# Changeset 11693

Ignore:
Timestamp:
2019-10-14T14:53:52+02:00 (14 months ago)
Message:

Macros renaming

Location:
NEMO/trunk/doc/latex
Files:
27 edited

Unmodified
Removed
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

 r11690 This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex

 r11690 \begin{figure}[!ht] \centering \includegraphics[width=0.66\textwidth]{ALGOS_ISO_triad} %\includegraphics[width=0.66\textwidth]{ALGOS_ISO_triad} \caption[Triads used in the Griffies's like iso-neutral diffision scheme for $u$- and $w$-components)]{ where $A_{e}$ is the eddy induced velocity coefficient, and $r_i$ and $r_j$ the slopes between the iso-neutral and the geopotential surfaces. %%gm wrong: to be modified with 2 2D streamfunctions \cmtgm{Wrong: to be modified with 2 2D streamfunctions} In other words, the eddy induced velocity can be derived from a vector streamfuntion, $\phi$, which is given by $\phi = A_e\,\textbf{r}$ as $\textbf{U}^* = \textbf{k} \times \nabla \phi$. %%end gm A traditional way to implement this additional advection is to add it to the eulerian velocity prior to \ie\ the variance of the tracer is preserved by the discretisation of the skew fluxes. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

 r11598 that is a Laplacian diffusion is applied on momentum along the coordinate directions. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex

 r11599 \clearpage %%%  Appendix put in gmcomment as it has not been updated for \zstar and s coordinate %%%  Appendix put in cmtgm 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 %\gmcomment{ %\cmtgm{ %% ================================================================================================= %gm comment \gmcomment{ \cmtgm{ The last equality comes from the following equation, \begin{flalign*} \label{subsec:INVARIANTS_2.6} \gmcomment{ \cmtgm{ A pressure gradient has no contribution to the evolution of the vorticity as the curl of a gradient is zero. In the $z$-coordinate, this property is satisfied locally on a C-grid with 2nd order finite differences %gm comment \gmcomment{ \cmtgm{ \begin{flalign*} \sum\limits_{i,j,k} \biggl\{   p_t\;\partial_t b_t   \biggr\}                                &&&\\ %} \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex

 r11599 the expression of the 3D divergence in the $s-$coordinates established above. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}

 r11690 \] \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

 r11599 \end{clines} \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

 r11690 A complete description of the use of this I/O server is presented in the next section. %\gmcomment{                    % start of gmcomment %\cmtgm{                    % start of gmcomment %% ================================================================================================= The maximum values from the run are also copied to the ocean.output file. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

 r11599 \] \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

 r11690 \end{description} \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}

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

 r11690 \end{figure} \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

 r11690 %ENDIF %\gmcomment{  word doc of runoffs: %In the current \NEMO\ setup river runoff is added to emp fluxes, these are then applied at just the sea surface as a volume change (in the variable volume case this is a literal volume change, and in the linear free surface case the free surface is moved) and a salt flux due to the concentration/dilution effect.  There is also an option to increase vertical mixing near river mouths; this gives the effect of having a 3d river.  All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface. %Our aim was to code the option to specify the temperature and salinity of river runoff, (as well as the amount), along with the depth that the river water will affect.  This would make it possible to model low salinity outflow, such as the Baltic, and would allow the ocean temperature to be affected by river runoff. %The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between. %To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the tra_sbc module.  We decided to separate them throughout the code, so that the variable emp represented solely evaporation minus precipitation fluxes, and a new 2d variable rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use emp or emps and the changes made are below: \cmtgm{  word doc of runoffs: In the current \NEMO\ setup river runoff is added to emp fluxes, these are then applied at just the sea surface as a volume change (in the variable volume case this is a literal volume change, and in the linear free surface case the free surface is moved) and a salt flux due to the concentration/dilution effect. There is also an option to increase vertical mixing near river mouths; this gives the effect of having a 3d river. All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface. Our aim was to code the option to specify the temperature and salinity of river runoff, (as well as the amount), along with the depth that the river water will affect. This would make it possible to model low salinity outflow, such as the Baltic, and would allow the ocean temperature to be affected by river runoff. The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between. To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the \mdl{tra_sbc} module. We decided to separate them throughout the code, so that the variable emp represented solely evaporation minus precipitation fluxes, and a new 2d variable rnf was added which represents the volume flux of river runoff (in $kg/m^2s$ to remain consistent with $emp$). This meant many uses of emp and emps needed to be changed, a list of all modules which use $emp$ or $emps$ and the changes made are below:} %% ================================================================================================= Two different bulk formulae are available: \begin{description} \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). A complete description is available in \citet{jenkins_JGR91}. \end{description} Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m. Then, the fluxes are spread over the same thickness (ie over one or several cells). If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature. This can lead to super-cool temperature in the top cell under melting condition. If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. There are 3 different ways to compute the exchange coeficient: \begin{description} \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. \begin{gather*} \begin{description} \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). A complete description is available in \citet{jenkins_JGR91}. \end{description} Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m. Then, the fluxes are spread over the same thickness (ie over one or several cells). If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature. This can lead to super-cool temperature in the top cell under melting condition. If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. There are 3 different ways to compute the exchange coeficient: \begin{description} \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. \begin{gather*} % \label{eq:SBC_isf_gamma_iso} \gamma^{T} = rn\_gammat0 \\ \gamma^{S} = rn\_gammas0 \end{gather*} This is the recommended formulation for ISOMIP. \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as \begin{gather*} \gamma^{T} = rn\_gammat0 \times u_{*} \\ \gamma^{S} = rn\_gammas0 \times u_{*} \end{gather*} where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: $\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}$ where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), $\Gamma_{Turb}$ the contribution of the ocean stability and $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. See \citet{holland.jenkins_JPO99} for all the details on this formulation. This formulation has not been extensively tested in \NEMO\ (not recommended). \end{description} \item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. \item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. \item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl})\\ \gamma^{T} = rn\_gammat0 \\ \gamma^{S} = rn\_gammas0 \end{gather*} This is the recommended formulation for ISOMIP. \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as \begin{gather*} \gamma^{T} = rn\_gammat0 \times u_{*} \\ \gamma^{S} = rn\_gammas0 \times u_{*} \end{gather*} where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: $\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}$ where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), $\Gamma_{Turb}$ the contribution of the ocean stability and $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. See \citet{holland.jenkins_JPO99} for all the details on this formulation. This formulation has not been extensively tested in \NEMO\ (not recommended). \end{description} \item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. \item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. \item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl}) \end{description} % in ocean-ice models. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

 r11598 The first four parameters define the stochastic part of equation of state. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

 r11690 restore this property. %%%gmcomment   :  Cross term are missing in the current implementation.... \cmtgm{Cross term are missing in the current implementation....} %% ================================================================================================= %!!        i.e. transport proportional to the along-slope density gradient %%%gmcomment   :  this section has to be really written \cmtgm{This section has to be really written} When applying an advective BBL (\np[=1..2]{nn_bbl_adv}{nn\_bbl\_adv}), \label{sec:TRA_zpshde} \gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, \cmtgm{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, I've changed "derivative" to "difference" and "mean" to "average"} Sensitivity of the advection schemes to the way horizontal averages are performed in the vicinity of partial cells should be further investigated in the near future. \gmcomment{gm :   this last remark has to be done} \onlyinsubfile{\input{../../global/epilogue}} \cmtgm{gm :   this last remark has to be done} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

 r11690 \clearpage %gm% Add here a small introduction to ZDF and naming of the different physics (similar to what have been written for TRA and DYN. \cmtgm{ Add here a small introduction to ZDF and naming of the different physics (similar to what have been written for TRA and DYN).} %% ================================================================================================= \end{figure} \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

 r11690 Unlike ordinary river points the Baltic inputs also include salinity and temperature data. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex

 r11598 It has not been implemented. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

 r11690 increment also applies to the time.step file which is otherwise updated every timestep. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

 r11690 an explicit computation of vertical advection relative to the moving s-surfaces. %\gmcomment{ %A key point here is that the $s$-coordinate depends on $(i,j)$ ==> horizontal pressure gradient... \cmtgm{A key point here is that the $s$-coordinate depends on $(i,j)$ ==> horizontal pressure gradient...} The generalized vertical coordinates used in ocean modelling are not orthogonal, which contrasts with many other applications in mathematical physics. and similar expressions are used for mixing and forcing terms. \gmcomment{ \cmtgm{ \colorbox{yellow}{ to be updated $= = >$} Add a few works on z and zps and s and underlies the differences between all of them Nevertheless it is currently not available in the iso-neutral case. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

 r11690 \begin{figure}[!t] \centering \includegraphics[width=0.66\textwidth]{MBZ_DYN_dynspg_ts} %\includegraphics[width=0.66\textwidth]{MBZ_DYN_dynspg_ts} \caption[Schematic of the split-explicit time stepping scheme for the barotropic and baroclinic modes, after \citet{Griffies2004?}]{ In particular, this means that in filtered case, the matrix to be inverted has to be recomputed at each time-step. \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

 r11690 % - daymod: definition of the time domain (nit000, nitend and the calendar) \gmcomment{STEVEN :maybe a picture of the directory structure in the introduction which \cmtgm{STEVEN :maybe a picture of the directory structure in the introduction which could be referred to here, would help  ==> to be added} %%gm %%gm   UPDATE the next paragraphs with time varying thickness ... %%gm \cmtgm{UPDATE the next paragraphs with time varying thickness ...} This scheme is rather time consuming since it requires a matrix inversion. Fast barotropic motions (such as tides) are also simulated with a better accuracy. %\gmcomment{ %\cmtgm{ \begin{figure} \centering the \nam{run}{run} namelist variables. \gmcomment{ \cmtgm{ add here how to force the restart to contain only one time step for operational purposes } \gmcomment{       % add a subsection here \cmtgm{       % add a subsection here %% ================================================================================================= }     %% end add \gmcomment{       % add implicit in vvl case  and Crant-Nicholson scheme \cmtgm{       % add implicit in vvl case  and Crant-Nicholson scheme Implicit time stepping in case of variable volume thickness. } \onlyinsubfile{\input{../../global/epilogue}} \subinc{\input{../../global/epilogue}} \end{document}
• ## NEMO/trunk/doc/latex/global/document.tex

• ## NEMO/trunk/doc/latex/global/new_cmds.tex

• ## NEMO/trunk/doc/latex/global/packages.tex

 r11688 %% Issue with fontawesome pkg: path to FontAwesome.otf has to be hard-coded \defaultfontfeatures{ Path = /usr/local/texlive/2019/texmf-dist/fonts/opentype/public/fontawesome/ Path = /home/ntmlod/.local/texlive2019/texmf-dist/fonts/opentype/public/fontawesome/ } \usepackage{academicons, fontawesome, newtxtext}
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