flux of locally referenced  
    389388potential density is zero, $i.e.$ 
    390 \begin{align} \label{Gf_property2} 
     389\begin{align} \label{eq:Gf_property2} 
    391390\begin{matrix} 
    392391&{_i^k {\mathbb{F}_u}_{i_p}^{k_p} (\rho)}  
     
    398397\end{matrix} 
    399398\end{align} 
    400 This result is trivially obtained using the \eqref{Gf_triads} applied to $T$ and $S$  
    401 and the definition of the triads' slopes \eqref{Gf_slopes}. 
     399This result is trivially obtained using the \autoref{eq:Gf_triads} applied to $T$ and $S$  
     400and the definition of the triads' slopes \autoref{eq:Gf_slopes}. 
    402401 
    403402\item[$\bullet$ conservation of tracer] The iso-neutral diffusion term conserve the  
    404403total tracer content, $i.e.$ 
    405 \begin{equation} \label{Gf_property1} 
     404\begin{equation} \label{eq:Gf_property1} 
    406405\sum_{i,j,k} \left\{ D_l^T \ b_T \right\} = 0 
    407406\end{equation} 
     
    411410\item[$\bullet$ decrease of tracer variance] The iso-neutral diffusion term does  
    412411not increase the total tracer variance, $i.e.$ 
    413 \begin{equation} \label{Gf_property1} 
     412\begin{equation} \label{eq:Gf_property1} 
    414413\sum_{i,j,k} \left\{ T \ D_l^T \ b_T \right\} \leq 0 
    415414\end{equation} 
    416 The property is demonstrated in the Appendix~\ref{Apdx_Gf_operator}. It is a  
     415The property is demonstrated in the \autoref{apdx:Gf_operator}. It is a  
    417416key property for a diffusion term. It means that the operator is also a dissipation  
    418417term, $i.e.$ it is a sink term for the square of the quantity on which it is applied.  
     
    422421\item[$\bullet$ self-adjoint operator] The iso-neutral diffusion operator is self-adjoint,  
    423422$i.e.$ 
    424 \begin{equation} \label{Gf_property1} 
     423\begin{equation} \label{eq:Gf_property1} 
    425424\sum_{i,j,k} \left\{ S \ D_l^T \ b_T \right\} = \sum_{i,j,k} \left\{ D_l^S \ T \ b_T \right\}  
    426425\end{equation} 
     
    428427operator. We just have to apply the same routine. This properties can be demonstrated  
    429428quite easily in a similar way the "non increase of tracer variance" property has been  
    430 proved (see Appendix~\ref{Apdx_Gf_operator}). 
     429proved (see \autoref{apdx:Gf_operator}). 
    431430\end{description} 
    432431 
     
    442441eddy induced velocity, the formulation of which depends on the slopes of iso- 
    443442neutral surfaces. Contrary to the case of iso-neutral mixing, the slopes used  
    444 here are referenced to the geopotential surfaces, $i.e.$ \eqref{Eq_ldfslp_geo}  
    445 is used in $z$-coordinate, and the sum \eqref{Eq_ldfslp_geo} 
    446 + \eqref{Eq_ldfslp_iso} in $z^*$ or $s$-coordinates.  
     443here are referenced to the geopotential surfaces, $i.e.$ \autoref{eq:ldfslp_geo}  
     444is used in $z$-coordinate, and the sum \autoref{eq:ldfslp_geo} 
     445+ \autoref{eq:ldfslp_iso} in $z^*$ or $s$-coordinates.  
    447446 
    448447The eddy induced velocity is given by:  
    449 \begin{equation} \label{Eq_eiv_v} 
     448\begin{equation} \label{eq:eiv_v} 
    450449\begin{split} 
    451450 u^* & = - \frac{1}{e_2\,e_{3}}          \;\partial_k \left( e_2 \, A_e \; r_i  \right)    
     
    467466A traditional way to implement this additional advection is to add it to the eulerian  
    468467velocity prior to compute the tracer advection. This allows us to take advantage of  
    469 all the advection schemes offered for the tracers (see \S\ref{TRA_adv}) and not just  
     468all the advection schemes offered for the tracers (see \autoref{sec:TRA_adv}) and not just  
    470469a $2^{nd}$ order advection scheme. This is particularly useful for passive tracers  
    471470where \emph{positivity} of the advection scheme is of paramount importance.  
    472 % give here the expression using the triads. It is different from the one given in \eqref{Eq_ldfeiv} 
     471% give here the expression using the triads. It is different from the one given in \autoref{eq:ldfeiv} 
    473472% see just below a copy of this equation: 
    474 %\begin{equation} \label{Eq_ldfeiv} 
     473%\begin{equation} \label{eq:ldfeiv} 
    475474%\begin{split} 
    476475% u^* & = \frac{1}{e_{2u}e_{3u}}\; \delta_k \left[e_{2u} \, A_{uw}^{eiv} \; \overline{r_{1w}}^{\,i+1/2} \right]\\ 
     
    479478%\end{split} 
    480479%\end{equation} 
    481 \begin{equation} \label{Eq_eiv_vd}   
     480\begin{equation} \label{eq:eiv_vd}   
    482481\textbf{F}_{eiv}^T   \equiv   \left( \begin{aligned}                                 
    483482 \sum_{\substack{i_p,\,k_p}} & 
     
    491490\end{equation} 
    492491 
    493 \ref{Griffies_JPO98} introduces another way to implement the eddy induced advection,  
     492\citep{Griffies_JPO98} introduces another way to implement the eddy induced advection,  
    494493the so-called skew form. It is based on a transformation of the advective fluxes  
    495494using the non-divergent nature of the eddy induced velocity.  
     
    522521and since the eddy induces velocity field is no-divergent, we end up with the skew  
    523522form of the eddy induced advective fluxes: 
    524 \begin{equation} \label{Eq_eiv_skew_continuous} 
     523\begin{equation} \label{eq:eiv_skew_continuous} 
    525524\textbf{F}_{eiv}^T = \begin{pmatrix}  
    526525           {+ e_{2} \, A_{e} \; r_i  \; \partial_k T}   \\ 
     
    529528\end{equation} 
    530529The tendency associated with eddy induced velocity is then simply the divergence  
    531 of the \eqref{Eq_eiv_skew_continuous} fluxes. It naturally conserves the tracer  
     530of the \autoref{eq:eiv_skew_continuous} fluxes. It naturally conserves the tracer  
    532531content, as it is expressed in flux form and, as the advective form, it preserve the  
    533 tracer variance. Another interesting property of \eqref{Eq_eiv_skew_continuous}  
     532tracer variance. Another interesting property of \autoref{eq:eiv_skew_continuous}  
    534533form is that when $A=A_e$, a simplification occurs in the sum of the iso-neutral  
    535534diffusion and eddy induced velocity terms: 
    536 \begin{flalign} \label{Eq_eiv_skew+eiv_continuous} 
     535\begin{flalign} \label{eq:eiv_skew+eiv_continuous} 
    537536\textbf{F}_{iso}^T + \textbf{F}_{eiv}^T &=  
    538537\begin{pmatrix}  
     
    554553has been used to reduce the computational time \citep{Griffies_JPO98}, but it is  
    555554not of practical use as usually $A \neq A_e$. Nevertheless this property can be used to  
    556 choose a discret form of  \eqref{Eq_eiv_skew_continuous} which is consistent with the  
    557 iso-neutral operator \eqref{Gf_operator}. Using the slopes \eqref{Gf_slopes}  
     555choose a discret form of  \autoref{eq:eiv_skew_continuous} which is consistent with the  
     556iso-neutral operator \autoref{eq:Gf_operator}. Using the slopes \autoref{eq:Gf_slopes}  
    558557and defining $A_e$ at $T$-point($i.e.$ as $A$, the eddy diffusivity coefficient), 
    559558the resulting discret form is given by: 
    560 \begin{equation} \label{Eq_eiv_skew}   
     559\begin{equation} \label{eq:eiv_skew}   
    561560\textbf{F}_{eiv}^T   \equiv   \frac{1}{4} \left( \begin{aligned}                                 
    562561 \sum_{\substack{i_p,\,k_p}} & 
     
    569568\end{aligned}   \right) 
    570569\end{equation} 
    571 Note that \eqref{Eq_eiv_skew} is valid in $z$-coordinate with or without partial cells.  
     570Note that \autoref{eq:eiv_skew} is valid in $z$-coordinate with or without partial cells.  
    572571In $z^*$ or $s$-coordinate, the slope between the level and the geopotential surfaces  
    573572must be added to $\mathbb{R}$ for the discret form to be exact.  
     
    575574Such a choice of discretisation is consistent with the iso-neutral operator as it uses the  
    576575same definition for the slopes. It also ensures the conservation of the tracer variance  
    577 (see Appendix \ref{Apdx_eiv_skew}), $i.e.$ it does not include a diffusive component  
     576(see Appendix \autoref{apdx:eiv_skew}), $i.e.$ it does not include a diffusive component  
    578577but is a "pure" advection term. 
    579578 
     
    586585% ================================================================ 
    587586\subsection{Discrete invariants of the iso-neutral diffrusion} 
    588 \label{Apdx_Gf_operator} 
     587\label{subsec:Gf_operator} 
    589588 
    590589Demonstration of the decrease of the tracer variance in the (\textbf{i},\textbf{j}) plane.  
     
    596595\int_D  D_l^T \; T \;dv   \leq 0 
    597596\end{align*} 
    598 The discrete form of its left hand side is obtained using \eqref{Eq_iso_flux} 
     597The discrete form of its left hand side is obtained using \autoref{eq:iso_flux} 
    599598 
    600599\begin{align*} 
     
    673672% 
    674673\allowdisplaybreaks 
    675 \intertext{Then outing in factor the triad in each of the four terms of the summation and substituting the triads by their expression given in \eqref{Gf_triads}. It becomes: } 
     674\intertext{Then outing in factor the triad in each of the four terms of the summation and substituting the triads by their expression given in \autoref{eq:Gf_triads}. It becomes: } 
    676675% 
    677676&\equiv -\sum_{i,k} 
     
    739738% ================================================================ 
    740739\subsection{Discrete invariants of the skew flux formulation} 
    741 \label{Apdx_eiv_skew} 
     740\label{subsec:eiv_skew} 
    742741 
    743742 
     
    750749\int_D \nabla \cdot \textbf{F}_{eiv}(T) \; T \;dv  \equiv 0 
    751750\end{align*} 
    752 The discrete form of its left hand side is obtained using \eqref{Eq_eiv_skew} 
     751The discrete form of its left hand side is obtained using \autoref{eq:eiv_skew} 
    753752\begin{align*} 
    754753 \sum\limits_{i,k} \sum_{\substack{i_p,\,k_p}}  \Biggl\{   \;\; 
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