New URL for NEMO forge!   http://forge.nemo-ocean.eu

Since March 2022 along with NEMO 4.2 release, the code development moved to a self-hosted GitLab.
This present forge is now archived and remained online for history.
Changeset 12928 for NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles – NEMO

Ignore:
Timestamp:
2020-05-14T21:46:00+02:00 (4 years ago)
Author:
smueller
Message:

Synchronizing with /NEMO/trunk@12925 (ticket #2170)

Location:
NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser
Files:
25 edited
1 copied

Legend:

Unmodified
Added
Removed

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser

    • Property svn:externals

      •  

        old new  
        66^/vendors/FCM@HEAD            ext/FCM 
        77^/vendors/IOIPSL@HEAD         ext/IOIPSL 
         8 
         9# SETTE 
         10^/utils/CI/sette@HEAD         sette 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

    r12178 r12928  
    113113\begin{figure}[!tb] 
    114114  \centering 
    115   \includegraphics[width=0.66\textwidth]{Fig_zgr} 
     115  \includegraphics[width=0.66\textwidth]{DOMCFG_zgr} 
    116116  \caption[DOMAINcfg: default vertical mesh for ORCA2]{ 
    117117    Default vertical mesh for ORCA2: 30 ocean levels (L30). 
    … …  
    444444\begin{figure}[!ht] 
    445445  \centering 
    446   \includegraphics[width=0.66\textwidth]{Fig_sco_function} 
     446  \includegraphics[width=0.66\textwidth]{DOMCFG_sco_function} 
    447447  \caption[DOMAINcfg: examples of the stretching function applied to a seamount]{ 
    448448    Examples of the stretching function applied to a seamount; 
    … …  
    493493\begin{figure}[!ht] 
    494494  \centering 
    495   \includegraphics[width=0.66\textwidth]{Fig_DOM_compare_coordinates_surface} 
     495  \includegraphics[width=0.66\textwidth]{DOMCFG_compare_coordinates_surface} 
    496496  \caption[DOMAINcfg: comparison of $s$- and $z$-coordinate]{ 
    497497    A comparison of the \citet{song.haidvogel_JCP94} $S$-coordinate (solid lines), 
    … …  
    530530This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. 
    531531 
    532 \onlyinsubfile{\input{../../global/epilogue}} 
     532\subinc{\input{../../global/epilogue}} 
    533533 
    534534\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_algos.tex

    r12178 r12928  
    311311\begin{figure}[!ht] 
    312312  \centering 
    313   \includegraphics[width=0.66\textwidth]{Fig_ISO_triad} 
     313  %\includegraphics[width=0.66\textwidth]{ALGOS_ISO_triad} 
    314314  \caption[Triads used in the Griffies's like iso-neutral diffision scheme for 
    315315    $u$- and $w$-components)]{ 
    … …  
    461461where $A_{e}$ is the eddy induced velocity coefficient, 
    462462and $r_i$ and $r_j$ the slopes between the iso-neutral and the geopotential surfaces. 
    463 %%gm wrong: to be modified with 2 2D streamfunctions 
     463\cmtgm{Wrong: to be modified with 2 2D streamfunctions} 
    464464In other words, the eddy induced velocity can be derived from a vector streamfuntion, $\phi$, 
    465465which is given by $\phi = A_e\,\textbf{r}$ as $\textbf{U}^*  = \textbf{k} \times \nabla \phi$. 
    466 %%end gm 
    467466 
    468467A traditional way to implement this additional advection is to add it to the eulerian velocity prior to 
    … …  
    822821\ie\ the variance of the tracer is preserved by the discretisation of the skew fluxes. 
    823822 
    824 \onlyinsubfile{\input{../../global/epilogue}} 
     823\subinc{\input{../../global/epilogue}} 
    825824 
    826825\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

    r12178 r12928  
    421421that is a Laplacian diffusion is applied on momentum along the coordinate directions. 
    422422 
    423 \onlyinsubfile{\input{../../global/epilogue}} 
     423\subinc{\input{../../global/epilogue}} 
    424424 
    425425\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_invariants.tex

    r12178 r12928  
    2525\clearpage 
    2626 
    27 %%%  Appendix put in gmcomment as it has not been updated for \zstar and s coordinate 
     27%%%  Appendix put in cmtgm as it has not been updated for \zstar and s coordinate 
    2828%I'm writting this appendix. It will be available in a forthcoming release of the documentation 
    2929 
    30 %\gmcomment{ 
     30%\cmtgm{ 
    3131 
    3232%% ================================================================================================= 
    … …  
    270270 
    271271%gm comment 
    272 \gmcomment{ 
     272\cmtgm{ 
    273273The last equality comes from the following equation, 
    274274\begin{flalign*} 
    … …  
    583583\label{subsec:INVARIANTS_2.6} 
    584584 
    585 \gmcomment{ 
     585\cmtgm{ 
    586586  A pressure gradient has no contribution to the evolution of the vorticity as the curl of a gradient is zero. 
    587587  In the $z$-coordinate, this property is satisfied locally on a C-grid with 2nd order finite differences 
    … …  
    694694 
    695695%gm comment 
    696 \gmcomment{ 
     696\cmtgm{ 
    697697  \begin{flalign*} 
    698698    \sum\limits_{i,j,k} \biggl\{   p_t\;\partial_t b_t   \biggr\}                                &&&\\ 
    … …  
    14791479%} 
    14801480 
    1481 \onlyinsubfile{\input{../../global/epilogue}} 
     1481\subinc{\input{../../global/epilogue}} 
    14821482 
    14831483\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_s_coord.tex

    r12178 r12928  
    584584the expression of the 3D divergence in the $s-$coordinates established above. 
    585585 
    586 \onlyinsubfile{\input{../../global/epilogue}} 
     586\subinc{\input{../../global/epilogue}} 
    587587 
    588588\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_triads.tex

    r12178 r12928  
    212212\begin{figure}[tb] 
    213213  \centering 
    214   \includegraphics[width=0.66\textwidth]{Fig_GRIFF_triad_fluxes} 
     214  \includegraphics[width=0.66\textwidth]{TRIADS_GRIFF_triad_fluxes} 
    215215  \caption[Triads arrangement and tracer gradients to give lateral and vertical tracer fluxes]{ 
    216216    (a) Arrangement of triads $S_i$ and tracer gradients to 
    … …  
    272272\begin{figure}[tb] 
    273273  \centering 
    274   \includegraphics[width=0.66\textwidth]{Fig_GRIFF_qcells} 
     274  \includegraphics[width=0.66\textwidth]{TRIADS_GRIFF_qcells} 
    275275  \caption[Triad notation for quarter cells]{ 
    276276    Triad notation for quarter cells. 
    … …  
    657657\begin{figure}[h] 
    658658  \centering 
    659   \includegraphics[width=0.66\textwidth]{Fig_GRIFF_bdry_triads} 
     659  \includegraphics[width=0.66\textwidth]{TRIADS_GRIFF_bdry_triads} 
    660660  \caption[Boundary triads]{ 
    661661    (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer points (black dots), 
    … …  
    808808\begin{figure}[h] 
    809809  \centering 
    810   \includegraphics[width=0.66\textwidth]{Fig_GRIFF_MLB_triads} 
     810  \includegraphics[width=0.66\textwidth]{TRIADS_GRIFF_MLB_triads} 
    811811  \caption[Definition of mixed-layer depth and calculation of linearly tapered triads]{ 
    812812    Definition of mixed-layer depth and calculation of linearly tapered triads. 
    … …  
    11771177\] 
    11781178 
    1179 \onlyinsubfile{\input{../../global/epilogue}} 
     1179\subinc{\input{../../global/epilogue}} 
    11801180 
    11811181\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_ASM.tex

    r12178 r12928  
    194194\end{clines} 
    195195 
    196 \onlyinsubfile{\input{../../global/epilogue}} 
     196\subinc{\input{../../global/epilogue}} 
    197197 
    198198\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_DIA.tex

    r12178 r12928  
    5555A complete description of the use of this I/O server is presented in the next section. 
    5656 
    57 %\gmcomment{                    % start of gmcomment 
     57%\cmtgm{                    % start of gmcomment 
    5858 
    5959%% ================================================================================================= 
    … …  
    15801580 
    15811581%% ================================================================================================= 
    1582 \section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})]{Harmonic analysis of tidal constituents (\protect\key{diaharm})} 
    1583 \label{sec:DIA_diag_harm} 
    1584  
    1585 \begin{listing} 
    1586   \nlst{nam_diaharm} 
    1587   \caption{\forcode{&nam_diaharm}} 
    1588   \label{lst:nam_diaharm} 
    1589 \end{listing} 
    1590  
    1591 A module is available to compute the amplitude and phase of tidal waves. 
    1592 This on-line Harmonic analysis is actived with \key{diaharm}. 
    1593  
    1594 Some parameters are available in namelist \nam{_diaharm}{\_diaharm}: 
    1595  
    1596  - \np{nit000_han}{nit000\_han} is the first time step used for harmonic analysis 
    1597  
    1598  - \np{nitend_han}{nitend\_han} is the  last time step used for harmonic analysis 
    1599  
    1600  - \np{nstep_han}{nstep\_han}  is the  time step frequency for harmonic analysis 
    1601  
    1602 % - \np{nb_ana}{nb\_ana}     is the number of harmonics to analyse 
    1603  
    1604  - \np{tname}{tname}       is an array with names of tidal constituents to analyse 
    1605  
    1606  \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000}{nit000} and \np{nitend}{nitend} of the simulation. 
    1607  The restart capability is not implemented. 
    1608  
    1609  The Harmonic analysis solve the following equation: 
    1610  
    1611  \[ 
    1612    h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i} 
    1613  \] 
    1614  
    1615 With $A_{j}$, $\nu_{j}$, $\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error. 
    1616 $h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\ 
    1617 We can rewrite this equation: 
    1618  
    1619 \[ 
    1620   h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i} 
    1621 \] 
    1622  
    1623 with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ and $\phi_{j}=arctan(S_{j}/C_{j})$. 
    1624  
    1625 We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave. 
    1626  
    1627 %% ================================================================================================= 
    16281582\section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})} 
    16291583\label{sec:DIA_diag_dct} 
    … …  
    19671921\begin{figure}[!t] 
    19681922  \centering 
    1969   \includegraphics[width=0.66\textwidth]{Fig_mask_subasins} 
     1923  \includegraphics[width=0.66\textwidth]{DIA_mask_subasins} 
    19701924  \caption[Decomposition of the World Ocean to compute transports as well as 
    19711925  the meridional stream-function]{ 
    … …  
    20221976 
    20231977%% ================================================================================================= 
    2024 \subsection{Top middle and bed hourly output} 
    2025  
    2026 \begin{listing} 
    2027   \nlst{nam_diatmb} 
    2028   \caption{\forcode{&nam_diatmb}} 
    2029   \label{lst:nam_diatmb} 
    2030 \end{listing} 
    2031  
    2032 A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables. 
    2033 This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs. 
    2034 The tidal signal is retained but the overall data usage is cut to just three vertical levels. 
    2035 Also the bottom level is calculated for each cell. 
    2036 This diagnostic is actived with the logical $ln\_diatmb$. 
    2037  
    2038 %% ================================================================================================= 
    20391978\subsection{Courant numbers} 
    20401979 
    … …  
    20612000The maximum values from the run are also copied to the ocean.output file. 
    20622001 
    2063 \onlyinsubfile{\input{../../global/epilogue}} 
     2002\subinc{\input{../../global/epilogue}} 
    20642003 
    20652004\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_DIU.tex

    r12178 r12928  
    160160\] 
    161161 
    162 \onlyinsubfile{\input{../../global/epilogue}} 
     162\subinc{\input{../../global/epilogue}} 
    163163 
    164164\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_DOM.tex

    r12178 r12928  
    6060\begin{figure} 
    6161  \centering 
    62   \includegraphics[width=0.33\textwidth]{Fig_cell} 
     62  \includegraphics[width=0.33\textwidth]{DOM_cell} 
    6363  \caption[Arrangement of variables in the unit cell of space domain]{ 
    6464    Arrangement of variables in the unit cell of space domain. 
    … …  
    151151\begin{figure} 
    152152  \centering 
    153   \includegraphics[width=0.5\textwidth]{Fig_zgr_e3} 
     153  \includegraphics[width=0.5\textwidth]{DOM_zgr_e3} 
    154154  \caption[Comparison of grid-point position, vertical grid-size and scale factors]{ 
    155155    Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical, 
    … …  
    265265\begin{figure} 
    266266  \centering 
    267   \includegraphics[width=0.33\textwidth]{Fig_index_hor} 
     267  \includegraphics[width=0.33\textwidth]{DOM_index_hor} 
    268268  \caption[Horizontal integer indexing]{ 
    269269    Horizontal integer indexing used in the \fortran\ code. 
    … …  
    316316\begin{figure} 
    317317  \centering 
    318   \includegraphics[width=0.33\textwidth]{Fig_index_vert} 
     318  \includegraphics[width=0.33\textwidth]{DOM_index_vert} 
    319319  \caption[Vertical integer indexing]{ 
    320320    Vertical integer indexing used in the \fortran\ code. 
    … …  
    474474\begin{figure} 
    475475  \centering 
    476   \includegraphics[width=0.5\textwidth]{Fig_z_zps_s_sps} 
     476  \includegraphics[width=0.5\textwidth]{DOM_z_zps_s_sps} 
    477477  \caption[Ocean bottom regarding coordinate systems ($z$, $s$ and hybrid $s-z$)]{ 
    478478    The ocean bottom as seen by the model: 
    … …  
    695695\end{description} 
    696696 
    697 \onlyinsubfile{\input{../../global/epilogue}} 
     697\subinc{\input{../../global/epilogue}} 
    698698 
    699699\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_DYN.tex

    r12178 r12928  
    6767Furthermore, the tendency terms associated with the 2D barotropic vorticity balance (when \texttt{trdvor?} is defined) 
    6868can be derived from the 3D terms. 
    69 \gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does 
    70 MISC correspond to "extracting tendency terms" or "vorticity balance"?} 
     69\cmtgm{STEVEN: not quite sure I've got the sense of the last sentence. 
     70  Does MISC correspond to "extracting tendency terms" or "vorticity balance"?} 
    7171 
    7272%% ================================================================================================= 
    … …  
    153153as changes in the divergence of the barotropic transport are absorbed into the change of the level thicknesses, 
    154154re-orientated downward. 
    155 \gmcomment{not sure of this...  to be modified with the change in emp setting} 
     155\cmtgm{not sure of this...  to be modified with the change in emp setting} 
    156156In the case of a linear free surface, the time derivative in \autoref{eq:DYN_wzv} disappears. 
    157157The upper boundary condition applies at a fixed level $z=0$. 
    … …  
    287287$u$ and $v$ are located at different grid points, 
    288288a price worth paying to avoid a double averaging in the pressure gradient term as in the $B$-grid. 
    289 \gmcomment{ To circumvent this, Adcroft (ADD REF HERE) 
     289\cmtgm{ To circumvent this, Adcroft (ADD REF HERE) 
    290290Nevertheless, this technique strongly distort the phase and group velocity of Rossby waves....} 
    291291 
    … …  
    311311\begin{figure}[!ht] 
    312312  \centering 
    313   \includegraphics[width=0.66\textwidth]{Fig_DYN_een_triad} 
     313  \includegraphics[width=0.66\textwidth]{DYN_een_triad} 
    314314  \caption[Triads used in the energy and enstrophy conserving scheme (EEN)]{ 
    315315    Triads used in the energy and enstrophy conserving scheme (EEN) for 
    … …  
    516516In the vertical, the centred $2^{nd}$ order evaluation of the advection is preferred, \ie\ $u_{uw}^{ubs}$ and 
    517517$u_{vw}^{ubs}$ in \autoref{eq:DYN_adv_cen2} are used. 
    518 UBS is diffusive and is associated with vertical mixing of momentum. \gmcomment{ gm  pursue the 
     518UBS is diffusive and is associated with vertical mixing of momentum. \cmtgm{ gm  pursue the 
    519519sentence:Since vertical mixing of momentum is a source term of the TKE equation...  } 
    520520 
    … …  
    534534there is also the possibility of using a $4^{th}$ order evaluation of the advective velocity as in ROMS. 
    535535This is an error and should be suppressed soon. 
    536 \gmcomment{action :  this have to be done} 
     536\cmtgm{action :  this have to be done} 
    537537 
    538538%% ================================================================================================= 
    … …  
    846846\begin{figure}[!t] 
    847847  \centering 
    848   \includegraphics[width=0.66\textwidth]{Fig_DYN_dynspg_ts} 
     848  \includegraphics[width=0.66\textwidth]{DYN_dynspg_ts} 
    849849  \caption[Split-explicit time stepping scheme for the external and internal modes]{ 
    850850    Schematic of the split-explicit time stepping scheme for the external and internal modes. 
    … …  
    915915it is still significant as shown by \citet{levier.treguier.ea_rpt07} in the case of an analytical barotropic Kelvin wave. 
    916916 
    917 \gmcomment{               %%% copy from griffies Book 
     917\cmtgm{               %%% copy from griffies Book 
    918918 
    919919\textbf{title: Time stepping the barotropic system } 
    … …  
    10431043 
    10441044%% gm %%======>>>>   given here the discrete eqs provided to the solver 
    1045 \gmcomment{               %%% copy from chap-model basics 
     1045\cmtgm{               %%% copy from chap-model basics 
    10461046  \[ 
    10471047    % \label{eq:DYN_spg_flt} 
    … …  
    10541054  and $\mathrm {\mathbf M}$ represents the collected contributions of the Coriolis, hydrostatic pressure gradient, 
    10551055  non-linear and viscous terms in \autoref{eq:MB_dyn}. 
    1056 }   %end gmcomment 
     1056}   %end cmtgm 
    10571057 
    10581058Note that in the linear free surface formulation (\texttt{vvl?} not defined), 
    … …  
    10821082no slip or partial slip boundary conditions are applied according to the user's choice (see \autoref{chap:LBC}). 
    10831083 
    1084 \gmcomment{ 
     1084\cmtgm{ 
    10851085  Hyperviscous operators are frequently used in the simulation of turbulent flows to 
    10861086  control the dissipation of unresolved small scale features. 
    … …  
    11831183the first derivative term normal to the coast depends on the free or no-slip lateral boundary conditions chosen, 
    11841184while the third derivative terms normal to the coast are set to zero (see \autoref{chap:LBC}). 
    1185 \gmcomment{add a remark on the the change in the position of the coefficient} 
     1185\cmtgm{add a remark on the the change in the position of the coefficient} 
    11861186 
    11871187%% ================================================================================================= 
    … …  
    12521252the snow-ice mass is taken into account when computing the surface pressure gradient. 
    12531253 
    1254 \gmcomment{ missing : the lateral boundary condition !!!   another external forcing 
     1254\cmtgm{ missing : the lateral boundary condition !!!   another external forcing 
    12551255 } 
    12561256 
    … …  
    14801480\begin{figure}[!ht] 
    14811481  \centering 
    1482   \includegraphics[width=0.66\textwidth]{Fig_WAD_dynhpg} 
     1482  \includegraphics[width=0.66\textwidth]{DYN_WAD_dynhpg} 
    14831483  \caption[Combinations controlling the limiting of the horizontal pressure gradient in 
    14841484  wetting and drying regimes]{ 
    … …  
    15961596and only array swapping and Asselin filtering is done in \mdl{dynnxt}. 
    15971597 
    1598 \onlyinsubfile{\input{../../global/epilogue}} 
     1598\subinc{\input{../../global/epilogue}} 
    15991599 
    16001600\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_LBC.tex

    r12178 r12928  
    2525\clearpage 
    2626 
    27 %gm% add here introduction to this chapter 
     27\cmtgm{Add here introduction to this chapter} 
    2828 
    2929%% ================================================================================================= 
    … …  
    7979\begin{figure}[!t] 
    8080  \centering 
    81   \includegraphics[width=0.66\textwidth]{Fig_LBC_uv} 
     81  \includegraphics[width=0.66\textwidth]{LBC_uv} 
    8282  \caption[Lateral boundary at $T$-level]{ 
    8383    Lateral boundary (thick line) at T-level. 
    … …  
    104104\begin{figure}[!p] 
    105105  \centering 
    106   \includegraphics[width=0.66\textwidth]{Fig_LBC_shlat} 
     106  \includegraphics[width=0.66\textwidth]{LBC_shlat} 
    107107  \caption[Lateral boundary conditions]{ 
    108108    Lateral boundary conditions 
    … …  
    201201\begin{figure}[!t] 
    202202  \centering 
    203   \includegraphics[width=0.66\textwidth]{Fig_LBC_jperio} 
     203  \includegraphics[width=0.66\textwidth]{LBC_jperio} 
    204204  \caption[Setting of east-west cyclic and symmetric across the Equator boundary conditions]{ 
    205205    Setting of (a) east-west cyclic (b) symmetric across the Equator boundary conditions} 
    … …  
    219219\begin{figure}[!t] 
    220220  \centering 
    221   \includegraphics[width=0.66\textwidth]{Fig_North_Fold_T} 
     221  \includegraphics[width=0.66\textwidth]{LBC_North_Fold_T} 
    222222  \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{ 
    223223    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$), 
    … …  
    272272\begin{figure}[!t] 
    273273  \centering 
    274   \includegraphics[width=0.66\textwidth]{Fig_mpp} 
     274  \includegraphics[width=0.66\textwidth]{LBC_mpp} 
    275275  \caption{Positioning of a sub-domain when massively parallel processing is used} 
    276276  \label{fig:LBC_mpp} 
    … …  
    325325\begin{figure}[!ht] 
    326326  \centering 
    327   \includegraphics[width=0.66\textwidth]{Fig_mppini2} 
     327  \includegraphics[width=0.66\textwidth]{LBC_mppini2} 
    328328  \caption[Atlantic domain defined for the CLIPPER projet]{ 
    329329    Example of Atlantic domain defined for the CLIPPER projet. 
    … …  
    596596\begin{figure}[!t] 
    597597  \centering 
    598   \includegraphics[width=0.66\textwidth]{Fig_LBC_bdy_geom} 
     598  \includegraphics[width=0.66\textwidth]{LBC_bdy_geom} 
    599599  \caption[Geometry of unstructured open boundary]{Example of geometry of unstructured open boundary} 
    600600  \label{fig:LBC_bdy_geom} 
    … …  
    631631\begin{figure}[!t] 
    632632  \centering 
    633   \includegraphics[width=0.66\textwidth]{Fig_LBC_nc_header} 
     633  \includegraphics[width=0.66\textwidth]{LBC_nc_header} 
    634634  \caption[Header for a \protect\ifile{coordinates.bdy} file]{ 
    635635    Example of the header for a \protect\ifile{coordinates.bdy} file} 
    … …  
    708708direction of rotation). %, e.g. anticlockwise or clockwise. 
    709709 
    710 \onlyinsubfile{\input{../../global/epilogue}} 
     710\subinc{\input{../../global/epilogue}} 
    711711 
    712712\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_LDF.tex

    r12178 r12928  
    6868\label{sec:LDF_slp} 
    6969 
    70 \gmcomment{ 
     70\cmtgm{ 
    7171  we should emphasize here that the implementation is a rather old one. 
    7272  Better work can be achieved by using \citet{griffies.gnanadesikan.ea_JPO98, griffies_bk04} iso-neutral scheme. 
    … …  
    8484$r_{1f}$, $r_{1vw}$, $r_{2t}$, $r_{2vw}$ for $v$. 
    8585 
    86 %gm% add here afigure of the slope in i-direction 
     86\cmtgm{Add here afigure of the slope in i-direction} 
    8787 
    8888%% ================================================================================================= 
    … …  
    9494the diffusive fluxes in the three directions are set to zero and $T$ is assumed to be horizontally uniform, 
    9595\ie\ a linear function of $z_T$, the depth of a $T$-point. 
    96 %gm { Steven : My version is obviously wrong since I'm left with an arbitrary constant which is the local vertical temperature gradient} 
     96\cmtgm{Steven : My version is obviously wrong since 
     97  I'm left with an arbitrary constant which is the local vertical temperature gradient} 
    9798 
    9899\begin{equation} 
    … …  
    112113\end{equation} 
    113114 
    114 %gm%  caution I'm not sure the simplification was a good idea! 
     115\cmtgm{Caution I'm not sure the simplification was a good idea!} 
    115116 
    116117These slopes are computed once in \rou{ldf\_slp\_init} when \np[=.true.]{ln_sco}{ln\_sco}, 
    … …  
    144145\end{equation} 
    145146 
    146 %gm% rewrite this as the explanation is not very clear !!! 
     147\cmtgm{rewrite this as the explanation is not very clear !!!} 
    147148%In practice, \autoref{eq:LDF_slp_iso} is of little help in evaluating the neutral surface slopes. Indeed, for an unsimplified equation of state, the density has a strong dependancy on pressure (here approximated as the depth), therefore applying \autoref{eq:LDF_slp_iso} using the $in situ$ density, $\rho$, computed at T-points leads to a flattening of slopes as the depth increases. This is due to the strong increase of the $in situ$ density with depth. 
    148149 
    … …  
    173174  will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes. 
    174175 
    175 %gm% 
    176176  Note: The solution for $s$-coordinate passes trough the use of different (and better) expression for 
    177177  the constraint on iso-neutral fluxes. 
    … …  
    182182    \alpha \ \textbf{F}(T) = \beta \ \textbf{F}(S) 
    183183  \] 
    184   % gm{  where vector F is ....} 
     184  \cmtgm{where vector F is ....} 
    185185 
    186186This constraint leads to the following definition for the slopes: 
    … …  
    229229This allows an iso-neutral diffusion scheme without additional background horizontal mixing. 
    230230This technique can be viewed as a diffusion operator that acts along large-scale 
    231 (2~$\Delta$x) \gmcomment{2deltax doesnt seem very large scale} iso-neutral surfaces. 
     231(2~$\Delta$x) \cmtgm{2deltax doesnt seem very large scale} iso-neutral surfaces. 
    232232The diapycnal diffusion required for numerical stability is thus minimized and its net effect on the flow is quite small when compared to the effect of an horizontal background mixing. 
    233233 
    … …  
    237237\begin{figure}[!ht] 
    238238  \centering 
    239   \includegraphics[width=0.66\textwidth]{Fig_LDF_ZDF1} 
     239  \includegraphics[width=0.66\textwidth]{LDF_ZDF1} 
    240240  \caption{Averaging procedure for isopycnal slope computation} 
    241241  \label{fig:LDF_ZDF1} 
    … …  
    263263\begin{figure}[!ht] 
    264264  \centering 
    265   \includegraphics[width=0.66\textwidth]{Fig_eiv_slp} 
     265  \includegraphics[width=0.66\textwidth]{LDF_eiv_slp} 
    266266  \caption[Vertical profile of the slope used for lateral mixing in the mixed layer]{ 
    267267    Vertical profile of the slope used for lateral mixing in the mixed layer: 
    … …  
    478478 
    479479%%gm  from Triad appendix  : to be incorporated.... 
    480 \gmcomment{ 
     480\cmtgm{ 
    481481  Values of iso-neutral diffusivity and GM coefficient are set as described in \autoref{sec:LDF_coef}. 
    482482  If none of the keys \key{traldf\_cNd}, N=1,2,3 is set (the default), spatially constant iso-neutral $A_l$ and 
    … …  
    544544\colorbox{yellow}{TBC} 
    545545 
    546 \onlyinsubfile{\input{../../global/epilogue}} 
     546\subinc{\input{../../global/epilogue}} 
    547547 
    548548\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_OBS.tex

    r12178 r12928  
    711711\begin{figure} 
    712712  \centering 
    713   \includegraphics[width=0.66\textwidth]{Fig_OBS_avg_rec} 
     713  \includegraphics[width=0.66\textwidth]{OBS_avg_rec} 
    714714  \caption[Observational weights with a rectangular footprint]{ 
    715715    Weights associated with each model grid box (blue lines and numbers) 
    … …  
    720720\begin{figure} 
    721721  \centering 
    722   \includegraphics[width=0.66\textwidth]{Fig_OBS_avg_rad} 
     722  \includegraphics[width=0.66\textwidth]{OBS_avg_rad} 
    723723  \caption[Observational weights with a radial footprint]{ 
    724724    Weights associated with each model grid box (blue lines and numbers) 
    … …  
    798798\begin{figure} 
    799799  \centering 
    800   \includegraphics[width=0.66\textwidth]{Fig_ASM_obsdist_local} 
     800  \includegraphics[width=0.66\textwidth]{OBS_obsdist_local} 
    801801  \caption[Observations with the geographical distribution]{ 
    802802    Example of the distribution of observations with 
    … …  
    825825\begin{figure} 
    826826  \centering 
    827   \includegraphics[width=0.66\textwidth]{Fig_ASM_obsdist_global} 
     827  \includegraphics[width=0.66\textwidth]{OBS_obsdist_global} 
    828828  \caption[Observations with the round-robin distribution]{ 
    829829    Example of the distribution of observations with 
    … …  
    855855 
    856856%% ================================================================================================= 
    857 \section{Standalone observation operator} 
     857\section{Standalone observation operator (\texttt{SAO})} 
    858858\label{sec:OBS_sao} 
    859859 
    … …  
    11641164\begin{figure} 
    11651165  \centering 
    1166   \includegraphics[width=0.66\textwidth]{Fig_OBS_dataplot_main} 
     1166  \includegraphics[width=0.66\textwidth]{OBS_dataplot_main} 
    11671167  \caption{Main window of dataplot} 
    11681168  \label{fig:OBS_dataplotmain} 
    … …  
    11741174\begin{figure} 
    11751175  \centering 
    1176   \includegraphics[width=0.66\textwidth]{Fig_OBS_dataplot_prof} 
     1176  \includegraphics[width=0.66\textwidth]{OBS_dataplot_prof} 
    11771177  \caption[Profile plot from dataplot]{ 
    11781178    Profile plot from dataplot produced by right clicking on a point in the main window} 
    … …  
    11801180\end{figure} 
    11811181 
    1182 \onlyinsubfile{\input{../../global/epilogue}} 
     1182\subinc{\input{../../global/epilogue}} 
    11831183 
    11841184\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_SBC.tex

    r12178 r12928  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2\usepackage{fontspec} 
     3\usepackage{fontawesome} 
    24 
    35\begin{document} 
    … …  
    4547 
    4648\begin{itemize} 
    47 \item a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk} with four possible bulk algorithms), 
     49\item a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk}), featuring a selection of four bulk parameterization algorithms, 
    4850\item a flux formulation (\np[=.true.]{ln_flx}{ln\_flx}), 
    4951\item a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler), 
    … …  
    504506\label{sec:SBC_flx} 
    505507 
     508% Laurent: DO NOT mix up ``bulk formulae'' (the classic equation) and the ``bulk 
     509% parameterization'' (i.e NCAR, COARE, ECMWF...) 
     510 
    506511\begin{listing} 
    507512  \nlst{namsbc_flx} 
    … …  
    520525See \autoref{subsec:SBC_ssr} for its specification. 
    521526 
    522 %% ================================================================================================= 
     527 
     528 
     529 
     530 
     531 
     532 
     533%% ================================================================================================= 
     534\pagebreak 
     535\newpage 
    523536\section[Bulk formulation (\textit{sbcblk.F90})]{Bulk formulation (\protect\mdl{sbcblk})} 
    524537\label{sec:SBC_blk} 
     538 
     539% L. Brodeau, December 2019... % 
    525540 
    526541\begin{listing} 
    … …  
    530545\end{listing} 
    531546 
    532 In the bulk formulation, the surface boundary condition fields are computed with bulk formulae using atmospheric fields 
    533 and ocean (and sea-ice) variables averaged over \np{nn_fsbc}{nn\_fsbc} time-step. 
    534  
    535 The atmospheric fields used depend on the bulk formulae used. 
    536 In forced mode, when a sea-ice model is used, a specific bulk formulation is used. 
    537 Therefore, different bulk formulae are used for the turbulent fluxes computation 
    538 over the ocean and over sea-ice surface. 
    539 For the ocean, four bulk formulations are available thanks to the \href{https://brodeau.github.io/aerobulk/}{Aerobulk} package (\citet{brodeau.barnier.ea_JPO16}): 
    540 the NCAR (formerly named CORE), COARE 3.0, COARE 3.5 and ECMWF bulk formulae. 
    541 The choice is made by setting to true one of the following namelist variable: 
    542  \np{ln_NCAR}{ln\_NCAR}, \np{ln_COARE_3p0}{ln\_COARE\_3p0},  \np{ln_COARE_3p5}{ln\_COARE\_3p5} and  \np{ln_ECMWF}{ln\_ECMWF}. 
    543 For sea-ice, three possibilities can be selected: 
    544 a constant transfer coefficient (1.4e-3; default value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations 
     547If the bulk formulation is selected (\np[=.true.]{ln_blk}{ln\_blk}), the air-sea 
     548fluxes associated with surface boundary conditions are estimated by means of the 
     549traditional \emph{bulk formulae}. As input, bulk formulae rely on a prescribed 
     550near-surface atmosphere state (typically extracted from a weather reanalysis) 
     551and the prognostic sea (-ice) surface state averaged over \np{nn_fsbc}{nn\_fsbc} 
     552time-step(s). 
     553 
     554% Turbulent air-sea fluxes are computed using the sea surface properties and 
     555% atmospheric SSVs at height $z$ above the sea surface, with the traditional 
     556% aerodynamic bulk formulae: 
     557 
     558Note: all the NEMO Fortran routines involved in the present section have been 
     559 initially developed (and are still developed in parallel) in 
     560 the \href{https://brodeau.github.io/aerobulk/}{\texttt{AeroBulk}} open-source project 
     561\citep{brodeau.barnier.ea_JPO17}. 
     562 
     563%%% Bulk formulae are this: 
     564\subsection{Bulk formulae}\label{subsec:SBC_blkform} 
     565% 
     566In NEMO, the set of equations that relate each component of the surface fluxes 
     567to the near-surface atmosphere and sea surface states writes 
     568% 
     569\begin{subequations}\label{eq_bulk} 
     570  \label{eq:SBC_bulk_form} 
     571  \begin{eqnarray} 
     572    \mathbf{\tau} &=& \rho~ C_D ~ \mathbf{U}_z  ~ U_B \\ 
     573    Q_H           &=& \rho~C_H~C_P~\big[ \theta_z - T_s \big] ~ U_B \\ 
     574    E             &=& \rho~C_E    ~\big[    q_s   - q_z \big] ~ U_B \\ 
     575    Q_L           &=& -L_v \, E \\ 
     576    % 
     577    Q_{sr}        &=& (1 - a) Q_{sw\downarrow} \\ 
     578    Q_{ir}        &=& \delta (Q_{lw\downarrow} -\sigma T_s^4) 
     579  \end{eqnarray} 
     580\end{subequations} 
     581% 
     582with 
     583   \[ \theta_z \simeq T_z+\gamma z \] 
     584   \[  q_s \simeq 0.98\,q_{sat}(T_s,p_a ) \] 
     585% 
     586from which, the the non-solar heat flux is \[ Q_{ns} = Q_L + Q_H + Q_{ir} \] 
     587% 
     588where $\mathbf{\tau}$ is the wind stress vector, $Q_H$ the sensible heat flux, 
     589$E$ the evaporation, $Q_L$ the latent heat flux, and $Q_{ir}$ the net longwave 
     590flux. 
     591% 
     592$Q_{sw\downarrow}$ and $Q_{lw\downarrow}$ are the surface downwelling shortwave 
     593and longwave radiative fluxes, respectively. 
     594% 
     595Note: a positive sign for $\mathbf{\tau}$, $Q_H$, $Q_L$, $Q_{sr}$ or $Q_{ir}$ 
     596implies a gain of the relevant quantity for the ocean, while a positive $E$ 
     597implies a freshwater loss for the ocean. 
     598% 
     599$\rho$ is the density of air. $C_D$, $C_H$ and $C_E$ are the bulk transfer 
     600coefficients for momentum, sensible heat, and moisture, respectively. 
     601% 
     602$C_P$ is the heat capacity of moist air, and $L_v$ is the latent heat of 
     603vaporization of water. 
     604% 
     605$\theta_z$, $T_z$ and $q_z$ are the potential temperature, absolute temperature, 
     606and specific humidity of air at height $z$ above the sea surface, 
     607respectively. $\gamma z$ is a temperature correction term which accounts for the 
     608adiabatic lapse rate and approximates the potential temperature at height 
     609$z$ \citep{josey.gulev.ea_2013}. 
     610% 
     611$\mathbf{U}_z$ is the wind speed vector at height $z$ above the sea surface 
     612(possibly referenced to the surface current $\mathbf{u_0}$, 
     613section \ref{s_res1}.\ref{ss_current}). 
     614% 
     615The bulk scalar wind speed, namely $U_B$, is the scalar wind speed, 
     616$|\mathbf{U}_z|$, with the potential inclusion of a gustiness contribution. 
     617% 
     618$a$ and $\delta$ are the albedo and emissivity of the sea surface, respectively.\\ 
     619% 
     620%$p_a$ is the mean sea-level pressure (SLP). 
     621% 
     622$T_s$ is the sea surface temperature. $q_s$ is the saturation specific humidity 
     623of air at temperature $T_s$; it includes a 2\% reduction to account for the 
     624presence of salt in seawater \citep{sverdrup.johnson.ea_1942,kraus.businger_QJRMS96}. 
     625Depending on the bulk parametrization used, $T_s$ can either be the temperature 
     626at the air-sea interface (skin temperature, hereafter SSST) or at typically a 
     627few tens of centimeters below the surface (bulk sea surface temperature, 
     628hereafter SST). 
     629% 
     630The SSST differs from the SST due to the contributions of two effects of 
     631opposite sign, the \emph{cool skin} and \emph{warm layer} (hereafter CS and WL, 
     632respectively, see section\,\ref{subsec:SBC_skin}). 
     633% 
     634Technically, when the ECMWF or COARE* bulk parametrizations are selected 
     635(\np[=.true.]{ln_ECMWF}{ln\_ECMWF} or \np[=.true.]{ln_COARE*}{ln\_COARE\*}), 
     636$T_s$ is the SSST, as opposed to the NCAR bulk parametrization 
     637(\np[=.true.]{ln_NCAR}{ln\_NCAR}) for which $T_s$ is the bulk SST (\ie~temperature 
     638at first T-point level). 
     639 
     640For more details on all these aspects the reader is invited to refer 
     641to \citet{brodeau.barnier.ea_JPO17}. 
     642 
     643 
     644 
     645\subsection{Bulk parametrizations}\label{subsec:SBC_blk_ocean} 
     646%%%\label{subsec:SBC_param} 
     647 
     648Accuracy of the estimate of surface turbulent fluxes by means of bulk formulae 
     649strongly relies on that of the bulk transfer coefficients: $C_D$, $C_H$ and 
     650$C_E$. They are estimated with what we refer to as a \emph{bulk 
     651parametrization} algorithm. When relevant, these algorithms also perform the 
     652height adjustment of humidity and temperature to the wind reference measurement 
     653height (from \np{rn_zqt}{rn\_zqt} to \np{rn_zu}{rn\_zu}). 
     654 
     655 
     656 
     657For the open ocean, four bulk parametrization algorithms are available in NEMO: 
     658\begin{itemize} 
     659\item NCAR, formerly known as CORE, \citep{large.yeager_rpt04,large.yeager_CD09} 
     660\item COARE 3.0 \citep{fairall.bradley.ea_JC03} 
     661\item COARE 3.6 \citep{edson.jampana.ea_JPO13} 
     662\item ECMWF (IFS documentation, cy45) 
     663\end{itemize} 
     664 
     665 
     666With respect to version 3, the principal advances in version 3.6 of the COARE 
     667bulk parametrization are built around improvements in the representation of the 
     668effects of waves on 
     669fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO17}. This includes 
     670improved relationships of surface roughness, and whitecap fraction on wave 
     671parameters. It is therefore recommended to chose version 3.6 over 3. 
     672 
     673 
     674 
     675 
     676\subsection{Cool-skin and warm-layer parametrizations}\label{subsec:SBC_skin} 
     677%\subsection[Cool-skin and warm-layer parameterizations 
     678%(\forcode{ln_skin_cs} \& \forcode{ln_skin_wl})]{Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \& \np{ln_skin_wl}{ln\_skin\_wl})} 
     679%\label{subsec:SBC_skin} 
     680% 
     681As opposed to the NCAR bulk parametrization, more advanced bulk 
     682parametrizations such as COARE3.x and ECMWF are meant to be used with the skin 
     683temperature $T_s$ rather than the bulk SST (which, in NEMO is the temperature at 
     684the first T-point level, see section\,\ref{subsec:SBC_blkform}). 
     685% 
     686As such, the relevant cool-skin and warm-layer parametrization must be 
     687activated through \np[=T]{ln_skin_cs}{ln\_skin\_cs} 
     688and \np[=T]{ln_skin_wl}{ln\_skin\_wl} to use COARE3.x or ECMWF in a consistent 
     689way. 
     690 
     691\texttt{\#LB: ADD BLBLA ABOUT THE TWO CS/WL PARAMETRIZATIONS (ECMWF and COARE) !!!} 
     692 
     693For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same 
     694basis: \citet{fairall.bradley.ea_JGR96}. With some minor updates based 
     695on \citet{zeng.beljaars_GRL05} for ECMWF, and \citet{fairall.ea_19} for COARE 
     6963.6. 
     697 
     698For the warm-layer scheme, ECMWF is based on \citet{zeng.beljaars_GRL05} with a 
     699recent update from \citet{takaya.bidlot.ea_JGR10} (consideration of the 
     700turbulence input from Langmuir circulation). 
     701 
     702Importantly, COARE warm-layer scheme \citep{fairall.ea_19} includes a prognostic 
     703equation for the thickness of the warm-layer, while it is considered as constant 
     704in the ECWMF algorithm. 
     705 
     706 
     707\subsection{Appropriate use of each bulk parametrization} 
     708 
     709\subsubsection{NCAR} 
     710 
     711NCAR bulk parametrizations (formerly known as CORE) is meant to be used with the 
     712CORE II atmospheric forcing \citep{large.yeager_CD09}. The expected sea surface 
     713temperature is the bulk SST. Hence the following namelist parameters must be 
     714set: 
     715% 
     716\begin{verbatim} 
     717  ... 
     718  ln_NCAR    = .true. 
     719  ... 
     720  rn_zqt     = 10.     ! Air temperature & humidity reference height (m) 
     721  rn_zu      = 10.     ! Wind vector reference height (m) 
     722  ... 
     723  ln_skin_cs = .false. ! use the cool-skin parameterization 
     724  ln_skin_wl = .false. ! use the warm-layer parameterization 
     725  ... 
     726  ln_humi_sph = .true. ! humidity "sn_humi" is specific humidity  [kg/kg] 
     727\end{verbatim} 
     728 
     729 
     730\subsubsection{ECMWF} 
     731% 
     732With an atmospheric forcing based on a reanalysis of the ECMWF, such as the 
     733Drakkar Forcing Set \citep{brodeau.barnier.ea_OM10}, we strongly recommend to 
     734use the ECMWF bulk parametrizations with the cool-skin and warm-layer 
     735parametrizations activated. In ECMWF reanalyzes, since air temperature and 
     736humidity are provided at the 2\,m height, and given that the humidity is 
     737distributed as the dew-point temperature, the namelist must be tuned as follows: 
     738% 
     739\begin{verbatim} 
     740  ... 
     741  ln_ECMWF   = .true. 
     742  ...      
     743  rn_zqt     =  2.     ! Air temperature & humidity reference height (m) 
     744  rn_zu      = 10.     ! Wind vector reference height (m) 
     745  ... 
     746  ln_skin_cs = .true. ! use the cool-skin parameterization 
     747  ln_skin_wl = .true. ! use the warm-layer parameterization 
     748  ... 
     749  ln_humi_dpt = .true. !  humidity "sn_humi" is dew-point temperature [K] 
     750  ... 
     751\end{verbatim} 
     752% 
     753Note: when \np{ln_ECMWF}{ln\_ECMWF} is selected, the selection 
     754of \np{ln_skin_cs}{ln\_skin\_cs} and \np{ln_skin_wl}{ln\_skin\_wl} implicitly 
     755triggers the use of the ECMWF cool-skin and warm-layer parametrizations, 
     756respectively (found in \textit{sbcblk\_skin\_ecmwf.F90}). 
     757 
     758 
     759\subsubsection{COARE 3.x} 
     760% 
     761Since the ECMWF parametrization is largely based on the COARE* parametrization, 
     762the two algorithms are very similar in terms of structure and closure 
     763approach. As such, the namelist tuning for COARE 3.x is identical to that of 
     764ECMWF: 
     765% 
     766\begin{verbatim} 
     767  ... 
     768  ln_COARE3p6 = .true. 
     769  ...      
     770  ln_skin_cs = .true. ! use the cool-skin parameterization 
     771  ln_skin_wl = .true. ! use the warm-layer parameterization 
     772  ... 
     773\end{verbatim} 
     774 
     775Note: when \np[=T]{ln_COARE3p0}{ln\_COARE3p0} is selected, the selection 
     776of \np{ln_skin_cs}{ln\_skin\_cs} and \np{ln_skin_wl}{ln\_skin\_wl} implicitly 
     777triggers the use of the COARE cool-skin and warm-layer parametrizations, 
     778respectively (found in \textit{sbcblk\_skin\_coare.F90}). 
     779 
     780 
     781%lulu 
     782 
     783 
     784 
     785% In a typical bulk algorithm, the BTCs under neutral stability conditions are 
     786% defined using \emph{in-situ} flux measurements while their dependence on the 
     787% stability is accounted through the \emph{Monin-Obukhov Similarity Theory} and 
     788% the \emph{flux-profile} relationships \citep[\eg{}][]{Paulson_1970}. BTCs are 
     789% functions of the wind speed and the near-surface stability of the atmospheric 
     790% surface layer (hereafter ASL), and hence, depend on $U_B$, $T_s$, $T_z$, $q_s$ 
     791% and $q_z$. 
     792 
     793 
     794 
     795\subsection{Prescribed near-surface atmospheric state} 
     796 
     797The atmospheric fields used depend on the bulk formulae used.  In forced mode, 
     798when a sea-ice model is used, a specific bulk formulation is used.  Therefore, 
     799different bulk formulae are used for the turbulent fluxes computation over the 
     800ocean and over sea-ice surface. 
     801% 
     802 
     803%The choice is made by setting to true one of the following namelist 
     804%variable: \np{ln_NCAR}{ln\_NCAR}, \np{ln_COARE_3p0}{ln\_COARE\_3p0}, \np{ln_COARE_3p6}{ln\_COARE\_3p6} 
     805%and \np{ln_ECMWF}{ln\_ECMWF}.  
    545806 
    546807Common options are defined through the \nam{sbc_blk}{sbc\_blk} namelist variables. 
    … …  
    553814    Variable description                 & Model variable & Units              & point \\ 
    554815    \hline 
    555     i-component of the 10m air velocity  & utau           & $m.s^{-1}$         & T     \\ 
     816    i-component of the 10m air velocity  & wndi           & $m.s^{-1}$         & T     \\ 
    556817    \hline 
    557     j-component of the 10m air velocity  & vtau           & $m.s^{-1}$         & T     \\ 
     818    j-component of the 10m air velocity  & wndj           & $m.s^{-1}$         & T     \\ 
    558819    \hline 
    559     10m air temperature                  & tair           & \r{}$K$            & T     \\ 
     820    10m air temperature                  & tair           & $K$               & T     \\ 
    560821    \hline 
    561     Specific humidity                    & humi           & \%                 & T     \\ 
     822    Specific humidity                    & humi           & $-$               & T     \\ 
     823    Relative humidity                    & ~              & $\%$              & T     \\ 
     824    Dew-point temperature                & ~              & $K$               & T     \\     
    562825    \hline 
    563     Incoming long wave radiation         & qlw            & $W.m^{-2}$         & T     \\ 
     826    Downwelling longwave radiation       & qlw            & $W.m^{-2}$         & T     \\ 
    564827    \hline 
    565     Incoming short wave radiation        & qsr            & $W.m^{-2}$         & T     \\ 
     828    Downwelling shortwave radiation      & qsr            & $W.m^{-2}$         & T     \\ 
    566829    \hline 
    567830    Total precipitation (liquid + solid) & precip         & $Kg.m^{-2}.s^{-1}$ & T     \\ 
    … …  
    584847 
    585848\np{cn_dir}{cn\_dir} is the directory of location of bulk files 
    586 \np{ln_taudif}{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.) 
     849%\np{ln_taudif}{ln\_taudif} is the flag to specify if we use High Frequency (HF) tau information (.true.) or not (.false.) 
    587850\np{rn_zqt}{rn\_zqt}: is the height of humidity and temperature measurements (m) 
    588851\np{rn_zu}{rn\_zu}: is the height of wind measurements (m) 
    … …  
    595858Its range must be between zero and one, and it is recommended to set it to 0 at low-resolution (ORCA2 configuration). 
    596859 
    597 As for the flux formulation, information about the input data required by the model is provided in 
     860As for the flux parametrization, information about the input data required by the model is provided in 
    598861the namsbc\_blk namelist (see \autoref{subsec:SBC_fldread}). 
    599862 
    600 %% ================================================================================================= 
    601 \subsection[Ocean-Atmosphere Bulk formulae (\textit{sbcblk\_algo\_coare.F90, sbcblk\_algo\_coare3p5.F90, sbcblk\_algo\_ecmwf.F90, sbcblk\_algo\_ncar.F90})]{Ocean-Atmosphere Bulk formulae (\mdl{sbcblk\_algo\_coare}, \mdl{sbcblk\_algo\_coare3p5}, \mdl{sbcblk\_algo\_ecmwf}, \mdl{sbcblk\_algo\_ncar})} 
    602 \label{subsec:SBC_blk_ocean} 
    603  
    604 Four different bulk algorithms are available to compute surface turbulent momentum and heat fluxes over the ocean. 
    605 COARE 3.0, COARE 3.5 and ECMWF schemes mainly differ by their roughness lenghts computation and consequently 
    606 their neutral transfer coefficients relationships with neutral wind. 
    607 \begin{itemize} 
    608 \item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
    609   They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
    610   They use an inertial dissipative method to compute the turbulent transfer coefficients 
    611   (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity. 
    612   This \citet{large.yeager_rpt04} dataset is available through 
    613   the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}. 
    614   Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
    615   This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
    616 \item COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}): See \citet{fairall.bradley.ea_JC03} for more details 
    617 \item COARE 3.5 (\np[=.true.]{ln_COARE_3p5}{ln\_COARE\_3p5}): See \citet{edson.jampana.ea_JPO13} for more details 
    618 \item ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}): Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation. 
    619   Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}. 
    620 \end{itemize} 
     863 
     864\subsubsection{Air humidity} 
     865 
     866Air humidity can be provided as three different parameters: specific humidity 
     867[kg/kg], relative humidity [\%], or dew-point temperature [K] (LINK to namelist 
     868parameters)... 
     869 
     870 
     871~\\ 
     872 
     873 
     874 
     875 
     876 
     877 
     878 
     879 
     880 
     881 
     882%% ================================================================================================= 
     883%\subsection[Ocean-Atmosphere Bulk formulae (\textit{sbcblk\_algo\_coare3p0.F90, sbcblk\_algo\_coare3p6.F90, %sbcblk\_algo\_ecmwf.F90, sbcblk\_algo\_ncar.F90})]{Ocean-Atmosphere Bulk formulae (\mdl{sbcblk\_algo\_coare3p0}, %\mdl{sbcblk\_algo\_coare3p6}, \mdl{sbcblk\_algo\_ecmwf}, \mdl{sbcblk\_algo\_ncar})} 
     884%\label{subsec:SBC_blk_ocean} 
     885 
     886%Four different bulk algorithms are available to compute surface turbulent momentum and heat fluxes over the ocean. 
     887%COARE 3.0, COARE 3.6 and ECMWF schemes mainly differ by their roughness lenghts computation and consequently 
     888%their neutral transfer coefficients relationships with neutral wind. 
     889%\begin{itemize} 
     890%\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
     891%  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
     892%  They use an inertial dissipative method to compute the turbulent transfer coefficients 
     893%  (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity. 
     894%  This \citet{large.yeager_rpt04} dataset is available through 
     895%  the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}. 
     896%  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
     897%  This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
     898%\item COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}): See \citet{fairall.bradley.ea_JC03} for more details 
     899%\item COARE 3.6 (\np[=.true.]{ln_COARE_3p6}{ln\_COARE\_3p6}): See \citet{edson.jampana.ea_JPO13} for more details 
     900%\item ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}): Based on \href{https://www.ecmwf.int/node/9204}{IFS (Cy40r1)} %implementation and documentation. 
     901%  Surface roughness lengths needed for the Obukhov length are computed 
     902%  following \citet{beljaars_QJRMS95}. 
     903%\end{itemize} 
    621904 
    622905%% ================================================================================================= 
    623906\subsection{Ice-Atmosphere Bulk formulae} 
    624907\label{subsec:SBC_blk_ice} 
     908 
     909 
     910\texttt{\#out\_of\_place:} 
     911 For sea-ice, three possibilities can be selected: 
     912a constant transfer coefficient (1.4e-3; default 
     913value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), 
     914and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations 
     915\texttt{\#out\_of\_place.} 
     916 
     917 
     918 
    625919 
    626920Surface turbulent fluxes between sea-ice and the atmosphere can be computed in three different ways: 
    … …  
    8801174%ENDIF 
    8811175 
    882 %\gmcomment{  word doc of runoffs: 
    883 %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. 
    884 %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. 
    885  
    886 %The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between. 
    887  
    888 %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: 
     1176\cmtgm{  word doc of runoffs: 
     1177In the current \NEMO\ setup river runoff is added to emp fluxes, 
     1178these are then applied at just the sea surface as a volume change (in the variable volume case 
     1179this is a literal volume change, and in the linear free surface case the free surface is moved) 
     1180and a salt flux due to the concentration/dilution effect. 
     1181There is also an option to increase vertical mixing near river mouths; 
     1182this gives the effect of having a 3d river. 
     1183All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and 
     1184at the same temperature as the sea surface. 
     1185Our aim was to code the option to specify the temperature and salinity of river runoff, 
     1186(as well as the amount), along with the depth that the river water will affect. 
     1187This would make it possible to model low salinity outflow, such as the Baltic, 
     1188and would allow the ocean temperature to be affected by river runoff. 
     1189 
     1190The depth option makes it possible to have the river water affecting just the surface layer, 
     1191throughout depth, or some specified point in between. 
     1192 
     1193To do this we need to treat evaporation/precipitation fluxes and river runoff differently in 
     1194the \mdl{tra_sbc} module. 
     1195We decided to separate them throughout the code, 
     1196so that the variable emp represented solely evaporation minus precipitation fluxes, 
     1197and a new 2d variable rnf was added which represents the volume flux of river runoff 
     1198(in $kg/m^2s$ to remain consistent with $emp$). 
     1199This meant many uses of emp and emps needed to be changed, 
     1200a list of all modules which use $emp$ or $emps$ and the changes made are below:} 
    8891201 
    8901202%% ================================================================================================= 
    … …  
    9081220  Two different bulk formulae are available: 
    9091221 
    910    \begin{description} 
    911    \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
    912      the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
    913    \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
    914      (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
    915      A complete description is available in \citet{jenkins_JGR91}. 
    916    \end{description} 
    917  
    918      Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
    919      Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. 
    920      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. 
    921      Then, the fluxes are spread over the same thickness (ie over one or several cells). 
    922      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. 
    923      This can lead to super-cool temperature in the top cell under melting condition. 
    924      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.\\ 
    925  
    926      Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
    927      There are 3 different ways to compute the exchange coeficient: 
    928    \begin{description} 
    929         \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}. 
    930      \begin{gather*} 
     1222  \begin{description} 
     1223  \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
     1224    the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
     1225  \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
     1226    (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
     1227    A complete description is available in \citet{jenkins_JGR91}. 
     1228  \end{description} 
     1229 
     1230  Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
     1231  Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. 
     1232  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. 
     1233  Then, the fluxes are spread over the same thickness (ie over one or several cells). 
     1234  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. 
     1235  This can lead to super-cool temperature in the top cell under melting condition. 
     1236  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.\\ 
     1237 
     1238  Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
     1239  There are 3 different ways to compute the exchange coeficient: 
     1240  \begin{description} 
     1241  \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}. 
     1242    \begin{gather*} 
    9311243       % \label{eq:SBC_isf_gamma_iso} 
    932        \gamma^{T} = rn\_gammat0 \\ 
    933        \gamma^{S} = rn\_gammas0 
    934      \end{gather*} 
    935      This is the recommended formulation for ISOMIP. 
    936    \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
    937      \begin{gather*} 
    938        \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
    939        \gamma^{S} = rn\_gammas0 \times u_{*} 
    940      \end{gather*} 
    941      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
    942      See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
    943    \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    944 \[ 
    945 \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
    946 \] 
    947      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), 
    948      $\Gamma_{Turb}$ the contribution of the ocean stability and 
    949      $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
    950      See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
    951      This formulation has not been extensively tested in \NEMO\ (not recommended). 
    952    \end{description} 
    953   \item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    954    The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    955    The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
    956    (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
    957    (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
    958    The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
    959   \item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    960    The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
    961    the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
    962    the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
    963    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    964   \item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    965    However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
    966    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    967    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})\\ 
     1244      \gamma^{T} = rn\_gammat0 \\ 
     1245      \gamma^{S} = rn\_gammas0 
     1246    \end{gather*} 
     1247    This is the recommended formulation for ISOMIP. 
     1248  \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
     1249    \begin{gather*} 
     1250      \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
     1251      \gamma^{S} = rn\_gammas0 \times u_{*} 
     1252    \end{gather*} 
     1253    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
     1254    See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
     1255  \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
     1256    \[ 
     1257      \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
     1258    \] 
     1259    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), 
     1260    $\Gamma_{Turb}$ the contribution of the ocean stability and 
     1261    $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
     1262    See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
     1263    This formulation has not been extensively tested in \NEMO\ (not recommended). 
     1264  \end{description} 
     1265\item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
     1266  The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
     1267  The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
     1268  (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
     1269  (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
     1270  The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
     1271\item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
     1272  The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
     1273  the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
     1274  the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
     1275  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     1276\item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
     1277  However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
     1278  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     1279  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}) 
    9681280\end{description} 
    9691281 
    … …  
    9861298\begin{figure}[!t] 
    9871299  \centering 
    988   \includegraphics[width=0.66\textwidth]{Fig_SBC_isf} 
     1300  \includegraphics[width=0.66\textwidth]{SBC_isf} 
    9891301  \caption[Ice shelf location and fresh water flux definition]{ 
    9901302    Illustration of the location where the fwf is injected and 
    … …  
    13071619\begin{figure}[!t] 
    13081620  \centering 
    1309   \includegraphics[width=0.66\textwidth]{Fig_SBC_diurnal} 
     1621  \includegraphics[width=0.66\textwidth]{SBC_diurnal} 
    13101622  \caption[Reconstruction of the diurnal cycle variation of short wave flux]{ 
    13111623    Example of reconstruction of the diurnal cycle variation of short wave flux from 
    … …  
    13411653\begin{figure}[!t] 
    13421654  \centering 
    1343   \includegraphics[width=0.66\textwidth]{Fig_SBC_dcy} 
     1655  \includegraphics[width=0.66\textwidth]{SBC_dcy} 
    13441656  \caption[Reconstruction of the diurnal cycle variation of short wave flux on an ORCA2 grid]{ 
    13451657    Example of reconstruction of the diurnal cycle variation of short wave flux from 
    … …  
    15211833% in ocean-ice models. 
    15221834 
    1523 \onlyinsubfile{\input{../../global/epilogue}} 
     1835\subinc{\input{../../global/epilogue}} 
    15241836 
    15251837\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_STO.tex

    r12178 r12928  
    205205The first four parameters define the stochastic part of equation of state. 
    206206 
    207 \onlyinsubfile{\input{../../global/epilogue}} 
     207\subinc{\input{../../global/epilogue}} 
    208208 
    209209\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_TRA.tex

    r12178 r12928  
    110110\begin{figure} 
    111111  \centering 
    112   \includegraphics[width=0.66\textwidth]{Fig_adv_scheme} 
     112  \includegraphics[width=0.66\textwidth]{TRA_adv_scheme} 
    113113  \caption[Ways to evaluate the tracer value and the amount of tracer exchanged]{ 
    114114    Schematic representation of some ways used to evaluate the tracer value at $u$-point and 
    … …  
    452452restore this property. 
    453453 
    454 %%%gmcomment   :  Cross term are missing in the current implementation.... 
     454\cmtgm{Cross term are missing in the current implementation....} 
    455455 
    456456%% ================================================================================================= 
    … …  
    880880\begin{figure} 
    881881  \centering 
    882   \includegraphics[width=0.66\textwidth]{Fig_TRA_Irradiance} 
     882  \includegraphics[width=0.66\textwidth]{TRA_Irradiance} 
    883883  \caption[Penetration profile of the downward solar irradiance calculated by four models]{ 
    884884    Penetration profile of the downward solar irradiance calculated by four models. 
    … …  
    904904\begin{figure} 
    905905  \centering 
    906   \includegraphics[width=0.66\textwidth]{Fig_TRA_geoth} 
     906  \includegraphics[width=0.66\textwidth]{TRA_geoth} 
    907907  \caption[Geothermal heat flux]{ 
    908908    Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{emile-geay.madec_OS09}. 
    … …  
    10201020\begin{figure} 
    10211021  \centering 
    1022   \includegraphics[width=0.33\textwidth]{Fig_BBL_adv} 
     1022  \includegraphics[width=0.33\textwidth]{TRA_BBL_adv} 
    10231023  \caption[Advective/diffusive bottom boundary layer]{ 
    10241024    Advective/diffusive Bottom Boundary Layer. 
    … …  
    10371037%!!        i.e. transport proportional to the along-slope density gradient 
    10381038 
    1039 %%%gmcomment   :  this section has to be really written 
     1039\cmtgm{This section has to be really written} 
    10401040 
    10411041When applying an advective BBL (\np[=1..2]{nn_bbl_adv}{nn\_bbl\_adv}), 
    … …  
    13741374\label{sec:TRA_zpshde} 
    13751375 
    1376 \gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, 
     1376\cmtgm{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, 
    13771377I've changed "derivative" to "difference" and "mean" to "average"} 
    13781378 
    … …  
    13941394\begin{figure} 
    13951395  \centering 
    1396   \includegraphics[width=0.33\textwidth]{Fig_partial_step_scheme} 
     1396  \includegraphics[width=0.33\textwidth]{TRA_partial_step_scheme} 
    13971397  \caption[Discretisation of the horizontal difference and average of tracers in 
    13981398  the $z$-partial step coordinate]{ 
    … …  
    14641464Sensitivity of the advection schemes to the way horizontal averages are performed in 
    14651465the vicinity of partial cells should be further investigated in the near future. 
    1466 \gmcomment{gm :   this last remark has to be done} 
    1467  
    1468 \onlyinsubfile{\input{../../global/epilogue}} 
     1466\cmtgm{gm :   this last remark has to be done} 
     1467 
     1468\subinc{\input{../../global/epilogue}} 
    14691469 
    14701470\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r12178 r12928  
    2828\clearpage 
    2929 
    30 %gm% Add here a small introduction to ZDF and naming of the different physics (similar to what have been written for TRA and DYN. 
     30\cmtgm{ Add here a small introduction to ZDF and naming of the different physics 
     31(similar to what have been written for TRA and DYN).} 
    3132 
    3233%% ================================================================================================= 
    … …  
    248249\begin{figure}[!t] 
    249250  \centering 
    250   \includegraphics[width=0.66\textwidth]{Fig_mixing_length} 
     251  \includegraphics[width=0.66\textwidth]{ZDF_mixing_length} 
    251252  \caption[Mixing length computation]{Illustration of the mixing length computation} 
    252253  \label{fig:ZDF_mixing_length} 
    … …  
    533534 in \citet{reffray.guillaume.ea_GMD15} for the \NEMO\ model. 
    534535 
    535 %% ================================================================================================= 
    536 \subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm})]{OSM: OSMosis boundary layer scheme (\protect\np{ln_zdfosm}{ln\_zdfosm})} 
     536% ------------------------------------------------------------------------------------------------------------- 
     537%        OSM OSMOSIS BL Scheme 
     538% ------------------------------------------------------------------------------------------------------------- 
     539\subsection[OSM: OSMOSIS boundary layer scheme (\forcode{ln_zdfosm = .true.})] 
     540{OSM: OSMOSIS boundary layer scheme (\protect\np{ln_zdfosm}{ln\_zdfosm})} 
    537541\label{subsec:ZDF_osm} 
    538542 
    … …  
    543547\end{listing} 
    544548 
    545 The OSMOSIS turbulent closure scheme is based on......   TBC 
     549%-------------------------------------------------------------------------------------------------------------- 
     550\paragraph{Namelist choices} 
     551Most of the namelist options refer to how to specify the Stokes 
     552surface drift and penetration depth. There are three options: 
     553\begin{description} 
     554  \item \protect\np[=0]{nn_osm_wave}{nn\_osm\_wave} Default value in \texttt{namelist\_ref}. In this case the Stokes drift is 
     555      assumed to be parallel to the surface wind stress, with 
     556      magnitude consistent with a constant turbulent Langmuir number 
     557    $\mathrm{La}_t=$ \protect\np{rn_m_la} {rn\_m\_la} i.e.\ 
     558    $u_{s0}=\tau/(\mathrm{La}_t^2\rho_0)$.  Default value of 
     559    \protect\np{rn_m_la}{rn\_m\_la} is 0.3. The Stokes penetration 
     560      depth $\delta = $ \protect\np{rn_osm_dstokes}{rn\_osm\_dstokes}; this has default value 
     561      of 5~m. 
     562 
     563  \item \protect\np[=1]{nn_osm_wave}{nn\_osm\_wave} In this case the Stokes drift is 
     564      assumed to be parallel to the surface wind stress, with 
     565      magnitude as in the classical Pierson-Moskowitz wind-sea 
     566      spectrum.  Significant wave height and 
     567      wave-mean period taken from this spectrum are used to calculate the Stokes penetration 
     568      depth, following the approach set out in  \citet{breivik.janssen.ea_JPO14}. 
     569 
     570    \item \protect\np[=2]{nn_osm_wave}{nn\_osm\_wave} In this case the Stokes drift is 
     571      taken from  ECMWF wave model output, though only the component parallel 
     572      to the wind stress is retained. Significant wave height and 
     573      wave-mean period from ECMWF wave model output are used to calculate the Stokes penetration 
     574      depth, again following \citet{breivik.janssen.ea_JPO14}. 
     575 
     576    \end{description} 
     577 
     578    Others refer to the treatment of diffusion and viscosity beneath 
     579    the surface boundary layer: 
     580\begin{description} 
     581   \item \protect\np{ln_kpprimix} {ln\_kpprimix}  Default is \np{.true.}. Switches on KPP-style Ri \#-dependent 
     582     mixing below the surface boundary layer. If this is set 
     583     \texttt{.true.}  the following variable settings are honoured: 
     584    \item \protect\np{rn_riinfty}{rn\_riinfty} Critical value of local Ri \# below which 
     585      shear instability increases vertical mixing from background value. 
     586    \item \protect\np{rn_difri} {rn\_difri} Maximum value of Ri \#-dependent mixing at $\mathrm{Ri}=0$. 
     587    \item \protect\np{ln_convmix}{ln\_convmix} If \texttt{.true.} then, where water column is unstable, specify 
     588       diffusivity equal to \protect\np{rn_dif_conv}{rn\_dif\_conv} (default value is 1 m~s$^{-2}$). 
     589 \end{description} 
     590 Diagnostic output is controlled by: 
     591  \begin{description} 
     592    \item \protect\np{ln_dia_osm}{ln\_dia\_osm} Default is \np{.false.}; allows XIOS output of OSMOSIS internal fields. 
     593  \end{description} 
     594Obsolete namelist parameters include: 
     595\begin{description} 
     596   \item \protect\np{ln_use_osm_la}\np{ln\_use\_osm\_la} With \protect\np[=0]{nn_osm_wave}{nn\_osm\_wave}, 
     597      \protect\np{rn_osm_dstokes} {rn\_osm\_dstokes} is always used to specify the Stokes 
     598      penetration depth. 
     599   \item \protect\np{nn_ave} {nn\_ave} Choice of averaging method for KPP-style Ri \# 
     600      mixing. Not taken account of. 
     601   \item \protect\np{rn_osm_hbl0} {rn\_osm\_hbl0} Depth of initial boundary layer is now set 
     602     by a density criterion similar to that used in calculating \emph{hmlp} (output as \texttt{mldr10\_1}) in \mdl{zdfmxl}. 
     603\end{description} 
     604 
     605\subsubsection{Summary} 
     606Much of the time the turbulent motions in the ocean surface boundary 
     607layer (OSBL) are not given by 
     608classical shear turbulence. Instead they are in a regime known as 
     609`Langmuir turbulence',  dominated by an 
     610interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.ea_JFM97}. 
     611This regime is characterised by strong vertical turbulent motion, and appears when the surface Stokes drift $u_{s0}$ is much greater than the friction velocity $u_{\ast}$. More specifically Langmuir turbulence is thought to be crucial where the turbulent Langmuir number $\mathrm{La}_{t}=(u_{\ast}/u_{s0}) > 0.4$. 
     612 
     613The OSMOSIS model is fundamentally based on results of Large Eddy 
     614Simulations (LES) of Langmuir turbulence and aims to fully describe 
     615this Langmuir regime. The description in this section is of necessity incomplete and further details are available in Grant. A (2019); in prep. 
     616 
     617The OSMOSIS turbulent closure scheme is a similarity-scale scheme in 
     618the same spirit as the K-profile 
     619parameterization (KPP) scheme of \citet{large.ea_RG97}. 
     620A specified shape of diffusivity, scaled by the (OSBL) depth 
     621$h_{\mathrm{BL}}$ and a turbulent velocity scale, is imposed throughout the 
     622boundary layer 
     623$-h_{\mathrm{BL}}<z<\eta$. The turbulent closure model 
     624also includes fluxes of tracers and momentum that are``non-local'' (independent of the local property gradient). 
     625 
     626Rather than the OSBL 
     627depth being diagnosed in terms of a bulk Richardson number criterion, 
     628as in KPP, it is set by a prognostic equation that is informed by 
     629energy budget considerations reminiscent of the classical mixed layer 
     630models of \citet{kraus.turner_tellus67}. 
     631The model also includes an explicit parametrization of the structure 
     632of the pycnocline (the stratified region at the bottom of the OSBL). 
     633 
     634Presently, mixing below the OSBL is handled by the Richardson 
     635number-dependent mixing scheme used in \citet{large.ea_RG97}. 
     636 
     637Convective parameterizations such as described in \ref{sec:ZDF_conv} 
     638below should not be used with the OSMOSIS-OBL model: instabilities 
     639within the OSBL are part of the model, while instabilities below the 
     640ML are handled by the Ri \# dependent scheme. 
     641 
     642\subsubsection{Depth and velocity scales} 
     643The model supposes a boundary layer of thickness $h_{\mathrm{bl}}$ enclosing a well-mixed layer of thickness $h_{\mathrm{ml}}$ and a relatively thin pycnocline at the base of thickness $\Delta h$; Fig.~\ref{fig: OSBL_structure} shows typical (a) buoyancy structure and (b) turbulent buoyancy flux profile for the unstable boundary layer (losing buoyancy at the surface; e.g.\ cooling). 
     644\begin{figure}[!t] 
     645  \begin{center} 
     646    %\includegraphics[width=0.7\textwidth]{ZDF_OSM_structure_of_OSBL} 
     647    \caption{ 
     648      \protect\label{fig: OSBL_structure} 
     649     The structure of the entraining  boundary layer. (a) Mean buoyancy profile. (b) Profile of the buoyancy flux. 
     650    } 
     651  \end{center} 
     652\end{figure} 
     653The pycnocline in the OSMOSIS scheme is assumed to have a finite thickness, and may include a number of model levels. This means that the OSMOSIS scheme must parametrize both the thickness of the pycnocline, and the turbulent fluxes within the pycnocline. 
     654 
     655Consideration of the power input by wind acting on the Stokes drift suggests that the Langmuir turbulence has velocity scale: 
     656\begin{equation}\label{eq:w_La} 
     657w_{*L}= \left(u_*^2 u_{s\,0}\right)^{1/3}; 
     658\end{equation} 
     659but at times the Stokes drift may be weak due to e.g.\ ice cover, short fetch, misalignment with the surface stress, etc.\ so  a composite velocity scale is assumed for the stable (warming) boundary layer: 
     660\begin{equation}\label{eq:composite-nu} 
     661  \nu_{\ast}= \left\{ u_*^3 \left[1-\exp(-.5 \mathrm{La}_t^2)\right]+w_{*L}^3\right\}^{1/3}. 
     662\end{equation} 
     663For the unstable boundary layer this is merged with the standard convective velocity scale $w_{*C}=\left(\overline{w^\prime b^\prime}_0 \,h_\mathrm{ml}\right)^{1/3}$, where $\overline{w^\prime b^\prime}_0$ is the upwards surface buoyancy flux, to give: 
     664\begin{equation}\label{eq:vel-scale-unstable} 
     665\omega_* = \left(\nu_*^3 + 0.5 w_{*C}^3\right)^{1/3}. 
     666\end{equation} 
     667 
     668\subsubsection{The flux gradient model} 
     669The flux-gradient relationships used in the OSMOSIS scheme take the form: 
     670% 
     671\begin{equation}\label{eq:flux-grad-gen} 
     672\overline{w^\prime\chi^\prime}=-K\frac{\partial\overline{\chi}}{\partial z} + N_{\chi,s} +N_{\chi,b} +N_{\chi,t}, 
     673\end{equation} 
     674% 
     675where $\chi$ is a general variable and $N_{\chi,s}, N_{\chi,b} \mathrm{and} N_{\chi,t}$  are the non-gradient terms, and represent the effects of the different terms in the turbulent flux-budget on the transport of $\chi$. $N_{\chi,s}$ represents the effects that the Stokes shear has on the transport of $\chi$, $N_{\chi,b}$  the effect of buoyancy, and $N_{\chi,t}$ the effect of the turbulent transport.  The same general form for the flux-gradient relationship is used to parametrize the transports of momentum, heat and salinity. 
     676 
     677In terms of the non-dimensionalized depth variables 
     678% 
     679\begin{equation}\label{eq:sigma} 
     680\sigma_{\mathrm{ml}}= -z/h_{\mathrm{ml}}; \;\sigma_{\mathrm{bl}}= -z/h_{\mathrm{bl}}, 
     681\end{equation} 
     682% 
     683in unstable conditions the eddy diffusivity ($K_d$) and eddy viscosity ($K_\nu$) profiles are parametrized as: 
     684% 
     685\begin{align}\label{eq:diff-unstable} 
     686K_d=&0.8\, \omega_*\, h_{\mathrm{ml}} \, \sigma_{\mathrm{ml}} \left(1-\beta_d \sigma_{\mathrm{ml}}\right)^{3/2} 
     687\\\label{eq:visc-unstable} 
     688K_\nu =& 0.3\, \omega_* \,h_{\mathrm{ml}}\, \sigma_{\mathrm{ml}} \left(1-\beta_\nu \sigma_{\mathrm{ml}}\right)\left(1-\tfrac{1}{2}\sigma_{\mathrm{ml}}^2\right) 
     689\end{align} 
     690% 
     691where $\beta_d$ and $\beta_\nu$ are parameters that are determined by matching Eqs \ref{eq:diff-unstable} and \ref{eq:visc-unstable} to the eddy diffusivity and viscosity at the base of the well-mixed layer, given by 
     692% 
     693\begin{equation}\label{eq:diff-wml-base} 
     694K_{d,\mathrm{ml}}=K_{\nu,\mathrm{ml}}=\,0.16\,\omega_* \Delta h. 
     695\end{equation} 
     696% 
     697For stable conditions the eddy diffusivity/viscosity profiles are given by: 
     698% 
     699\begin{align}\label{diff-stable} 
     700K_d= & 0.75\,\, \nu_*\, h_{\mathrm{ml}}\,\,  \exp\left[-2.8 \left(h_{\mathrm{bl}}/L_L\right)^2\right]\sigma_{\mathrm{ml}} \left(1-\sigma_{\mathrm{ml}}\right)^{3/2} \\\label{eq:visc-stable} 
     701K_\nu = & 0.375\,\,  \nu_*\, h_{\mathrm{ml}} \,\, \exp\left[-2.8 \left(h_{\mathrm{bl}}/L_L\right)^2\right] \sigma_{\mathrm{ml}} \left(1-\sigma_{\mathrm{ml}}\right)\left(1-\tfrac{1}{2}\sigma_{\mathrm{ml}}^2\right). 
     702\end{align} 
     703% 
     704The shape of the eddy viscosity and diffusivity profiles is the same as the shape in the unstable OSBL. The eddy diffusivity/viscosity depends on the stability parameter $h_{\mathrm{bl}}/{L_L}$ where $ L_L$ is analogous to the Obukhov length, but for Langmuir turbulence: 
     705\begin{equation}\label{eq:L_L} 
     706  L_L=-w_{*L}^3/\left<\overline{w^\prime b^\prime}\right>_L, 
     707\end{equation} 
     708with the mean turbulent buoyancy flux averaged over the boundary layer given in terms of its surface value $\overline{w^\prime b^\prime}_0$ and (downwards) )solar irradiance $I(z)$ by 
     709\begin{equation} \label{eq:stable-av-buoy-flux} 
     710\left<\overline{w^\prime b^\prime}\right>_L = \tfrac{1}{2} {\overline{w^\prime b^\prime}}_0-g\alpha_E\left[\tfrac{1}{2}(I(0)+I(-h))-\left<I\right>\right]. 
     711\end{equation} 
     712% 
     713In unstable conditions the eddy diffusivity and viscosity depend on stability through the velocity scale $\omega_*$, which depends on the two velocity scales $\nu_*$ and $w_{*C}$. 
     714 
     715Details of the non-gradient terms in \eqref{eq:flux-grad-gen} and of the fluxes within the pycnocline $-h_{\mathrm{bl}}<z<h_{\mathrm{ml}}$ can be found in Grant (2019). 
     716 
     717\subsubsection{Evolution of the boundary layer depth} 
     718 
     719The prognostic equation for the depth of the neutral/unstable boundary layer is given by \citep{grant+etal18}, 
     720 
     721\begin{equation} \label{eq:dhdt-unstable} 
     722%\frac{\partial h_\mathrm{bl}}{\partial t} + \mathbf{U}_b\cdot\nabla h_\mathrm{bl}= W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}} 
     723\frac{\partial h_\mathrm{bl}}{\partial t} = W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}} 
     724\end{equation} 
     725where $h_\mathrm{bl}$ is the horizontally-varying depth of the OSBL, 
     726$\mathbf{U}_b$ and $W_b$ are the mean horizontal and vertical 
     727velocities at the base of the OSBL, ${\overline{w^\prime 
     728    b^\prime}}_\mathrm{ent}$ is the buoyancy flux due to entrainment 
     729and $\Delta B_\mathrm{bl}$ is the difference between the buoyancy 
     730averaged over the depth of the OSBL (i.e.\ including the ML and 
     731pycnocline) and the buoyancy just below the base of the OSBL. This 
     732equation for the case when the pycnocline has a finite thickness, 
     733based on the potential energy budget of the OSBL, is the leading term 
     734\citep{grant+etal18} of a generalization of that used in mixed-layer 
     735models e.g.\ \citet{kraus.turner_tellus67}, in which the thickness of the pycnocline is taken to be zero. 
     736 
     737The entrainment flux for the combination of convective and Langmuir turbulence is given by 
     738\begin{equation} \label{eq:entrain-flux} 
     739  {\overline{w^\prime b^\prime}}_\mathrm{ent} = -\alpha_{\mathrm{B}} {\overline{w^\prime b^\prime}}_0 - \alpha_{\mathrm{S}} \frac{u_*^3}{h_{\mathrm{ml}}} 
     740  + G\left(\delta/h_{\mathrm{ml}} \right)\left[\alpha_{\mathrm{S}}e^{-1.5\, \mathrm{La}_t}-\alpha_{\mathrm{L}} \frac{w_{\mathrm{*L}}^3}{h_{\mathrm{ml}}}\right] 
     741\end{equation} 
     742where the factor $G\equiv 1 - \mathrm{e}^ {-25\delta/h_{\mathrm{bl}}}(1-4\delta/h_{\mathrm{bl}})$ models the lesser efficiency of Langmuir mixing when the boundary-layer depth is much greater than the Stokes depth, and $\alpha_{\mathrm{B}}$, $\alpha_{S}$  and $\alpha_{\mathrm{L}}$ depend on the ratio of the appropriate eddy turnover time to the inertial timescale $f^{-1}$. Results from the LES suggest $\alpha_{\mathrm{B}}=0.18 F(fh_{\mathrm{bl}}/w_{*C})$, $\alpha_{S}=0.15 F(fh_{\mathrm{bl}}/u_*$  and $\alpha_{\mathrm{L}}=0.035 F(fh_{\mathrm{bl}}/u_{*L})$, where $F(x)\equiv\tanh(x^{-1})^{0.69}$. 
     743 
     744For the stable boundary layer, the equation for the depth of the OSBL is: 
     745 
     746\begin{equation}\label{eq:dhdt-stable} 
     747\max\left(\Delta B_{bl},\frac{w_{*L}^2}{h_\mathrm{bl}}\right)\frac{\partial h_\mathrm{bl}}{\partial t} = \left(0.06 + 0.52\,\frac{ h_\mathrm{bl}}{L_L}\right) \frac{w_{*L}^3}{h_\mathrm{bl}} +\left<\overline{w^\prime b^\prime}\right>_L. 
     748\end{equation} 
     749 
     750Equation. \ref{eq:dhdt-unstable} always leads to the depth of the entraining OSBL increasing (ignoring the effect of the mean vertical motion), but the change in the thickness of the stable OSBL given by Eq. \ref{eq:dhdt-stable} can be positive or negative, depending on the magnitudes of $\left<\overline{w^\prime b^\prime}\right>_L$ and $h_\mathrm{bl}/L_L$. The rate at which the depth of the OSBL can decrease is limited by choosing an effective buoyancy $w_{*L}^2/h_\mathrm{bl}$, in place of $\Delta B_{bl}$ which will be $\approx 0$ for the collapsing OSBL. 
     751 
    546752 
    547753%% ================================================================================================= 
    … …  
    551757\begin{figure}[!t] 
    552758  \centering 
    553   \includegraphics[width=0.66\textwidth]{Fig_ZDF_TKE_time_scheme} 
     759  \includegraphics[width=0.66\textwidth]{ZDF_TKE_time_scheme} 
    554760  \caption[Subgrid kinetic energy integration in GLS and TKE schemes]{ 
    555761    Illustration of the subgrid kinetic energy integration in GLS and TKE schemes and 
    … …  
    663869\begin{figure}[!htb] 
    664870  \centering 
    665   \includegraphics[width=0.66\textwidth]{Fig_npc} 
     871  \includegraphics[width=0.66\textwidth]{ZDF_npc} 
    666872  \caption[Unstable density profile treated by the non penetrative convective adjustment algorithm]{ 
    667873    Example of an unstable density profile treated by 
    … …  
    8081014\begin{figure}[!t] 
    8091015  \centering 
    810   \includegraphics[width=0.66\textwidth]{Fig_zdfddm} 
     1016  \includegraphics[width=0.66\textwidth]{ZDF_ddm} 
    8111017  \caption[Diapycnal diffusivities for temperature and salt in regions of salt fingering and 
    8121018  diffusive convection]{ 
    … …  
    12861492\begin{figure}[!t] 
    12871493  \centering 
    1288   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_coeff} 
     1494  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_coeff} 
    12891495  \caption[Partitioning coefficient used to partition vertical velocities into parts]{ 
    12901496    The value of the partitioning coefficient (\cf) used to partition vertical velocities into 
    … …  
    13261532\begin{figure}[!t] 
    13271533  \centering 
    1328   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_overflow_frames} 
     1534  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_overflow_frames} 
    13291535  \caption[OVERFLOW: time-series of temperature vertical cross-sections]{ 
    13301536    A time-series of temperature vertical cross-sections for the OVERFLOW test case. 
    … …  
    14061612\begin{figure}[!t] 
    14071613  \centering 
    1408   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_overflow_all_rdt} 
     1614  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_overflow_all_rdt} 
    14091615  \caption[OVERFLOW: sample temperature vertical cross-sections from mid- and end-run]{ 
    14101616    Sample temperature vertical cross-sections from mid- and end-run using 
    … …  
    14191625\begin{figure}[!t] 
    14201626  \centering 
    1421   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_maxCf} 
     1627  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_maxCf} 
    14221628  \caption[OVERFLOW: maximum partitioning coefficient during a series of test runs]{ 
    14231629    The maximum partitioning coefficient during a series of test runs with 
    … …  
    14301636\begin{figure}[!t] 
    14311637  \centering 
    1432   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_maxCf_loc} 
     1638  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_maxCf_loc} 
    14331639  \caption[OVERFLOW: maximum partitioning coefficient for the case overlaid]{ 
    14341640    The maximum partitioning coefficient for the \forcode{nn_rdt=10.0} case overlaid with 
    … …  
    14371643\end{figure} 
    14381644 
    1439 \onlyinsubfile{\input{../../global/epilogue}} 
     1645\subinc{\input{../../global/epilogue}} 
    14401646 
    14411647\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r12178 r12928  
    9393\begin{figure}[!t] 
    9494  \centering 
    95   \includegraphics[width=0.66\textwidth]{Fig_ORCA_NH_mesh} 
     95  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_mesh} 
    9696  \caption[ORCA mesh conception]{ 
    9797    ORCA mesh conception. 
    … …  
    120120\begin{figure}[!tbp] 
    121121  \centering 
    122   \includegraphics[width=0.66\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
    123   \includegraphics[width=0.66\textwidth]{Fig_ORCA_aniso} 
     122  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_msh05_e1_e2} 
     123  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_aniso} 
    124124  \caption[Horizontal scale factors and ratio of anisotropy for ORCA 0.5\deg\ mesh]{ 
    125125    \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and 
    … …  
    264264\begin{figure}[!t] 
    265265  \centering 
    266   \includegraphics[width=0.66\textwidth]{Fig_GYRE} 
     266  \includegraphics[width=0.66\textwidth]{CFGS_GYRE} 
    267267  \caption[Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54]{ 
    268268    Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54. 
    … …  
    292292Unlike ordinary river points the Baltic inputs also include salinity and temperature data. 
    293293 
    294 \onlyinsubfile{\input{../../global/epilogue}} 
     294\subinc{\input{../../global/epilogue}} 
    295295 
    296296\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_conservation.tex

    r12178 r12928  
    334334It has not been implemented. 
    335335 
    336 \onlyinsubfile{\input{../../global/epilogue}} 
     336\subinc{\input{../../global/epilogue}} 
    337337 
    338338\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_misc.tex

    r12178 r12928  
    9494\begin{figure}[!tbp] 
    9595  \centering 
    96   \includegraphics[width=0.66\textwidth]{Fig_Gibraltar} 
    97   \includegraphics[width=0.66\textwidth]{Fig_Gibraltar2} 
     96  \includegraphics[width=0.66\textwidth]{MISC_Gibraltar} 
     97  \includegraphics[width=0.66\textwidth]{MISC_Gibraltar2} 
    9898  \caption[Two methods to defined the Gibraltar strait]{ 
    9999    Example of the Gibraltar strait defined in a 1\deg\ $\times$ 1\deg\ mesh. 
    … …  
    111111\begin{figure}[!tbp] 
    112112  \centering 
    113   \includegraphics[width=0.66\textwidth]{Fig_closea_mask_example} 
     113  \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example} 
    114114  \caption[Mask fields for the \protect\mdl{closea} module]{ 
    115115    Example of mask fields for the \protect\mdl{closea} module. 
    … …  
    362362 
    363363%% ================================================================================================= 
    364 \subsection{Control print} 
    365  
    366 The \np{ln_ctl}{ln\_ctl} switch was originally used as a debugging option in two modes: 
    367  
    368 \begin{enumerate} 
    369 \item {\np{ln_ctl}{ln\_ctl}: compute and print the trends averaged over the interior domain in all TRA, DYN, LDF and 
    370 ZDF modules. 
    371 This option is very helpful when diagnosing the origin of an undesired change in model results. } 
    372  
    373 \item {also \np{ln_ctl}{ln\_ctl} but using the nictl and njctl namelist parameters to check the source of differences between 
    374 mono and multi processor runs.} 
     364\subsection{Status and debugging information output} 
     365 
     366 
     367NEMO can produce a range of text information output either: in the main output 
     368file (ocean.output) written by the normal reporting processor (narea == 1) or various 
     369specialist output files (e.g. layout.dat, run.stat, tracer.stat etc.). Some, for example 
     370run.stat and tracer.stat, contain globally collected values for which a single file is 
     371sufficient. Others, however, contain information that could, potentially, be different 
     372for each processing region. For computational efficiency, the default volume of text 
     373information produced is reduced to just a few files from the narea=1 processor. 
     374 
     375When more information is required for monitoring or debugging purposes, the various 
     376forms of output can be selected via the \np{sn\_cfctl} structure. As well as simple 
     377on-off switches this structure also allows selection of a range of processors for 
     378individual reporting (where appropriate) and a time-increment option to restrict 
     379globally collected values to specified time-step increments. 
     380 
     381Most options within the structure are influenced by the top-level switches shown here 
     382with their default settings: 
     383 
     384\begin{verbatim} 
     385   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
     386     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
     387\end{verbatim} 
     388 
     389The first switch is a convenience option which can be used to switch on and off all 
     390sub-options. However, if it is false then switching off all sub-options is only done 
     391if \texttt{sn_cfctl%l\_config} is also false. Specifically, the logic is: 
     392 
     393\begin{verbatim} 
     394  IF ( sn_cfctl%l_allon ) THEN 
     395    set all suboptions .TRUE. 
     396    and set procmin, procmax and procincr so that all regions are selected ([0,10000000,1], respectively) 
     397  ELSEIF ( sn_cfctl%l_config ) THEN 
     398    honour individual settings of the suboptions from the namelist 
     399  ELSE 
     400    set all suboptions .FALSE. 
     401  ENDIF 
     402\end{verbatim} 
     403 
     404Details of the suboptions follow but first an explanation of the stand-alone option: 
     405\texttt{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks 
     406carried out in \textt{stpctl.F90}. These checks detect probable numerical instabilites 
     407by searching for excessive sea surface heights or velocities and salinity values 
     408outside a sensible physical range. If breaches are detected then the default behaviour 
     409is to locate and report the local indices of the grid-point in breach. These indices 
     410are included in the error message that precedes the model shutdown. When true, 
     411\texttt{sn_cfctl%l_glochk} modifies this action by performing a global location of 
     412the various minimum and maximum values and the global indices are reported. This has 
     413some value in locating the most severe error in cases where the first detected error 
     414may not be the worst culprit. 
     415 
     416\subsubsection{Control print suboptions} 
     417 
     418The options that can be individually selected fall into three categories: 
     419 
     420\begin{enumerate} \item{Time step progress information} This category includes 
     421\texttt{run.stat} and \texttt{tracer.stat} files which record certain physical and 
     422passive tracer metrics (respectively). Typical contents of \texttt{run.stat} include 
     423global maximums of ssh, velocity; and global minimums and maximums of temperature 
     424and salinity.  A netCDF version of \texttt{run.stat} (\texttt{run.stat.nc}) is also 
     425produced with the same time-series data and this can easily be expanded to include 
     426extra monitoring information.  \texttt{tracer.stat} contains the volume-weighted 
     427average tracer value for each passive tracer. Collecting these metrics involves 
     428global communications and will impact on model efficiency so both these options are 
     429disabled by default by setting the respective options, \texttt{sn\_cfctl%runstat} and 
     430\texttt{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or 
     431both of these options and setting the \texttt{sn\_cfctl%timincr} entry to an integer 
     432value greater than one. This increment determines the time-step frequency at which 
     433the global metrics are collected and reported.  This increment also applies to the 
     434time.step file which is otherwise updated every timestep. 
     435\item{One-time configuration information/progress logs} 
     436 
     437Some run-time configuration information and limited progress information is always 
     438produced by the first ocean process. This includes the \texttt{ocean.output} file 
     439which reports on all the namelist options read by the model and remains open to catch 
     440any warning or error messages generated during execution. A \texttt{layout.dat} 
     441file is also produced which details the MPI-decomposition used by the model. The 
     442suboptions: \texttt{sn\_cfctl%oceout} and \texttt{sn\_cfctl%layout} can be used 
     443to activate the creation of these files by all ocean processes.  For example, 
     444when \texttt{sn\_cfctl%oceout} is true all processors produce their own version of 
     445\texttt{ocean.output}.  All files, beyond the the normal reporting processor (narea == 1), are 
     446named with a \_XXXX extension to their name, where XXXX is a 4-digit area number (with 
     447leading zeros, if required). This is useful as a debugging aid since all processes can 
     448report their local conditions. Note though that these files are buffered on most UNIX 
     449systems so bug-hunting efforts using this facility should also utilise the \fortran: 
     450 
     451\begin{verbatim}  
     452   CALL FLUSH(numout) 
     453\end{verbatim} 
     454 
     455statement after any additional write statements to ensure that file contents reflect 
     456the last model state. Associated with the \texttt{sn\_cfctl%oceout} option is the 
     457additional \texttt{sn\_cfctl%oasout} suboption. This does not activate its own output 
     458file but rather activates the writing of addition information regarding the OASIS 
     459configuration when coupling via oasis and the sbccpl routine. This information is 
     460written to any active \texttt{ocean.output} files. 
     461\item{Control sums of trends for debugging} 
     462 
     463NEMO includes an option for debugging reproducibility differences between 
     464a MPP and mono-processor runs.  This is somewhat dated and clearly only 
     465useful for this purpose when dealing with configurations that can be run 
     466on a single processor. The full details can be found in this report: \href{ 
     467http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Documentation/prtctl_NEMO_doc_v2.pdf}{The 
     468control print option in NEMO} The switches to activate production of the control sums 
     469of trends for either the physics or passive tracers are the \texttt{sn\_cfctl%prtctl} 
     470and \texttt{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its 
     471original intention, the ability to produce these control sums of trends in specific 
     472areas provides another tool for diagnosing model behaviour.  If only the output from a 
     473select few regions is required then additional options are available to activate options 
     474for only a simple subset of processing regions. These are: \texttt{sn\_cfctl%procmin}, 
     475\texttt{sn\_cfctl%procmax} and \texttt{sn\_cfctl%procincr} which can be used to specify 
     476the minimum and maximum active areas and the increment. The default values are set 
     477such that all regions will be active. Note this subsetting can also be used to limit 
     478which additional \texttt{ocean.output} and \texttt{layout.dat} files are produced if 
     479those suboptions are active. 
     480 
    375481\end{enumerate} 
    376482 
    377 However, in recent versions it has also been used to force all processors to assume the 
    378 reporting role. Thus when \np{ln_ctl}{ln\_ctl} is true all processors produce their own versions 
    379 of files such as: ocean.output, layout.dat, etc.  All such files, beyond the the normal 
    380 reporting processor (narea == 1), are named with a \_XXXX extension to their name, where 
    381 XXXX is a 4-digit area number (with leading zeros, if required). Other reporting files 
    382 such as run.stat (and its netCDF counterpart: run.stat.nc) and tracer.stat contain global 
    383 information and are only ever produced by the reporting master (narea == 1). For version 
    384 4.0 a start has been made to return \np{ln_ctl}{ln\_ctl} to its original function by introducing 
    385 a new control structure which allows finer control over which files are produced. This 
    386 feature is still evolving but it does already allow the user to: select individually the 
    387 production of run.stat and tracer.stat files and to toggle the production of other files 
    388 on processors other than the reporting master. These other reporters can be a simple 
    389 subset of processors as defined by a minimum, maximum and incremental processor number. 
    390  
    391 Note, that production of the run.stat and tracer.stat files require global communications. 
    392 For run.stat, these are global min and max operations to find metrics such as the gloabl 
    393 maximum velocity. For tracer.stat these are global sums of tracer fields. To improve model 
    394 performance these operations are disabled by default and, where necessary, any use of the 
    395 global values have been replaced with local calculations. For example, checks on the CFL 
    396 criterion are now done on the local domain and only reported if a breach is detected. 
    397  
    398 Experienced users may wish to still monitor this information as a check on model progress. 
    399 If so, the best compromise will be to activate the files with: 
    400  
    401 \begin{verbatim} 
    402      sn_cfctl%l_config = .TRUE. 
    403        sn_cfctl%l_runstat = .TRUE. 
    404        sn_cfctl%l_trcstat = .TRUE. 
    405 \end{verbatim} 
    406  
    407 and to use the new time increment setting to ensure the values are collected and reported 
    408 at a suitably long interval. For example: 
    409  
    410 \begin{verbatim} 
    411        sn_cfctl%ptimincr  = 25 
    412 \end{verbatim} 
    413  
    414 will carry out the global communications and write the information every 25 timesteps. This 
    415 increment also applies to the time.step file which is otherwise updated every timestep. 
    416  
    417 \onlyinsubfile{\input{../../global/epilogue}} 
     483 
     484   sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only 
     485   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
     486     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
     487       sn_cfctl%l_runstat = .FALSE. ! switches and which areas produce reports with the proc integer settings. 
     488       sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure 
     489       sn_cfctl%l_oceout  = .FALSE. ! that  all areas report. 
     490       sn_cfctl%l_layout  = .FALSE. ! 
     491       sn_cfctl%l_prtctl  = .FALSE. ! 
     492       sn_cfctl%l_prttrc  = .FALSE. ! 
     493       sn_cfctl%l_oasout  = .FALSE. ! 
     494       sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0] 
     495       sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000] 
     496       sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
     497       sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
     498 
     499 
     500 
     501\subinc{\input{../../global/epilogue}} 
    418502 
    419503\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r12178 r12928  
    130130\begin{figure} 
    131131  \centering 
    132   \includegraphics[width=0.66\textwidth]{Fig_I_ocean_bc} 
     132  \includegraphics[width=0.66\textwidth]{MB_ocean_bc} 
    133133  \caption[Ocean boundary conditions]{ 
    134134    The ocean is bounded by two surfaces, $z = - H(i,j)$ and $z = \eta(i,j,t)$, 
    … …  
    327327\begin{figure} 
    328328  \centering 
    329   \includegraphics[width=0.33\textwidth]{Fig_I_earth_referential} 
     329  \includegraphics[width=0.33\textwidth]{MB_earth_referential} 
    330330  \caption[Geographical and curvilinear coordinate systems]{ 
    331331    the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear 
    … …  
    579579an explicit computation of vertical advection relative to the moving s-surfaces. 
    580580 
    581 %\gmcomment{ 
    582 %A key point here is that the $s$-coordinate depends on $(i,j)$ ==> horizontal pressure gradient... 
     581\cmtgm{A key point here is that the $s$-coordinate depends on $(i,j)$ 
     582  ==> horizontal pressure gradient...} 
    583583The generalized vertical coordinates used in ocean modelling are not orthogonal, 
    584584which contrasts with many other applications in mathematical physics. 
    … …  
    680680and similar expressions are used for mixing and forcing terms. 
    681681 
    682 \gmcomment{ 
     682\cmtgm{ 
    683683  \colorbox{yellow}{ to be updated $= = >$} 
    684684  Add a few works on z and zps and s and underlies the differences between all of them 
    … …  
    692692\begin{figure} 
    693693  \centering 
    694   \includegraphics[width=0.66\textwidth]{Fig_z_zstar} 
     694  \includegraphics[width=0.66\textwidth]{MB_z_zstar} 
    695695  \caption[Curvilinear z-coordinate systems (\{non-\}linear free-surface cases and re-scaled \zstar)]{ 
    696696    \begin{enumerate*}[label=(\textit{\alph*})] 
    … …  
    11501150Nevertheless it is currently not available in the iso-neutral case. 
    11511151 
    1152 \onlyinsubfile{\input{../../global/epilogue}} 
     1152\subinc{\input{../../global/epilogue}} 
    11531153 
    11541154\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r12178 r12928  
    147147\begin{figure}[!t] 
    148148  \centering 
    149   \includegraphics[width=0.66\textwidth]{Fig_DYN_dynspg_ts} 
     149  %\includegraphics[width=0.66\textwidth]{MBZ_DYN_dynspg_ts} 
    150150  \caption[Schematic of the split-explicit time stepping scheme for 
    151151  the barotropic and baroclinic modes, after \citet{Griffies2004?}]{ 
    … …  
    311311In particular, this means that in filtered case, the matrix to be inverted has to be recomputed at each time-step. 
    312312 
    313 \onlyinsubfile{\input{../../global/epilogue}} 
     313\subinc{\input{../../global/epilogue}} 
    314314 
    315315\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r12178 r12928  
    3131% - daymod: definition of the time domain (nit000, nitend and the calendar) 
    3232 
    33 \gmcomment{STEVEN :maybe a picture of the directory structure in the introduction which 
     33\cmtgm{STEVEN :maybe a picture of the directory structure in the introduction which 
    3434could be referred to here, would help  ==> to be added} 
    3535 
    … …  
    158158\end{equation} 
    159159 
    160 %%gm 
    161 %%gm   UPDATE the next paragraphs with time varying thickness ... 
    162 %%gm 
     160\cmtgm{UPDATE the next paragraphs with time varying thickness ...} 
    163161 
    164162This scheme is rather time consuming since it requires a matrix inversion. 
    … …  
    213211Fast barotropic motions (such as tides) are also simulated with a better accuracy. 
    214212 
    215 %\gmcomment{ 
     213%\cmtgm{ 
    216214\begin{figure} 
    217215  \centering 
    218   \includegraphics[width=0.66\textwidth]{Fig_TimeStepping_flowchart_v4} 
     216  \includegraphics[width=0.66\textwidth]{TD_TimeStepping_flowchart_v4} 
    219217  \caption[Leapfrog time stepping sequence with split-explicit free surface]{ 
    220218    Sketch of the leapfrog time stepping sequence in \NEMO\ with split-explicit free surface. 
    … …  
    276274\begin{figure} 
    277275  \centering 
    278   \includegraphics[width=0.66\textwidth]{Fig_MLF_forcing} 
     276  \includegraphics[width=0.66\textwidth]{TD_MLF_forcing} 
    279277  \caption[Forcing integration methods for modified leapfrog (top and bottom)]{ 
    280278    Illustration of forcing integration methods. 
    … …  
    328326the \nam{run}{run} namelist variables. 
    329327 
    330 \gmcomment{ 
     328\cmtgm{ 
    331329add here how to force the restart to contain only one time step for operational purposes 
    332330 
    … …  
    338336} 
    339337 
    340 \gmcomment{       % add a subsection here 
     338\cmtgm{       % add a subsection here 
    341339 
    342340%% ================================================================================================= 
    … …  
    353351}     %% end add 
    354352 
    355 \gmcomment{       % add implicit in vvl case  and Crant-Nicholson scheme 
     353\cmtgm{       % add implicit in vvl case  and Crant-Nicholson scheme 
    356354 
    357355Implicit time stepping in case of variable volume thickness. 
    … …  
    404402} 
    405403 
    406 \onlyinsubfile{\input{../../global/epilogue}} 
     404\subinc{\input{../../global/epilogue}} 
    407405 
    408406\end{document} 
Note: See TracChangeset for help on using the changeset viewer.