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- 2021-04-07T15:48:38+02:00 (3 years ago)
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NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/main/settings.tex
r14328 r14676 5 5 \def\spcup{\vspace*{2.15cm}} 6 6 \def\hdg{NEMO ocean engine} 7 %\def\shdg{} 8 \def\spcdn{\vspace*{1cm}} 9 \def\autwd{0.25\linewidth} 10 \def\lnlg{270pt} 11 \def\abswd{0.65\linewidth} 7 %\def\shdg{} %% No subheading 8 \def\spcdn{\vspace*{1.00cm}} 9 \def\autwd{0.25\linewidth}\def\lnlg{270pt}\def\abswd{0.65\linewidth} 12 10 13 11 %% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) 14 \def\clr{1 ,.60,0,.4}12 \def\clr{1.0,0.6,0.0,0.4} 15 13 16 14 %% IPSL publication number -
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NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex
r14328 r14676 6 6 \label{apdx:DOMCFG} 7 7 8 % {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains } \\9 10 8 \chaptertoc 11 9 … … 14 12 {\footnotesize 15 13 \begin{tabularx}{\textwidth}{l||X|X} 16 Release & Author(s) & Modifications \\ 17 \hline 18 {\em next}& {\em Pierre Mathiot} & {\em add ice shelf and closed sea option description } \\ 19 {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains } \\ 20 {\em 3.6} & {\em ...} & {\em ...} \\ 21 {\em 3.4} & {\em ...} & {\em ...} \\ 22 {\em <=3.4} & {\em ...} & {\em ...} 14 Release & Author(s) & Modifications \\ 15 \hline 16 {\em next} & {\em Pierre Mathiot} & {\em Add ice shelf and closed sea option description } \\ 17 {\em 4.0} & {\em Andrew Coward} & {\em Creation from materials removed from \autoref{chap:DOM} 18 that are still relevant to the DOMAINcfg tool 19 when setting up new domains } 23 20 \end{tabularx} 24 21 } … … 45 42 46 43 \begin{listing} 47 % \nlst{namdom_domcfg}48 44 \begin{forlines} 49 45 !----------------------------------------------------------------------- … … 412 408 413 409 \begin{listing} 414 % \nlst{namzgr_sco_domcfg}415 410 \caption{\forcode{&namzgr_sco_domcfg}} 416 411 \label{lst:namzgr_sco_domcfg} … … 592 587 the \textit{isfdraft\_meter} file (Netcdf format). This file need to include the \textit{isf\_draft} variable. 593 588 A positive value will mean ice shelf/ocean or ice shelf bedrock interface below the reference 0m ssh. 594 The exact shape of the ice shelf cavity (grounding line position and minimum thickness of the water column under an ice shelf, ...) can be specify in \nam{zgr_isf}{zgr _isf}.589 The exact shape of the ice shelf cavity (grounding line position and minimum thickness of the water column under an ice shelf, ...) can be specify in \nam{zgr_isf}{zgr\_isf}. 595 590 596 591 \begin{listing} … … 616 611 \end{listing} 617 612 618 The options available to define the shape of the under ice shelf cavities are listed in \nam{zgr_isf}{zgr _isf} (\texttt{DOMAINcfg} only, \autoref{lst:namzgr_isf}).619 620 621 622 623 624 625 626 627 628 Where $h_{isf} < MAX(e3t\_1d(1),\np{rn_isfdep_min}{rn\_isfdep\_min}$), $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}.629 630 631 632 633 634 635 636 637 638 639 613 The options available to define the shape of the under ice shelf cavities are listed in \nam{zgr_isf}{zgr\_isf} (\texttt{DOMAINcfg} only, \autoref{lst:namzgr_isf}). 614 615 \subsection{Model ice shelf draft definition} 616 \label{subsec:zgrisf_isfd} 617 618 First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry. 619 There are 3 compulsory steps to achieve this: 620 621 \begin{description} 622 \item{\np{rn_isfdep_min}{rn\_isfdep\_min}:} this is the minimum ice shelf draft. This is to make sure there is no ridiculous thin ice shelf. If \np{rn_isfdep_min}{rn\_isfdep\_min} is smaller than the surface level, \np{rn_isfdep_min}{rn\_isfdep\_min} is set to $e3t\_1d(1)$. 623 Where $h_{isf} < MAX(e3t\_1d(1),rn\_isfdep\_min)$, $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}. 624 625 \item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position. 626 Where the difference between the bathymetry and the ice shelf draft is smaller than \np{rn_glhw_min}{rn\_glhw\_min}, the cell are grounded (ie masked). 627 This step is needed to take into account possible small mismatch between ice shelf draft value and bathymetry value (sources are coming from different grid, different data processes, rounding error, ...). 628 629 \item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is the minimum water column thickness in the cavity. 630 Where the water column thickness is lower than \np{rn_isfhw_min}{rn\_isfhw\_min}, the ice shelf draft is adjusted to match this criterion. 631 If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked. 632 \end{description} 633 634 Once all these adjustements are made, if the water column thickness contains one cell wide channels, these channels can be closed using \np{ln_isfchannel}{ln\_isfchannel}. 640 635 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 636 \subsection{Model top level definition} 637 After the definition of the ice shelf draft, the tool defines the top level. 638 The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points. 639 To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\ 640 641 The process is the following: 642 \begin{description} 643 \item{step 1:} The top level is defined in the same way as the bottom level is defined. 644 \item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf) 645 \item{step 3:} The tools make sure, the top level is above or equal to the bottom level 646 \item{step 4:} If the water column at a U- or V- point is one wet cell wide, the ice shelf draft is adjusted. So the actual top cell become fully open and the new 647 top cell thickness is set to the minimum cell thickness allowed (following the same logic as for the bottom partial cell). This step is iterated 4 times to ensure the condition is fullfill along the 4 sides of the cell. 648 \end{description} 649 650 In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourging ice shelf draft). 651 The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells. 652 Some limiters in meter or levels on the digging allowed by the tool are available (respectively, \np{rn_zisfmax}{rn\_zisfmax} or \np{rn_kisfmax}{rn\_kisfmax}). 653 This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels. 654 655 \subsection{Subglacial lakes} 656 Despite careful setting of your ice shelf draft and bathymetry input file as well as setting described in \autoref{subsec:zgrisf_isfd}, some situation are unavoidable. 657 For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling, 658 you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded). 659 If you do so, the subglacial lakes will show up (Vostock for example). An other possibility is with coarse vertical resolution, some ice shelves could be cut in 2 parts: 660 one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\ 661 662 The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes. 663 This may be useful for esthetical reason or for stability reasons: 664 665 \begin{description} 666 \item $\bullet$ In a subglacial lakes, in case of very weak circulation (often the case), the only heat flux is the conductive heat flux through the ice sheet. 667 This will lead to constant freezing until water reaches -20C. 668 This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}). 669 \item $\bullet$ In case of coupling with an ice sheet model, 670 the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example), 671 and so if for any reason both a connected at some point, the model is likely to fall over.\\ 672 \end{description} 678 673 679 674 \section{Closed sea definition} … … 707 702 \end{listing} 708 703 709 The options available to define the closed seas and how closed sea net fresh water input will be redistributed by NEMO are listed in \nam{ clo}{dom_clo} (\texttt{DOMAINcfg} only).704 The options available to define the closed seas and how closed sea net fresh water input will be redistributed by NEMO are listed in \nam{dom_clo}{dom\_clo} (\texttt{DOMAINcfg} only). 710 705 The individual definition of each closed sea is managed by \np{sn_lake}{sn\_lake}. In this fields the user needs to define:\\ 711 706 \begin{description} -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/apdx_triads.tex
r14328 r14676 2 2 3 3 \begin{document} 4 5 %% Local cmds6 \newcommand{\rML}[1][i]{\ensuremath{_{\mathrm{ML}\,#1}}}7 \newcommand{\rMLt}[1][i]{\tilde{r}_{\mathrm{ML}\,#1}}8 %% Move to ../../global/new_cmds.tex to avoid error with \listoffigures9 %\newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}10 \newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}}11 \newcommand{\triadt}[5]{\ensuremath{{}_{#1}^{#2}{\tilde{\mathbb{#3}}}_{#4}^{\,#5}}}12 \newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}}13 \newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}}14 4 15 5 \chapter{Iso-Neutral Diffusion and Eddy Advection using Triads} … … 34 24 35 25 %% ================================================================================================= 36 \section[Choice of \forcode{namtra \_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters}26 \section[Choice of \forcode{namtra_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters} 37 27 38 28 Two scheme are available to perform the iso-neutral diffusion. -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_DIU.tex
r14328 r14676 50 50 51 51 This namelist contains only two variables: 52 52 53 \begin{description} 53 54 \item [{\np{ln_diurnal}{ln\_diurnal}}] A logical switch for turning on/off both the cool skin and warm layer. -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_DOM.tex
r14328 r14676 377 377 in which case \np{cn_cfg}{cn\_cfg} and \np{nn_cfg}{nn\_cfg} are set from these values accordingly). 378 378 379 The global lateral boundary condition type is selected from 8 options using parameter \texttt{jperio}.379 The global lateral boundary condition type is selected from 8 options using parameters \texttt{l\_Iperio}, \texttt{l\_Jperio}, \texttt{l\_NFold} and \texttt{c\_NFtype}. 380 380 See \autoref{sec:LBC_jperio} for details on the available options and 381 the corresponding values for \texttt{ jperio}.381 the corresponding values for \texttt{l\_Iperio}, \texttt{l\_Jperio}, \texttt{l\_NFold} and \texttt{c\_NFtype}. 382 382 383 383 %% ================================================================================================= … … 394 394 395 395 \begin{clines} 396 int jpiglo, jpjglo, jpkglo /* global domain sizes */ 397 int jperio /* lateral global domain b.c. */ 398 double glamt, glamu, glamv, glamf /* geographic longitude (t,u,v and f points respectively) */ 399 double gphit, gphiu, gphiv, gphif /* geographic latitude */ 400 double e1t, e1u, e1v, e1f /* horizontal scale factors */ 401 double e2t, e2u, e2v, e2f /* horizontal scale factors */ 396 integer Ni0glo, NjOglo, jpkglo /* global domain sizes (without MPI halos) */ 397 logical l\_Iperio, l\_Jperio /* lateral global domain b.c.: i- j-periodicity */ 398 logical l\_NFold /* lateral global domain b.c.: North Pole folding */ 399 char(1) c\_NFtype /* type of North pole Folding: T or F point */ 400 real glamt, glamu, glamv, glamf /* geographic longitude (t,u,v and f points respectively) */ 401 real gphit, gphiu, gphiv, gphif /* geographic latitude */ 402 real e1t, e1u, e1v, e1f /* horizontal scale factors */ 403 real e2t, e2u, e2v, e2f /* horizontal scale factors */ 402 404 \end{clines} 403 405 -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_LBC.tex
r14328 r14676 159 159 160 160 %% ================================================================================================= 161 \section{Model domain boundary condition (\forcode{jperio})}161 \section{Model domain boundary condition} 162 162 \label{sec:LBC_jperio} 163 163 … … 168 168 169 169 %% ================================================================================================= 170 \subsection{Closed, cyclic (\forcode{ jperio={0,1,2,7}})}170 \subsection{Closed, cyclic (\forcode{l_Iperio,l_jperio})} 171 171 \label{subsec:LBC_jperio012} 172 172 173 173 The choice of closed or cyclic model domain boundary condition is made by 174 setting \forcode{ jperio} to 0, 1, 2 or 7in namelist \nam{cfg}{cfg}.174 setting \forcode{l_Iperio,l_jperio} to true or false in namelist \nam{cfg}{cfg}. 175 175 Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}. 176 176 The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$, … … 181 181 \begin{description} 182 182 183 \item [For closed boundary (\forcode{ jperio=0})], solid walls are imposed at all model boundaries:183 \item [For closed boundary (\forcode{l_Iperio = .false.,l_jperio = .false.})], solid walls are imposed at all model boundaries: 184 184 first and last rows and columns are set to zero. 185 185 186 \item [For cyclic east-west boundary (\forcode{ jperio=1})], first and last rows are set to zero (closed) whilst the first column is set to186 \item [For cyclic east-west boundary (\forcode{l_Iperio = .true.,l_jperio = .false.})], first and last rows are set to zero (closed) whilst the first column is set to 187 187 the value of the last-but-one column and the last column to the value of the second one 188 188 (\autoref{fig:LBC_jperio}-a). 189 189 Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end. 190 190 191 \item [For cyclic north-south boundary (\forcode{ jperio=2})], first and last columns are set to zero (closed) whilst the first row is set to191 \item [For cyclic north-south boundary (\forcode{l_Iperio = .false.,l_jperio = .true.})], first and last columns are set to zero (closed) whilst the first row is set to 192 192 the value of the last-but-one row and the last row to the value of the second one 193 193 (\autoref{fig:LBC_jperio}-a). 194 194 Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end. 195 195 196 \item [Bi-cyclic east-west and north-south boundary (\forcode{ jperio=7})] combines cases 1 and 2.196 \item [Bi-cyclic east-west and north-south boundary (\forcode{l_Iperio = .true.,l_jperio = .true.})] combines cases 1 and 2. 197 197 198 198 \end{description} … … 207 207 208 208 %% ================================================================================================= 209 \subsection{North-fold (\forcode{ jperio={3,6}})}209 \subsection{North-fold (\forcode{l_NFold = .true.})} 210 210 \label{subsec:LBC_north_fold} 211 211 … … 220 220 \includegraphics[width=0.66\textwidth]{LBC_North_Fold_T} 221 221 \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{ 222 North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($ jperio=4$),222 North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($c\_NFtype='T'$), 223 223 as used in ORCA 2\deg, 1/4\deg and 1/12\deg. 224 224 Pink shaded area corresponds to the inner domain mask (see text).} -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_OBS.tex
r14328 r14676 913 913 914 914 \begin{listing} 915 % \nlst{namsao}916 915 \begin{forlines} 917 916 !---------------------------------------------------------------------- -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_SBC.tex
r14328 r14676 975 975 M2, S2, N2, K2, nu2, mu2, 2N2, L2, T2, eps2, lam2, R2, M3, MKS2, MN4, MS4, M4, 976 976 N4, S4, M6, and M8; see file \textit{tide.h90} and \mdl{tide\_mod} for further 977 information and references\footnote{As a legacy option \np{ln_tide_var} can be977 information and references\footnote{As a legacy option \np{ln_tide_var}{ln\_tide\_var} can be 978 978 set to \forcode{0}, in which case the 19 tidal constituents (M2, N2, 2N2, S2, 979 979 K2, K1, O1, Q1, P1, M4, Mf, Mm, Msqm, Mtm, S1, MU2, NU2, L2, and T2; see file … … 1179 1179 %% ================================================================================================= 1180 1180 \section[Ice Shelf (ISF)]{Interaction with ice shelves (ISF)} 1181 \label{sec: isf}1181 \label{sec:SBC_isf} 1182 1182 1183 1183 \begin{listing} … … 1197 1197 1198 1198 \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .true.} activates the ocean/ice shelf thermodynamics interactions at the ice shelf/ocean interface. 1199 If \np{ln_isfcav_mlt} \forcode{ = .false.}, thermodynamics interactions are desctivated but the ocean dynamics inside the cavity is still active.1199 If \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .false.}, thermodynamics interactions are desctivated but the ocean dynamics inside the cavity is still active. 1200 1200 The logical flag \np{ln_isfcav}{ln\_isfcav} control whether or not the ice shelf cavities are closed. \np{ln_isfcav}{ln\_isfcav} is not defined in the namelist but in the domcfg.nc input file.\\ 1201 1201 1202 1202 3 options are available to represent to ice-shelf/ocean fluxes at the interface: 1203 1203 \begin{description} 1204 \item[\np{cn_isfcav_mlt} \forcode{ = 'spe'}]:1204 \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'spe'}]: 1205 1205 The fresh water flux is specified by a forcing fields \np{sn_isfcav_fwf}{sn\_isfcav\_fwf}. Convention of the input file is: positive toward the ocean (i.e. positive for melting and negative for freezing). 1206 1206 The latent heat fluxes is derived from the fresh water flux. 1207 1207 The heat content flux is derived from the fwf flux assuming a temperature set to the freezing point in the top boundary layer (\np{rn_htbl}{rn\_htbl}) 1208 1208 1209 \item[\np{cn_isfcav_mlt} \forcode{ = 'oasis'}]:1209 \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'oasis'}]: 1210 1210 The \forcode{'oasis'} is a prototype of what could be a method to spread precipitation on Antarctic ice sheet as ice shelf melt inside the cavity when a coupled model Atmosphere/Ocean is used. 1211 1211 It has not been tested and therefore the model will stop if you try to use it. 1212 1212 Actions will be undertake in 2020 to build a comprehensive interface to do so for Greenland, Antarctic and ice shelf (cav), ice shelf (par), icebergs, subglacial runoff and runoff. 1213 1213 1214 \item[\np{cn_isfcav_mlt} \forcode{ = '2eq'}]:1214 \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}]: 1215 1215 The heat flux and the fresh water flux (negative for melting) resulting from ice shelf melting/freezing are parameterized following \citet{Grosfeld1997}. 1216 1216 This formulation is based on a balance between the vertical diffusive heat flux across the ocean top boundary layer (\autoref{eq:ISOMIP1}) … … 1231 1231 and $\gamma$ the thermal exchange coefficient. 1232 1232 1233 \item[\np{cn_isfcav_mlt} \forcode{ = '3eq'}]:1233 \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'}]: 1234 1234 For realistic studies, the heat and freshwater fluxes are parameterized following \citep{Jenkins2001}. This formulation is based on three equations: 1235 1235 a balance between the vertical diffusive heat flux across the boundary layer … … 1287 1287 If \np{rn_htbl}{rn\_htbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 1288 1288 1289 Each melt formula (\np{cn_isfcav_mlt} \forcode{ = '3eq'} or \np{cn_isfcav_mlt}\forcode{ = '2eq'}) depends on an exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice.1289 Each melt formula (\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'} or \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}) depends on an exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 1290 1290 Below, the exchange coeficient $\Gamma^{T}$ and $\Gamma^{S}$ are respectively defined by \np{rn_gammat0}{rn\_gammat0} and \np{rn_gammas0}{rn\_gammas0}. 1291 1291 There are 3 different ways to compute the exchange velocity: 1292 1292 1293 1293 \begin{description} 1294 \item[\np{cn_gammablk} \forcode{='spe'}]:1294 \item[\np{cn_gammablk}{cn\_gammablk}\forcode{='spe'}]: 1295 1295 The salt and heat exchange coefficients are constant and defined by: 1296 1296 \[ … … 1302 1302 This is the recommended formulation for ISOMIP. 1303 1303 1304 \item[\np{cn_gammablk} \forcode{='vel'}]:1304 \item[\np{cn_gammablk}{cn\_gammablk}\forcode{='vel'}]: 1305 1305 The salt and heat exchange coefficients are velocity dependent and defined as 1306 1306 \[ … … 1313 1313 See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application and ISOMIP+/MISOMIP configuration. 1314 1314 1315 \item[\np{cn_gammablk} \forcode{'vel\_stab'}]:1315 \item[\np{cn_gammablk}{cn\_gammablk}\forcode{'vel\_stab'}]: 1316 1316 The salt and heat exchange coefficients are velocity and stability dependent and defined as: 1317 1317 \[ … … 1329 1329 \begin{description} 1330 1330 1331 \item[\np{cn_isfpar_mlt} \forcode{ = 'bg03'}]:1331 \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'bg03'}]: 1332 1332 The ice shelf cavities are not represented. 1333 1333 The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 1334 1334 The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 1335 1335 (\np{sn_isfpar_zmax}{sn\_isfpar\_zmax}) and the base of the ice shelf along the calving front 1336 (\np{sn_isfpar_zmin}{sn\_isfpar\_zmin}) as in (\np{cn_isfpar_mlt} \forcode{ = 'spe'}).1336 (\np{sn_isfpar_zmin}{sn\_isfpar\_zmin}) as in (\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'}). 1337 1337 The effective melting length (\np{sn_isfpar_Leff}{sn\_isfpar\_Leff}) is read from a file. 1338 1338 This parametrisation has not been tested since a while and based on \citet{Favier2019}, 1339 1339 this parametrisation should probably not be used. 1340 1340 1341 \item[\np{cn_isfpar_mlt} \forcode{ = 'spe'}]:1341 \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'}]: 1342 1342 The ice shelf cavity is not represented. 1343 1343 The fwf (\np{sn_isfpar_fwf}{sn\_isfpar\_fwf}) is prescribed and distributed along the ice shelf edge between … … 1346 1346 The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 1347 1347 1348 \item[\np{cn_isfpar_mlt} \forcode{ = 'oasis'}]:1348 \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'oasis'}]: 1349 1349 The \forcode{'oasis'} is a prototype of what could be a method to spread precipitation on Antarctic ice sheet as ice shelf melt inside the cavity when a coupled model Atmosphere/Ocean is used. 1350 1350 It has not been tested and therefore the model will stop if you try to use it. … … 1353 1353 \end{description} 1354 1354 1355 \np{cn_isfcav_mlt} \forcode{ = '2eq'}, \np{cn_isfcav_mlt}\forcode{ = '3eq'} and \np{cn_isfpar_mlt}\forcode{ = 'bg03'} compute a melt rate based on1355 \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}, \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'} and \np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'bg03'} compute a melt rate based on 1356 1356 the water mass properties, ocean velocities and depth. 1357 1357 The resulting fluxes are thus highly dependent of the model resolution (horizontal and vertical) and 1358 1358 realism of the water masses onto the shelf.\\ 1359 1359 1360 \np{cn_isfcav_mlt} \forcode{ = 'spe'} and \np{cn_isfpar_mlt}\forcode{ = 'spe'} read the melt rate from a file.1360 \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'spe'} and \np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'} read the melt rate from a file. 1361 1361 You have total control of the fwf forcing. 1362 1362 This can be useful if the water masses on the shelf are not realistic or … … 1437 1437 \end{description} 1438 1438 1439 If \np{ln_iscpl} \forcode{ = .true.}, the isf draft is assume to be different at each restart step with1439 If \np{ln_iscpl}{ln\_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with 1440 1440 potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics. 1441 1441 The wetting and drying scheme, applied on the restart, is very simple. The 6 different possible cases for the tracer and ssh are: … … 1482 1482 1483 1483 In order to remove the trend and keep the conservation level as close to 0 as possible, 1484 a simple conservation scheme is available with \np{ln_isfcpl_cons} \forcode{ = .true.}.1484 a simple conservation scheme is available with \np{ln_isfcpl_cons}{ln\_isfcpl\_cons}\forcode{ = .true.}. 1485 1485 The heat/salt/vol. gain/loss are diagnosed, as well as the location. 1486 1486 A correction increment is computed and applied each time step during the model run. -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_TRA.tex
r14328 r14676 733 733 (see \autoref{sec:SBC_rnf} for further detail of how it acts on temperature and salinity tendencies) 734 734 \item [\textit{fwfisf}] The mass flux associated with ice shelf melt, 735 (see \autoref{sec: isf} for further details on how the ice shelf melt is computed and applied).735 (see \autoref{sec:SBC_isf} for further details on how the ice shelf melt is computed and applied). 736 736 \end{labeling} 737 737 -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_ZDF.tex
r14328 r14676 2 2 3 3 \begin{document} 4 5 %% Custom aliases6 \newcommand{\cf}{\ensuremath{C\kern-0.14em f}}7 4 8 5 \chapter{Vertical Ocean Physics (ZDF)} … … 1083 1080 \label{lst:namdrg} 1084 1081 \end{listing} 1082 1085 1083 \begin{listing} 1086 1084 \nlst{namdrg_top} … … 1088 1086 \label{lst:namdrg_top} 1089 1087 \end{listing} 1088 1090 1089 \begin{listing} 1091 1090 \nlst{namdrg_bot} … … 1562 1561 by only a few extra physics choices namely: 1563 1562 1564 \begin{ verbatim}1563 \begin{forlines} 1565 1564 ln_dynldf_OFF = .false. 1566 1565 ln_dynldf_lap = .true. … … 1570 1569 nn_fct_h = 2 1571 1570 nn_fct_v = 2 1572 \end{ verbatim}1571 \end{forlines} 1573 1572 1574 1573 \noindent which were chosen to provide a slightly more stable and less noisy solution. The -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_misc.tex
r14328 r14676 12 12 {\footnotesize 13 13 \begin{tabularx}{\textwidth}{l||X|X} 14 Release & Author(s) & Modifications\\14 Release & Author(s) & Modifications \\ 15 15 \hline 16 {\em X.X} & {\em Pierre Mathiot} & { update of the closed sea section}17 {\em 4.0} & {\em ... } & {\em ...} \\18 {\em 3.6} & {\em ... } & {\em ...} \\19 {\em 3.4} & {\em ... } & {\em ...} \\20 {\em <=3.4} & {\em ... } & {\em ...}16 {\em X.X} & {\em Pierre Mathiot} & {Update of the closed sea section} \\ 17 {\em 4.0} & {\em ... } & {\em ... } \\ 18 {\em 3.6} & {\em ... } & {\em ... } \\ 19 {\em 3.4} & {\em ... } & {\em ... } \\ 20 {\em <=3.4} & {\em ... } & {\em ... } 21 21 \end{tabularx} 22 22 } -
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r14328 r14676 83 83 84 84 %\nlst{nam_dynspg} 85 85 86 Options are defined through the \nam{_dynspg}{\_dynspg} namelist variables. 86 87 The surface pressure gradient term is related to the representation of the free surface (\autoref{sec:MB_hor_pg}). -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/NEMO/subfiles/chap_time_domain.tex
r14328 r14676 12 12 {\footnotesize 13 13 \begin{tabularx}{0.5\textwidth}{l||X|X} 14 Release & Author(s) & 14 Release & Author(s) & 15 15 Modifications \\ 16 16 \hline 17 {\em 4.0} & {\em J\'{e}r\^{o}me Chanut \newline Tim Graham} & 17 {\em 4.0} & {\em J\'{e}r\^{o}me Chanut \newline Tim Graham} & 18 18 {\em Review \newline Update } \\ 19 {\em 3.6} & {\em Christian \'{E}th\'{e} } & 19 {\em 3.6} & {\em Christian \'{E}th\'{e} } & 20 20 {\em Update } \\ 21 {\em $\leq$ 3.4} & {\em Gurvan Madec } & 21 {\em $\leq$ 3.4} & {\em Gurvan Madec } & 22 22 {\em First version } \\ 23 23 \end{tabularx} … … 44 44 45 45 The time stepping used in \NEMO\ is a three level scheme that can be represented as follows: 46 46 47 \begin{equation} 47 48 \label{eq:TD} 48 49 x^{t + \rdt} = x^{t - \rdt} + 2 \, \rdt \ \text{RHS}_x^{t - \rdt, \, t, \, t + \rdt} 49 50 \end{equation} 51 50 52 where $x$ stands for $u$, $v$, $T$ or $S$; 51 53 RHS is the \textbf{R}ight-\textbf{H}and-\textbf{S}ide of the corresponding time evolution equation; … … 97 99 first designed by \citet{robert_JMSJ66} and more comprehensively studied by \citet{asselin_MWR72}, 98 100 is a kind of laplacian diffusion in time that mixes odd and even time steps: 101 99 102 \begin{equation} 100 103 \label{eq:TD_asselin} 101 104 x_F^t = x^t + \gamma \, \lt[ x_F^{t - \rdt} - 2 x^t + x^{t + \rdt} \rt] 102 105 \end{equation} 106 103 107 where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient. 104 108 $\gamma$ is initialized as \np{rn_atfp}{rn\_atfp} (namelist parameter). … … 132 136 The conditions for stability of second and fourth order horizontal diffusion schemes are 133 137 \citep{griffies_bk04}: 138 134 139 \begin{equation} 135 140 \label{eq:TD_euler_stability} … … 140 145 \end{cases} 141 146 \end{equation} 147 142 148 where $e$ is the smallest grid size in the two horizontal directions and 143 149 $A^h$ is the mixing coefficient. … … 151 157 To overcome the stability constraint, a backward (or implicit) time differencing scheme is used. 152 158 This scheme is unconditionally stable but diffusive and can be written as follows: 159 153 160 \begin{equation} 154 161 \label{eq:TD_imp} … … 168 175 where RHS is the right hand side of the equation except for the vertical diffusion term. 169 176 We rewrite \autoref{eq:TD_imp} as: 177 170 178 \begin{equation} 171 179 \label{eq:TD_imp_mat} 172 180 -c(k + 1) \; T^{t + 1}(k + 1) + d(k) \; T^{t + 1}(k) - \; c(k) \; T^{t + 1}(k - 1) \equiv b(k) 173 181 \end{equation} 182 174 183 where 184 175 185 \[ 176 186 c(k) = A_w^{vT} (k) \, / \, e_{3w} (k) \text{,} \quad … … 239 249 $Q$ is redistributed over several time step. 240 250 In the modified LF-RA environment, these two formulations have been replaced by: 251 241 252 \begin{gather} 242 253 \label{eq:TD_forcing} … … 246 257 - \gamma \, \rdt \, \lt( Q^{t + \rdt / 2} - Q^{t - \rdt / 2} \rt) 247 258 \end{gather} 259 248 260 The change in the forcing formulation given by \autoref{eq:TD_forcing} 249 261 (see \autoref{fig:TD_MLF_forcing}) has a significant effect: … … 375 387 % 376 388 \end{flalign*} 389 377 390 \begin{flalign*} 378 391 \allowdisplaybreaks … … 387 400 % 388 401 \end{flalign*} 402 389 403 \begin{flalign*} 390 404 \allowdisplaybreaks -
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r11591 r14676 1 %% Engine (folder name)2 \def \engine{SI3}1 %% Engine 2 \def\eng{SI3} 3 3 4 %% Title and cover page settings 5 \def \spacetop{ \vspace*{1.2cm} } 6 \def \heading{Sea Ice modelling Integrated Initiative (SI$^3$)} 7 \def \subheading{The NEMO sea ice engine} 8 \def \spacedown{ \vspace*{ 1cm} } 9 \def \authorswidth{0.2\linewidth} 10 \def \rulelenght{230pt} 11 \def \abstractwidth{0.65\linewidth} 4 %% Cover page 5 \def\spcup{\vspace*{1.20cm}} 6 \def \hdg{Sea Ice modelling Integrated Initiative (SI$^3$)} 7 \def\shdg{The NEMO sea ice engine } 8 \def\spcdn{\vspace*{1.00cm}} 9 \def\autwd{0.20\linewidth}\def\lnlg{230pt}\def\abswd{0.65\linewidth} 12 10 13 %% Color for document(frontpage banner, links and chapter boxes)14 \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{0, 0, 0, 0.4}}11 %% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) 12 \def\clr{0.0,0.0,0.0,0.4} 15 13 16 14 %% IPSL publication number 17 \def \ipslnum{31}15 \def\ipsl{31} 18 16 19 %% Zenodo ID, i.e. doi:10.5281/zenodo.\ ([0-9]*\)20 \def 17 %% Zenodo ID, i.e. doi:10.5281/zenodo.\zid 18 \def\zid{1471689} -
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r11171 r14676 185 185 journal = {Global Biogeochemical Cycles}, 186 186 publisher = {American Geophysical Union (AGU)} 187 } 188 189 @techreport{ gibson_trpt86, 190 title = "Standards for software development and maintenance", 191 pages = "21", 192 series = "ECMWF Technical Memoranda", 193 number = "120", 194 author = "J. K. Gibson", 195 institution = "ECMWF Operations Department; Reading, United Kingdom", 196 year = "1986", 197 month = "aug", 198 doi = "10.21957/gi113q4gn" 187 199 } 188 200 -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/TOP/main/settings.tex
r11591 r14676 1 %% Engine (folder name)2 \def \engine{TOP}1 %% Engine 2 \def\eng{TOP} 3 3 4 %% Title and cover page settings 5 \def \spacetop{ \vspace*{1.3cm} } 6 \def \heading{Tracers in Ocean Paradigm (TOP)} 7 \def \subheading{The NEMO passive tracers engine} 8 \def \spacedown{ \vspace*{ 1cm} } 9 \def \authorswidth{0.15\linewidth} 10 \def \rulelenght{110pt} 11 \def \abstractwidth{0.7\linewidth} 4 %% Cover page 5 \def\spcup{\vspace*{1.30cm}} 6 \def \hdg{Tracers in Ocean Paradigm (TOP)} 7 \def\shdg{The NEMO passive tracers engine} 8 \def\spcdn{\vspace*{1.00cm}} 9 \def\autwd{0.15\linewidth}\def\lnlg{110pt}\def\abswd{0.70\linewidth} 12 10 13 %% Color for document(frontpage banner, links and chapter boxes)14 \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, 0, 1, .4}}11 %% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) 12 \def\clr{1.0,0.0,1.0,0.4} 15 13 16 14 %% IPSL publication number 17 \def \ipslnum{28}15 \def\ipsl{28} 18 16 19 %% Zenodo ID, i.e. doi:10.5281/zenodo.\ ([0-9]*\)20 \def 17 %% Zenodo ID, i.e. doi:10.5281/zenodo.\zid 18 \def\zid{1471700} -
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NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/TOP/subfiles/model_description.tex
r14113 r14676 9 9 \newcommand{\Dcq}{\Delta ^{14}\mathrm{C}} 10 10 \newcommand{\Rq}{\mathrm{^{14}{R}}} 11 \newcommand{\CODE}[1]{\textsc{#1}}12 %\newcommand{\CODE}[1]{\textcolor{black}{\textsc{#1}}\xspace}13 11 14 12 \chapter{Model Description} … … 28 26 where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations, see equations 5.10 and 5.11 in \citep{nemo_manual} 29 27 30 {S(C)} , the first term on the right hand side of \ref{Eq_tracer}; is the SMS - Source Minus Sink - inherent to the tracer. In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decay through mortality and grazing. In the case of a tracer comprising carbon, {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biological processes. In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay. 31 32 The second term (within brackets) represents the advection of the tracer in the three directions. It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$ 28 {S(C)} , the first term on the right hand side of \autoref{Eq_tracer}; is the SMS - Source Minus Sink - inherent to the tracer. 29 In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decay through mortality and grazing. 30 In the case of a tracer comprising carbon, {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biological processes. 31 In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay. 32 33 The second term (within brackets) represents the advection of the tracer in the three directions. 34 It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$ 33 35 34 36 The third term represents the change due to lateral diffusion. … … 46 48 \label{sec:TopInt} 47 49 48 TOP is the NEMO hardwired interface toward biogeochemical models and provide the physical constraints/boundaries for oceanic tracers. It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules. 50 TOP is the NEMO hardwired interface toward biogeochemical models and provide the physical constraints/boundaries for oceanic tracers. 51 It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules. 49 52 50 53 This component of the NEMO framework allows one to exploit available modules and further develop a range of applications, spanning from the implementation of a dye passive tracer to evaluate dispersion processes (by means of MY\_TRC), track water masses age (AGE module), assess the ocean interior penetration of persistent chemical compounds (e.g., gases like CFC or even PCBs), up to the full set of equations involving marine biogeochemical cycles. … … 61 64 \item \textbf{AGE} : Water age tracking 62 65 \item \textbf{MY\_TRC} : Template for creation of new modules and external BGC models coupling 63 \item \textbf{PISCES} : Built in BGC model. See \citep{aumont_2015} for a throughout description. 66 \item \textbf{PISCES} : Built in BGC model. 67 See \citep{aumont_2015} for a throughout description. 64 68 \end{itemize} 65 69 % ---------------------------------------------------------- … … 69 73 The passive tracer transport component shares the same advection/diffusion routines with the dynamics, with specific treatment of some features like the surface boundary conditions, or the positivity of passive tracers concentrations. 70 74 71 \subsection{Advection}75 \subsection{Advection} 72 76 %------------------------------------------namtrc_adv---------------------------------------------------- 73 77 \nlst{namtrc_adv} 74 78 %------------------------------------------------------------------------------------------------------------- 75 The advection schemes used for the passive tracers are the same than the ones for $T$ and $S$ and described in section 5.1 of \citep{nemo_manual}. The choice of an advection scheme can be selected independently and can differ from the ones used for active tracers. This choice is made in the \textit{namtrc\_adv} namelist, by setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, the same way of what is done for dynamics. 76 cen2, MUSCL2, and UBS are not \textit{positive} schemes meaning that negative values can appear in an initially strictly positive tracer field which is advected, implying that false extrema are permitted. Their use is not recommended on passive tracers 77 78 \subsection{ Lateral diffusion} 79 The advection schemes used for the passive tracers are the same than the ones for $T$ and $S$ and described in section 5.1 of \citep{nemo_manual}. 80 The choice of an advection scheme can be selected independently and can differ from the ones used for active tracers. 81 This choice is made in the \textit{namtrc\_adv} namelist, by setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, the same way of what is done for dynamics. 82 cen2, MUSCL2, and UBS are not \textit{positive} schemes meaning that negative values can appear in an initially strictly positive tracer field which is advected, implying that false extrema are permitted. 83 Their use is not recommended on passive tracers 84 85 \subsection{Lateral diffusion} 79 86 %------------------------------------------namtrc_ldf---------------------------------------------------- 80 87 \nlst{namtrc_ldf} 81 88 %------------------------------------------------------------------------------------------------------------- 82 In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set in the \nam{namtra_ldf}{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 83 89 In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. 90 However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. 91 The choice of numerical scheme is then set in the \forcode{&namtra_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 84 92 85 93 %-----------------We also offers the possibility to increase zonal equatorial diffusion for passive tracers by introducing an enhanced zonal diffusivity coefficent in the equatorial domain which can be defined by the equation below : … … 88 96 %-----------------\end{equation} 89 97 90 \subsection{Tracer damping}98 \subsection{Tracer damping} 91 99 92 100 %------------------------------------------namtrc_dmp---------------------------------------------------- … … 94 102 %------------------------------------------------------------------------------------------------------------- 95 103 96 The use of newtonian damping to climatological fields or observations is also coded, sharing the same routine dans active tracers. Boolean variables are defined in the namelist\_top\_ref to select the tracers on which restoring is applied 97 Options are defined through the \nam{namtrc_dmp}{namtrc\_dmp} namelist variables. The restoring term is added when the namelist parameter \np{ln\_trcdmp} is set to true. The restoring coefficient is a three-dimensional array read in a file, which name is specified by the namelist variable \np{cn\_resto\_tr}. This netcdf file can be generated using the DMP\_TOOLS tool. 98 99 \subsection{ Tracer positivity} 104 The use of newtonian damping to climatological fields or observations is also coded, sharing the same routine dans active tracers. 105 Boolean variables are defined in the namelist\_top\_ref to select the tracers on which restoring is applied 106 Options are defined through the \nam{trc_dmp}{trc\_dmp} namelist variables. 107 The restoring term is added when the namelist parameter \np{ln\_trcdmp} is set to true. 108 The restoring coefficient is a three-dimensional array read in a file, which name is specified by the namelist variable \np{cn\_resto\_tr}. 109 This netcdf file can be generated using the DMP\_TOOLS tool. 110 111 \subsection{Tracer positivity} 100 112 101 113 %------------------------------------------namtrc_rad---------------------------------------------------- … … 103 115 %------------------------------------------------------------------------------------------------------------- 104 116 105 Sometimes, numerical scheme can generates negative values of passive tracers concentration that must be positive. For exemple, isopycnal diffusion can created extrema. The trcrad routine artificially corrects negative concentrations with a very crude solution that either sets negative concentration to zero without adjusting the tracer budget, or by removing negative concentration and keeping mass conservation. 106 The treatment of negative concentrations is an option and can be selected in the namelist \nam{namtrc_rad}{namtrc\_rad} by setting the parameter \np{ln\_trcrad} to true. 117 Sometimes, numerical scheme can generates negative values of passive tracers concentration that must be positive. 118 For exemple, isopycnal diffusion can created extrema. 119 The trcrad routine artificially corrects negative concentrations with a very crude solution that either sets negative concentration to zero without adjusting the tracer budget, or by removing negative concentration and keeping mass conservation. 120 The treatment of negative concentrations is an option and can be selected in the namelist \nam{trc_rad}{trc\_rad} by setting the parameter \np{ln\_trcrad} to true. 107 121 108 122 \section{The SMS modules} … … 119 133 %---------------------------------------------------------------------------------------------------------- 120 134 121 122 An `ideal age' tracer is integrated online in TOP when \textit{ln\_age} = \texttt{.true.} in namelist \textit{namtrc}. This tracer marks the length of time in units of years that fluid has spent in the interior of the ocean, insulated from exposure to the atmosphere. Thus, away from the surface for $z<-H_{\mathrm{Age}}$ where $H_{\mathrm{Age}}$ is specified by the \textit{namage} namelist variable \textit{rn\_age\_depth}, whose default value is 10~m, there is a source $\mathrm{SMS_{\mathrm{Age}}}$ of the age tracer $A$: 135 An `ideal age' tracer is integrated online in TOP when \textit{ln\_age} = \texttt{.true.} in namelist \textit{namtrc}. 136 This tracer marks the length of time in units of years that fluid has spent in the interior of the ocean, insulated from exposure to the atmosphere. 137 Thus, away from the surface for $z<-H_{\mathrm{Age}}$ where $H_{\mathrm{Age}}$ is specified by the \textit{namage} namelist variable \textit{rn\_age\_depth}, whose default value is 10~m, there is a source $\mathrm{SMS_{\mathrm{Age}}}$ of the age tracer $A$: 138 123 139 \begin{equation} 124 140 \label{eq:TOP-age-interior} 125 141 \mathrm{SMS_{\mathrm{Age}}} = 1 \mathrm{yr}\;^{-1} = 1/T_{\mathrm{year}}, 126 \end{equation} 127 where the length of the current year $T_{\mathrm{year}} = 86400*N_{\mathrm{days\;in\;current\; year}}\;\mathrm{s}$, where $N_{\mathrm{days\;in\;current\; year}}$ may be 366 or 365 depending on whether the current year is a leap year or not. 128 Near the surface, for $z>-H_{\mathrm{Age}}$, ideal age is relaxed back to zero: 142 \end{equation} 143 144 where the length of the current year $T_{\mathrm{year}} = 86400*N_{\mathrm{days\;in\;current\; year}}\;\mathrm{s}$, where $N_{\mathrm{days\;in\;current\; year}}$ may be 366 or 365 depending on whether the current year is a leap year or not. 145 Near the surface, for $z>-H_{\mathrm{Age}}$, ideal age is relaxed back to zero: 146 129 147 \begin{equation} 130 148 \label{eq:TOP-age-surface} 131 149 \mathrm{SMS_{\mathrm{Age}}} = -\lambda_{\mathrm{Age}}A, 132 \end{equation} 133 where the relaxation rate $\lambda_{\mathrm{Age}}$ (units $\mathrm{s}\;^{-1}$) is specified by the \textit{namage} namelist variable \textit{rn\_age\_kill\_rate} and has a default value of 1/7200~s. Since this relaxation is applied explicitly, this relaxation rate in principle should not exceed $1/\Delta t$, where $\Delta t$ is the time step used to step forward passive tracers (2 * \textit{nn\_dttrc * rn\_rdt} when the default leapfrog time-stepping scheme is employed). 134 135 Currently the 1-dimensional reference depth of the grid boxes is used rather than the dynamically evolving depth to determine whether the age tracer is incremented or relaxed to zero. This means that the tracer only works correctly in z-coordinates. To ensure that the forcing is independent of the level thicknesses, where the tracer cell at level $k$ has its upper face $z=-depw(k)$ above the depth $-H_{\mathrm{Age}}$, but its lower face $z=-depw(k+1)$ below that depth, then the age source 136 \begin{equation} 150 \end{equation} 151 152 where the relaxation rate $\lambda_{\mathrm{Age}}$ (units $\mathrm{s}\;^{-1}$) is specified by the \textit{namage} namelist variable \textit{rn\_age\_kill\_rate} and has a default value of 1/7200~s. 153 Since this relaxation is applied explicitly, this relaxation rate in principle should not exceed $1/\Delta t$, where $\Delta t$ is the time step used to step forward passive tracers (2 * \textit{nn\_dttrc * rn\_rdt} when the default leapfrog time-stepping scheme is employed). 154 155 Currently the 1-dimensional reference depth of the grid boxes is used rather than the dynamically evolving depth to determine whether the age tracer is incremented or relaxed to zero. 156 This means that the tracer only works correctly in z-coordinates. 157 To ensure that the forcing is independent of the level thicknesses, where the tracer cell at level $k$ has its upper face $z=-depw(k)$ above the depth $-H_{\mathrm{Age}}$, but its lower face $z=-depw(k+1)$ below that depth, then the age source 158 159 \begin{equation} 137 160 \label{eq:TOP-age-mixed} 138 161 \mathrm{SMS_{\mathrm{Age}}} = -f_{\mathrm{kill}}\lambda_{\mathrm{Age}}A +f_{\mathrm{add}}/T_{\mathrm{year}} , 139 \end{equation} 140 where 141 \begin{align} 162 \end{equation} 163 164 where 165 166 \begin{align} 142 167 f_{\mathrm{kill}} &= e3t_k^{-1}(H_{\mathrm{Age}} - depw(k)) , \\ 143 168 f_{\mathrm{add}} &= 1 - f_{\mathrm{kill}}. 144 145 146 147 169 \end{align} 170 171 172 This implementation was first used in the CORE-II intercomparison runs described e.g.\ in \citet{danabasoglu_2014}. 148 173 149 174 \subsection{Inert carbons tracer} … … 155 180 156 181 Chlorofluorocarbons 11 and 12 (CFC-11 and CFC-12), and sulfur hexafluoride (SF6), are synthetic chemicals manufactured for industrial and domestic applications from the early 20th century onwards. 157 CFC-11 (CCl$_{3}$F) is a volatile liquid at room temperature, and was widely used in refrigeration. CFC-12 (CCl$_{2}$F$_{2}$) is a gas at room temperature, and, like CFC-11, was widely used as a refrigerant, 158 and additionally as an aerosol propellant. SF6 (SF$_{6}$) is also a gas at room temperature, with a range of applications based around its property as an excellent electrical insulator (often replacing more toxic alternatives). 159 All three are relatively inert chemicals that are both non-toxic and non-flammable, and their wide use has led to their accumulation within the Earth's atmosphere. Large-scale production of CFC-11 and CFC-12 began in the 1930s, while production of SF6 began in the 1950s, and their atmospheric concentration time-histories are shown in Figure \ref{img_cfcatm}. 182 CFC-11 (CCl$_{3}$F) is a volatile liquid at room temperature, and was widely used in refrigeration. 183 CFC-12 (CCl$_{2}$F$_{2}$) is a gas at room temperature, and, like CFC-11, was widely used as a refrigerant, 184 and additionally as an aerosol propellant. 185 SF6 (SF$_{6}$) is also a gas at room temperature, with a range of applications based around its property as an excellent electrical insulator (often replacing more toxic alternatives). 186 All three are relatively inert chemicals that are both non-toxic and non-flammable, and their wide use has led to their accumulation within the Earth's atmosphere. 187 Large-scale production of CFC-11 and CFC-12 began in the 1930s, while production of SF6 began in the 1950s, and their atmospheric concentration time-histories are shown in Figure \autoref{img_cfcatm}. 160 188 As can be seen in the figure, while the concentration of SF6 continues to rise to the present day, the concentrations of both CFC-11 and CFC-12 have levelled off and declined since around the 1990s. 161 189 These declines have been driven by the Montreal Protocol (effective since August 1989), which has banned the production of CFC-11 and CFC-12 (as well as other CFCs) because of their role in the depletion of 162 stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases 190 stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. 191 Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases 163 192 than CO$_{2}$ (especially SF6), although their relatively low atmospheric concentrations limit their role in climate change. \\ 164 193 … … 171 200 % This release began in the 1930s for CFC-11 and CFC-12, and the 1950s for SF6, and 172 201 % regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12, 173 % and is still increasing, and SF6 (see Figure \ ref{img_cfcatm}). \\202 % and is still increasing, and SF6 (see Figure \autoref{img_cfcatm}). \\ 174 203 175 204 The ocean is a notable sink for all three gases, and their relatively recent occurrence in the atmosphere, coupled to the ease of making high precision measurements of their dissolved concentrations, has made them … … 177 206 Because they only enter the ocean via surface air-sea exchange, and are almost completely chemically and biologically inert, their distribution within the ocean interior reveals its ventilation via transport and mixing. 178 207 Measuring the dissolved concentrations of the gases -- as well as the mixing ratios between them -- shows circulation pathways within the ocean as well as water mass ages (i.e. the time since last contact with the 179 atmosphere). This feature of the gases has made them valuable across a wide range of oceanographic problems. One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and 208 atmosphere). 209 This feature of the gases has made them valuable across a wide range of oceanographic problems. 210 One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and 180 211 ventilation of models, key for understanding the behaviour of wider modelled marine biogeochemistry (e.g. \citep{dutay_2002,palmieri_2015}). \\ 181 212 182 Modelling these gases (henceforth CFCs) in NEMO is done within the passive tracer transport module, TOP, using the conservation state equation \ ref{Eq_tracer}213 Modelling these gases (henceforth CFCs) in NEMO is done within the passive tracer transport module, TOP, using the conservation state equation \autoref{Eq_tracer} 183 214 184 215 Advection and diffusion of the CFCs in NEMO are calculated by the physical module, OPA, … … 198 229 \end{eqnarray} 199 230 200 Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \ ref{equ_Kw};201 $C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ ref{equ_C_sat};231 Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \autoref{equ_Kw}; 232 $C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \autoref{equ_C_sat}; 202 233 $C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{-3}$); 203 234 and $f_{i}$ is the fractional sea-ice cover of the local ocean (ranging between 0.0 for ice-free ocean, … … 211 242 \end{eqnarray} 212 243 213 Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \ ref{equ_Sol_CFC};244 Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \autoref{equ_Sol_CFC}; 214 245 and $P_{cfc}$ is the atmosphere concentration of the CFC (in parts per trillion by volume, pptv). 215 246 This latter concentration is provided to the model by the historical time-series of \citet{bullister_2017}. … … 231 262 $a$ is a constant re-estimated by \citet{wanninkhof_2014} to 0.251 (in $\frac{cm~h^{-1}}{(m~s^{-1})^{2}}$); 232 263 and $u$ is the 10~m wind speed in m~s$^{-1}$ from either an atmosphere model or reanalysis atmospheric forcing. 233 $Sc$ is the Schmidt number, and is calculated as follow, using coefficients from \citet{wanninkhof_2014} (see Table \ ref{tab_Sc}).264 $Sc$ is the Schmidt number, and is calculated as follow, using coefficients from \citet{wanninkhof_2014} (see Table \autoref{tab_Sc}). 234 265 235 266 \begin{eqnarray} … … 238 269 \end{eqnarray} 239 270 240 The solubility, $Sol$, used in Equation \ ref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$,271 The solubility, $Sol$, used in Equation \autoref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$, 241 272 and is specific for each gas. 242 273 It has been experimentally estimated by \citet{warner_1985} as a function of temperature … … 260 291 261 292 Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature; 262 and the $a_{x}$ and $b_{x}$ coefficients are specific for each gas (see Table \ ref{tab_ref_CFC}).293 and the $a_{x}$ and $b_{x}$ coefficients are specific for each gas (see Table \autoref{tab_ref_CFC}). 263 294 This is then converted to mol~m$^{-3}$~pptv$^{-1}$ assuming a constant atmospheric surface pressure of 1~atm. 264 295 The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes. 265 Consequently, this translates to a pattern of solubility where it is greatest in cold, polar regions (see Figure \ ref{img_cfcsol}).296 Consequently, this translates to a pattern of solubility where it is greatest in cold, polar regions (see Figure \autoref{img_cfcsol}). 266 297 267 298 % AXY: not 100% sure about the units below; they might be in nanomol, or in seconds or years 268 299 269 300 The standard outputs of the CFC module are seawater CFC concentrations (in mol~m$^{-3}$), the net air-sea flux (in mol~m$^{-2}$~d$^{-1}$) and the cumulative net air-sea flux (in mol~m$^{-2}$). 270 Using XIOS, it is possible to obtain outputs such as the vertical integral of CFC concentrations (in mol~m$^{-2}$; see Figure \ ref{img_cfcinv}).301 Using XIOS, it is possible to obtain outputs such as the vertical integral of CFC concentrations (in mol~m$^{-2}$; see Figure \autoref{img_cfcinv}). 271 302 This property, when divided by the surface CFC concentration, estimates the local penetration depth (in m) of the CFC. 272 303 … … 285 316 286 317 \begin{table}[!t] 287 \caption{Coefficients for fit of the CFCs solubility (Eq. \ ref{equ_Sol_CFC}).}318 \caption{Coefficients for fit of the CFCs solubility (Eq. \autoref{equ_Sol_CFC}).} 288 319 \vskip4mm 289 320 \centering … … 302 333 303 334 \begin{table}[!t] 304 \caption{Coefficients for fit of the CFCs Schmidt number (Eq. \ ref{equ_Sc}). }335 \caption{Coefficients for fit of the CFCs Schmidt number (Eq. \autoref{equ_Sc}). } 305 336 \vskip4mm 306 337 \centering … … 353 384 %---------------------------------------------------------------------------------------------------------- 354 385 355 The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions. 386 The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. 387 It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions. 356 388 357 389 \subsubsection{Method} 358 390 359 Let $\Rq$ represent the ratio of $\cq$ atoms to the total number of carbon atoms in the sample, i.e. $\cq/\mathrm{C}$. Then, radiocarbon anomalies are reported as 391 Let $\Rq$ represent the ratio of $\cq$ atoms to the total number of carbon atoms in the sample, i.e. $\cq/\mathrm{C}$. 392 Then, radiocarbon anomalies are reported as 393 360 394 \begin{equation} 361 395 \Dcq = \left( \frac{\Rq}{\Rq_\mathrm{ref}} - 1 \right) 10^3, \label{eq:c14dcq} 362 396 \end{equation} 363 where $\Rq_{\textrm{ref}}$ is a reference ratio. For the purpose of ocean ventilation studies $\Rq_{\textrm{ref}}$ is set to one. 397 398 where $\Rq_{\textrm{ref}}$ is a reference ratio. 399 For the purpose of ocean ventilation studies $\Rq_{\textrm{ref}}$ is set to one. 364 400 365 401 Here we adopt the approach of \cite{fiadeiro_1982} and \cite{toggweiler_1989a,toggweiler_1989b} in which the ratio $\Rq$ is transported rather than the individual concentrations C and $\cq$. 366 This approach calls for a strong assumption, i.e., that of a homogeneous and constant dissolved inorganic carbon (DIC) field \citep{toggweiler_1989a,mouchet_2013}. While in terms of 367 oceanic $\Dcq$, it yields similar results to approaches involving carbonate chemistry, it underestimates the bomb radiocarbon inventory because it assumes a constant air-sea $\cd$ disequilibrium (Mouchet, 2013). Yet, field reconstructions of the ocean bomb $\cq$ inventory are also biased low \citep{naegler_2009} since they assume that the anthropogenic perturbation did not affect ocean DIC since the pre-bomb epoch. For these reasons, bomb $\cq$ inventories obtained with the present method are directly comparable to reconstructions based on field measurements. 368 369 This simplified approach also neglects the effects of fractionation (e.g., air-sea exchange) and of biological processes. Previous studies by \cite{bacastow_1990} and \cite{joos_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not. 402 This approach calls for a strong assumption, i.e., that of a homogeneous and constant dissolved inorganic carbon (DIC) field \citep{toggweiler_1989a,mouchet_2013}. 403 While in terms of 404 oceanic $\Dcq$, it yields similar results to approaches involving carbonate chemistry, it underestimates the bomb radiocarbon inventory because it assumes a constant air-sea $\cd$ disequilibrium (Mouchet, 2013). 405 Yet, field reconstructions of the ocean bomb $\cq$ inventory are also biased low \citep{naegler_2009} since they assume that the anthropogenic perturbation did not affect ocean DIC since the pre-bomb epoch. 406 For these reasons, bomb $\cq$ inventories obtained with the present method are directly comparable to reconstructions based on field measurements. 407 408 This simplified approach also neglects the effects of fractionation (e.g., air-sea exchange) and of biological processes. 409 Previous studies by \cite{bacastow_1990} and \cite{joos_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not. 370 410 Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{stuiver_1977} the model results are directly comparable to observations. 371 411 … … 373 413 374 414 The equation governing the transport of $\Rq$ in the ocean is 415 375 416 \begin{equation} 376 417 \frac{\partial}{\partial t} {\Rq} = - \bigtriangledown \cdot ( \mathbf{u} \Rq - \mathbf{K} \cdot \bigtriangledown \Rq ) - \lambda \Rq, \label{eq:quick} 377 418 \end{equation} 419 378 420 where $\lambda$ is the radiocarbon decay rate, ${\mathbf{u}}$ the 3-D velocity field, and $\mathbf{K}$ the diffusivity tensor. 379 421 380 At the air-sea interface a Robin boundary condition \citep{haine_2006} is applied to \ eqref{eq:quick}, i.e., the flux422 At the air-sea interface a Robin boundary condition \citep{haine_2006} is applied to \autoref{eq:quick}, i.e., the flux 381 423 through the interface is proportional to the difference in the ratios between 382 424 the ocean and the atmosphere 425 383 426 \begin{equation} 384 427 \mathcal{\!F} = \kappa_{R} (\Rq - \Rq_{a} ), \label{eq:BCR} 385 428 \end{equation} 386 where $\mathcal{\!F}$ is the flux out of the ocean, and $\Rq_{a}$ is the atmospheric $\cq/\mathrm{C}$ ratio. The transfer velocity $ \kappa_{R} $ for the radiocarbon ratio in \eqref{eq:BCR} is computed as 429 430 where $\mathcal{\!F}$ is the flux out of the ocean, and $\Rq_{a}$ is the atmospheric $\cq/\mathrm{C}$ ratio. 431 The transfer velocity $ \kappa_{R} $ for the radiocarbon ratio in \autoref{eq:BCR} is computed as 432 387 433 \begin{equation} 388 434 \kappa_{R} = \frac{\kappa_{\cd} K_0}{\overline{\Ct}} \, \pacd \label{eq:Rspeed} 389 435 \end{equation} 436 390 437 with $\kappa_{\cd}$ the carbon dioxide transfer or piston velocity, $K_0$ the $\cd$ solubility in seawater, $\pacd$ the atmospheric $\cd$ pressure at sea level, and $\overline{\Ct}$ the average sea-surface dissolved inorganic carbon concentration. 391 438 392 393 The $\cd$ transfer velocity is based on the empirical formulation of \cite{wanninkhof_1992} with chemical enhancement \citep{wanninkhof_1996,wanninkhof_2014}. The original formulation is modified to account for the reduction of the air-sea exchange rate in the presence of sea ice. Hence 439 The $\cd$ transfer velocity is based on the empirical formulation of \cite{wanninkhof_1992} with chemical enhancement \citep{wanninkhof_1996,wanninkhof_2014}. 440 The original formulation is modified to account for the reduction of the air-sea exchange rate in the presence of sea ice. 441 Hence 442 394 443 \begin{equation} 395 444 \kappa_\cd=\left( K_W\,\mathrm{w}^2 + b \right)\, (1-f_\mathrm{ice})\,\sqrt{660/Sc}, \label{eq:wanc14} 396 445 \end{equation} 397 446 with $\mathrm{w}$ the wind magnitude, $f_\mathrm{ice}$ the fractional ice cover, and $Sc$ the Schmidt number. 398 $K_W$ in \ eqref{eq:wanc14} is an empirical coefficient with dimension of an inverse velocity.447 $K_W$ in \autoref{eq:wanc14} is an empirical coefficient with dimension of an inverse velocity. 399 448 The chemical enhancement term $b$ is represented as a function of temperature $T$ \citep{wanninkhof_1992} 400 449 \begin{equation} … … 402 451 \end{equation} 403 452 404 %We compare the results of equilibrium and transient experiments obtained with both methods in section \ ref{sec:UNDEU}.453 %We compare the results of equilibrium and transient experiments obtained with both methods in section \autoref{sec:UNDEU}. 405 454 406 455 % … … 413 462 \label{sec:param} 414 463 % 415 The radiocarbon decay rate (\CODE{rlam14}; in \texttt{trcnam\_c14} module) is set to $\lambda=(1/8267)$ yr$^{-1}$ \citep{stuiver_1977}, which corresponds to a half-life of 5730 yr.\\[1pt] 416 % 417 The Schmidt number $Sc$, Eq. \eqref{eq:wanc14}, is calculated with the help of the formulation of \cite{wanninkhof_2014}. The $\cd$ solubility $K_0$ in \eqref{eq:Rspeed} is taken from \cite{weiss_1974}. $K_0$ and $Sc$ are computed with the OGCM temperature and salinity fields (\texttt{trcsms\_c14} module).\\[1pt] 464 The radiocarbon decay rate (\forcode{rlam14}; in \texttt{trcnam\_c14} module) is set to $\lambda=(1/8267)$ yr$^{-1}$ \citep{stuiver_1977}, which corresponds to a half-life of 5730 yr.\\[1pt] 465 % 466 The Schmidt number $Sc$, Eq. \autoref{eq:wanc14}, is calculated with the help of the formulation of \cite{wanninkhof_2014}. 467 The $\cd$ solubility $K_0$ in \autoref{eq:Rspeed} is taken from \cite{weiss_1974}. $K_0$ and $Sc$ are computed with the OGCM temperature and salinity fields (\texttt{trcsms\_c14} module).\\[1pt] 418 468 % 419 469 The following parameters intervening in the air-sea exchange rate are set in \texttt{namelist\_c14}: 470 420 471 \begin{itemize} 421 \item The reference DIC concentration $\overline{\Ct}$ (\ CODE{xdicsur}) intervening in \eqref{eq:Rspeed} is classically set to 2 mol m$^{-3}$ \citep{toggweiler_1989a,orr_2001,butzin_2005}.422 % 423 \item The value of the empirical coefficient $K_W$ (\ CODE{xkwind}) in \eqref{eq:wanc14} depends on the wind field and on the model upper ocean mixing rate \citep{toggweiler_1989a,wanninkhof_1992,naegler_2009,wanninkhof_2014}.472 \item The reference DIC concentration $\overline{\Ct}$ (\forcode{xdicsur}) intervening in \autoref{eq:Rspeed} is classically set to 2 mol m$^{-3}$ \citep{toggweiler_1989a,orr_2001,butzin_2005}. 473 % 474 \item The value of the empirical coefficient $K_W$ (\forcode{xkwind}) in \autoref{eq:wanc14} depends on the wind field and on the model upper ocean mixing rate \citep{toggweiler_1989a,wanninkhof_1992,naegler_2009,wanninkhof_2014}. 424 475 It should be adjusted so that the globally averaged $\cd$ piston velocity is $\kappa_\cd = 16.5\pm 3.2$ cm/h \citep{naegler_2009}. 425 %The sensitivity to this parametrization is discussed in section \ ref{sec:result}.426 % 427 \item Chemical enhancement (term $b$ in Eq. \ ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}.476 %The sensitivity to this parametrization is discussed in section \autoref{sec:result}. 477 % 478 \item Chemical enhancement (term $b$ in Eq. \autoref{eq:wanchem}) may be set on/off by means of the logical variable \forcode{ln\_chemh}. 428 479 \end{itemize} 429 480 430 481 % 431 482 \paragraph{Experiment type} 432 The type of experiment is determined by the value given to \CODE{kc14typ} in \texttt{namelist\_c14}. There are three possibilities: 483 The type of experiment is determined by the value given to \forcode{kc14typ} in \texttt{namelist\_c14}. 484 There are three possibilities: 485 433 486 \begin{enumerate} 434 \item natural $\Dcq$: \CODE{kc14typ}=0435 \item bomb $\Dcq$: \CODE{kc14typ}=1436 \item transient paleo-historical $\Dcq$: \ CODE{kc14typ}=2487 \item natural $\Dcq$: \forcode{kc14typ}=0 488 \item bomb $\Dcq$: \forcode{kc14typ}=1 489 \item transient paleo-historical $\Dcq$: \forcode{kc14typ}=2 437 490 \end{enumerate} 438 % 491 492 % 439 493 \textbf{Natural or Equilibrium radiocarbon} 440 \CODE{kc14typ}=0 441 442 Unless otherwise specified in \texttt{namelist\_c14}, the atmospheric $\Rq_a$ (\CODE{rc14at}) is set to one, the atmospheric $\cd$ (\CODE{pco2at}) to 280 ppm, and the ocean $\Rq$ is initialized with \CODE{rc14init=0.85}, i.e., $\Dcq=$-150\textperthousand \cite[typical for deep-ocean, Fig 6 in][]{key_2004}. 443 444 Equilibrium experiment should last until 98\% of the ocean volume exhibit a drift of less than 0.001\textperthousand/year \citep{orr_2000}; this is usually achieved after few kyr (Fig. \ref{fig:drift}). 445 % 494 \forcode{kc14typ}=0 495 496 Unless otherwise specified in \texttt{namelist\_c14}, the atmospheric $\Rq_a$ (\forcode{rc14at}) is set to one, the atmospheric $\cd$ (\forcode{pco2at}) to 280 ppm, and the ocean $\Rq$ is initialized with \forcode{rc14init=0.85}, i.e., $\Dcq=$-150\textperthousand \cite[typical for deep-ocean, Fig 6 in][]{key_2004}. 497 498 Equilibrium experiment should last until 98\% of the ocean volume exhibit a drift of less than 0.001\textperthousand/year \citep{orr_2000}; this is usually achieved after few kyr (Fig. \autoref{fig:drift}). 499 % 500 446 501 \begin{figure}[!h] 447 502 \begin{center} … … 449 504 \end{center} 450 505 \vspace{-4ex} 451 \caption{ Time evolution of $\Rq$ inventory anomaly for equilibrium run with homogeneous ocean initial state. The anomaly (or drift) is given in \% change in total ocean inventory per 50 years. Time on x-axis is in simulation year.\label{fig:drift} } 506 \caption{ Time evolution of $\Rq$ inventory anomaly for equilibrium run with homogeneous ocean initial state. 507 The anomaly (or drift) is given in \% change in total ocean inventory per 50 years. 508 Time on x-axis is in simulation year.\label{fig:drift} } 452 509 \end{figure} 453 510 454 511 \textbf{Transient: Bomb} 455 512 \label{sec:bomb} 456 \ CODE{kc14typ}=1513 \forcode{kc14typ}=1 457 514 458 515 \begin{figure}[!h] … … 461 518 \end{center} 462 519 \vspace{-4ex} 463 \caption{Atmospheric $\Dcq$ (solid; left axis) and $\cd$ (dashed; right axis) forcing for the $\cq$-bomb experiments. The $\Dcq$ is illustrated for the three zonal bands (upper, middle, and lower curves correspond to latitudes $> 20$N, $\in [20\mathrm{S},20\mathrm{N}]$, and $< 20$S, respectively.} \label{fig:bomb} 520 \caption{Atmospheric $\Dcq$ (solid; left axis) and $\cd$ (dashed; right axis) forcing for the $\cq$-bomb experiments. 521 The $\Dcq$ is illustrated for the three zonal bands (upper, middle, and lower curves correspond to latitudes $> 20$N, $\in [20\mathrm{S},20\mathrm{N}]$, and $< 20$S, respectively.} \label{fig:bomb} 464 522 \end{figure} 465 523 466 Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}). 467 468 An exception to this rule is when wishing to perform a perturbation bomb experiment as was possible with the package \texttt{C14b}. It is still possible to easily set-up that type of transient experiment for which no previous run is needed. In addition to the instructions as given in this section it is however necessary to adapt the \texttt{atmc14.dat} file so that it does no longer contain any negative $\Dcq$ values (Suess effect in the pre-bomb period). 469 470 The model is integrated from a given initial date following the observed records provided from 1765 AD on ( Fig. \ref{fig:bomb}). 471 The file \texttt{atmc14.dat} \cite[][\& I. Levin, personal comm.]{enting_1994} provides atmospheric $\Dcq$ for three latitudinal bands: 90S-20S, 20S-20N \& 20N-90N. 472 Atmospheric $\cd$ in the file \texttt{splco2.dat} is obtained from a spline fit through ice core data and direct atmospheric measurements \cite[][\& J. Orr, personal comm.]{orr_2000}. 524 Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\forcode{ln\_rsttr} should be set to \texttt{.TRUE.}). 525 526 An exception to this rule is when wishing to perform a perturbation bomb experiment as was possible with the package \texttt{C14b}. 527 It is still possible to easily set-up that type of transient experiment for which no previous run is needed. 528 In addition to the instructions as given in this section it is however necessary to adapt the \texttt{atmc14.dat} file so that it does no longer contain any negative $\Dcq$ values (Suess effect in the pre-bomb period). 529 530 The model is integrated from a given initial date following the observed records provided from 1765 AD on ( Fig. \autoref{fig:bomb}). 531 The file \texttt{atmc14.dat} \cite[][\& I. 532 Levin, personal comm.]{enting_1994} provides atmospheric $\Dcq$ for three latitudinal bands: 90S-20S, 20S-20N \& 20N-90N. 533 Atmospheric $\cd$ in the file \texttt{splco2.dat} is obtained from a spline fit through ice core data and direct atmospheric measurements \cite[][\& J. 534 Orr, personal comm.]{orr_2000}. 473 535 Dates in these forcing files are expressed as yr AD. 474 536 475 537 To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully: 538 476 539 \begin{itemize} 477 \item Specify the starting date of the experiment: \ CODE{nn\_date0} in \texttt{namelist}. \CODE{nn\_date0} is written as Year0101 where Year may take any positive value (AD).478 \item Then the parameters \ CODE{nn\_rstctl} in \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line) must be \textbf{set to 0} at the start of the experiment (force the date to \CODE{nn\_date0} for the \textbf{first} experiment year).479 \item These two parameters (\ CODE{nn\_rstctl} and \CODE{nn\_rsttr}) have then to be \textbf{set to 2} for the following years (the date must be read in the restart file).540 \item Specify the starting date of the experiment: \forcode{nn\_date0} in \texttt{namelist}. \forcode{nn\_date0} is written as Year0101 where Year may take any positive value (AD). 541 \item Then the parameters \forcode{nn\_rstctl} in \texttt{namelist} (on-line) and \forcode{nn\_rsttr} in \texttt{namelist\_top} (off-line) must be \textbf{set to 0} at the start of the experiment (force the date to \forcode{nn\_date0} for the \textbf{first} experiment year). 542 \item These two parameters (\forcode{nn\_rstctl} and \forcode{nn\_rsttr}) have then to be \textbf{set to 2} for the following years (the date must be read in the restart file). 480 543 \end{itemize} 481 If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. Note that \CODE{tyrc14\_beg} (\texttt{namelist\_c14}) is not used in this context. 544 545 If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. 546 Note that \forcode{tyrc14\_beg} (\texttt{namelist\_c14}) is not used in this context. 482 547 483 548 % 484 549 \textbf{Transient: Past} 485 \ CODE{kc14typ}=2550 \forcode{kc14typ}=2 486 551 % 487 552 \begin{figure}[!h] … … 490 555 \end{center} 491 556 \vspace{-4ex} 492 \caption{Atmospheric $\Dcq$ (solid) and $\cd$ (dashed) forcing for the Paleo experiments. The $\cd$ scale is given on the right axis.} \label{fig:paleo} 557 \caption{Atmospheric $\Dcq$ (solid) and $\cd$ (dashed) forcing for the Paleo experiments. 558 The $\cd$ scale is given on the right axis.} \label{fig:paleo} 493 559 \end{figure} 494 560 495 This experiment type does not need a previous equilibrium run. It should start 5--6 kyr earlier than the period to be analyzed. 496 Atmospheric $\Rq_a$ and $\cd$ are prescribed from forcing files. The ocean $\Rq$ is initialized with the value attributed to \CODE{rc14init} in \texttt{namelist\_c14}. 561 This experiment type does not need a previous equilibrium run. 562 It should start 5--6 kyr earlier than the period to be analyzed. 563 Atmospheric $\Rq_a$ and $\cd$ are prescribed from forcing files. 564 The ocean $\Rq$ is initialized with the value attributed to \forcode{rc14init} in \texttt{namelist\_c14}. 497 565 498 566 The file \texttt{intcal13.14c} \citep{reimer_2013} contains atmospheric $\Dcq$ from 0 to 50 kyr cal BP\footnote{cal BP: number of years before 1950 AD}. 499 The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP \citep{ahn_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP. 567 The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. 568 The content of this file is based on the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP \citep{ahn_2008}. 569 These atmospheric values are reproduced in Fig. \autoref{fig:paleo}. 570 Dates in these files are expressed as yr BP. 500 571 501 572 To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully. 502 The true experiment starting date is given by \CODE{tyrc14\_beg} (in yr BP) in \texttt{namelist\_c14}. In consequence, \CODE{nn\_date0} in \texttt{namelist} MUST be set to 00010101.\\ 503 Then the parameters \CODE{nn\_rstctl} in \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line) must be set to 0 at the start of the experiment (force the date to \CODE{nn\_date0} for the first experiment year). These two parameters have then to be set to 2 for the following years (read the date in the restart file). \\ 504 If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. 573 The true experiment starting date is given by \forcode{tyrc14\_beg} (in yr BP) in \texttt{namelist\_c14}. 574 In consequence, \forcode{nn\_date0} in \texttt{namelist} MUST be set to 00010101.\\ 575 Then the parameters \forcode{nn\_rstctl} in \texttt{namelist} (on-line) and \forcode{nn\_rsttr} in \texttt{namelist\_top} (off-line) must be set to 0 at the start of the experiment (force the date to \forcode{nn\_date0} for the first experiment year). 576 These two parameters have then to be set to 2 for the following years (read the date in the restart file). \\ 577 If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. 505 578 506 579 % 507 580 \paragraph{Model output} 508 581 \label{sec:output} 509 All output fields in Table \ref{tab:out} are routinely computed. It depends on the actual settings in \texttt{iodef.xml} whether they are stored or not. 582 583 All output fields in Table \autoref{tab:out} are routinely computed. 584 It depends on the actual settings in \texttt{iodef.xml} whether they are stored or not. 510 585 % 511 586 \begin{table}[!h] 512 587 \begin{center} 513 \caption{Standard output fields for the C14 package \label{tab:out}. 514 } 588 \caption{Standard output fields for the C14 package \label{tab:out}.} 515 589 %\begin{small} 516 590 \renewcommand{\arraystretch}{1.3}% 517 591 \begin{tabular}[h]{|l*{3}{|c}|l|} 518 592 \hline 519 Field & Type & Dim & Units & Description\\ \hline520 RC14 & ptrc & 3-D & - & Radiocarbon ratio\\521 DeltaC14 & diad & 3-D & \textperthousand & $\Dcq$\\522 C14Age & diad & 3-D & yr & Radiocarbon age\\523 RAge & diad & 2-D & yr & Reservoir age\\524 qtr\_c14 & diad & 2-D & m$^{-2}$ yr$^{-1}$ & Air-to-sea net $\Rq$ flux\\525 qint\_c14 & diad & 2-D & m$^{-2}$ & Cumulative air-to-sea $\Rq$ flux\\526 AtmCO2 & scalar & 0-D & ppm & Global atmospheric $\cd$\\527 AtmC14 & scalar & 0-D & \textperthousand & Global atmospheric $\Dcq$\\528 K\_CO2 & scalar & 0-D & cm h$^{-1}$& Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\529 K\_C14 & scalar & 0-D &m yr$^{-1}$ & Global $\Rq$ transfer velocity ($ \overline{\kappa_R}$)\\530 C14Inv & scalar & 0-D & $10^{26}$ atoms & Ocean radiocarbon inventory\\ \hline593 Field & Type & Dim & Units & Description \\ \hline 594 RC14 & ptrc & 3-D & - & Radiocarbon ratio \\ 595 DeltaC14 & diad & 3-D & \textperthousand & $\Dcq$ \\ 596 C14Age & diad & 3-D & yr & Radiocarbon age \\ 597 RAge & diad & 2-D & yr & Reservoir age \\ 598 qtr\_c14 & diad & 2-D & m$^{-2}$ yr$^{-1}$ & Air-to-sea net $\Rq$ flux \\ 599 qint\_c14 & diad & 2-D & m$^{-2}$ & Cumulative air-to-sea $\Rq$ flux \\ 600 AtmCO2 & scalar & 0-D & ppm & Global atmospheric $\cd$ \\ 601 AtmC14 & scalar & 0-D & \textperthousand & Global atmospheric $\Dcq$ \\ 602 K\_CO2 & scalar & 0-D & cm h$^{-1}$ & Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\ 603 K\_C14 & scalar & 0-D & m yr$^{-1}$ & Global $\Rq$ transfer velocity ($ \overline{\kappa_R}$) \\ 604 C14Inv & scalar & 0-D & $10^{26}$ atoms & Ocean radiocarbon inventory \\ \hline 531 605 \end{tabular} 532 606 %\end{small} … … 539 613 The radiocarbon age is computed as $(-1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. 540 614 541 The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{stuiver_1977} 615 The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. 616 It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{stuiver_1977} 617 542 618 \begin{align} 543 619 {^{14}\tau_\mathrm{c}}= -8033 \; \ln \left(1 + \frac{\Dcq}{10^3}\right), \label{eq:convage} 544 620 \end{align} 545 where ${^{14}\tau_\mathrm{c}}$ is expressed in years B.P. Here we do not use that convention and compute reservoir ages with the mean lifetime $1/\lambda$. Conversion from one scale to the other is readily performed. The conventional radiocarbon age is lower than the radiocarbon age by $\simeq3\%$. 621 622 where ${^{14}\tau_\mathrm{c}}$ is expressed in years B.P. 623 Here we do not use that convention and compute reservoir ages with the mean lifetime $1/\lambda$. 624 Conversion from one scale to the other is readily performed. 625 The conventional radiocarbon age is lower than the radiocarbon age by $\simeq3\%$. 546 626 547 627 The ocean radiocarbon inventory is computed as 628 548 629 \begin{equation} 549 630 N_A \Rq_\mathrm{oxa} \overline{\Ct} \left( \int_\Omega \Rq d\Omega \right) /10^{26}, \label{eq:inv} 550 631 \end{equation} 551 where $N_A$ is the Avogadro's number ($N_A=6.022\times10^{23}$ at/mol), $\Rq_\mathrm{oxa}$ is the oxalic acid radiocarbon standard \cite[$\Rq_\mathrm{oxa}=1.176\times10^{-12}$;][]{stuiver_1977}, and $\Omega$ is the ocean volume. Bomb $\cq$ inventories are traditionally reported in units of $10^{26}$ atoms, hence the denominator in \eqref{eq:inv}. 552 553 All transformations from second to year, and inversely, are performed with the help of the physical constant \CODE{rsiyea} the sideral year length expressed in seconds\footnote{The variable (\CODE{nyear\_len}) which reports the length in days of the previous/current/future year (see \textrm{oce\_trc.F90}) is not a constant. }. 632 633 where $N_A$ is the Avogadro's number ($N_A=6.022\times10^{23}$ at/mol), $\Rq_\mathrm{oxa}$ is the oxalic acid radiocarbon standard \cite[$\Rq_\mathrm{oxa}=1.176\times10^{-12}$;][]{stuiver_1977}, and $\Omega$ is the ocean volume. 634 Bomb $\cq$ inventories are traditionally reported in units of $10^{26}$ atoms, hence the denominator in \autoref{eq:inv}. 635 636 All transformations from second to year, and inversely, are performed with the help of the physical constant \forcode{rsiyea} the sideral year length expressed in seconds\footnote{The variable (\forcode{nyear\_len}) which reports the length in days of the previous/current/future year (see \textrm{oce\_trc.F90}) is not a constant. }. 554 637 555 638 The global transfer velocities represent time-averaged\footnote{the actual duration is set in \texttt{iodef.xml}} global integrals of the transfer rates: 556 \begin{equation} 639 640 \begin{equation} 557 641 \overline{\kappa_{\cd}}= \int_\mathcal{S} \kappa_{\cd} d\mathcal{S} \text{ and } \overline{\kappa_R}= \int_\mathcal{S} \kappa_R d\mathcal{S} 558 642 \end{equation} … … 561 645 \subsection{PISCES biogeochemical model} 562 646 563 PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). The model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. 647 PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). 648 The model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. 564 649 Two versions of PISCES are available in NEMO v4.0 : 565 650 566 PISCES-v2, by setting in namelist\_pisces\_ref \np{ln\_p4z} to true, can be seen as one of the many Monod models \citep{monod_1958}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twenty-four prognostic variables (tracers) including two phytoplankton compartments (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. 567 568 PISCES-QUOTA has been built on the PISCES-v2 model described in \citet{aumont_2015}. PISCES-QUOTA has thirty-nine prognostic compartments. Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus, iron, chlorophyll and silicon biomasses (the latter only for diatoms). This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted by the model. Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{sterner_2003,woods_2013,meunier_2014}. As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{takahashi_1985} and the -O/C ratio is set to 1.34 \citep{kortzinger_2001}. No silicified zooplankton is assumed. The bacterial pool is not yet explicitly modeled. 569 570 There are three non-living compartments: Semi-labile dissolved organic matter, small sinking particles, and large sinking particles. As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCES-v2. Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{honjo_1996,armstrong_2001}). The latter particles are assumed to sink at the same speed as the large organic matter particles. All the non-living compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM. 571 651 PISCES-v2, by setting in namelist\_pisces\_ref \np{ln\_p4z} to true, can be seen as one of the many Monod models \citep{monod_1958}. 652 It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. 653 There are twenty-four prognostic variables (tracers) including two phytoplankton compartments (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and mesozooplankton) and a description of the carbonate chemistry. 654 Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. 655 On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. 656 Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. 657 658 PISCES-QUOTA has been built on the PISCES-v2 model described in \citet{aumont_2015}. 659 PISCES-QUOTA has thirty-nine prognostic compartments. 660 Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. 661 Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. 662 For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus, iron, chlorophyll and silicon biomasses (the latter only for diatoms). 663 This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted by the model. 664 Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{sterner_2003,woods_2013,meunier_2014}. 665 As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. 666 In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{takahashi_1985} and the -O/C ratio is set to 1.34 \citep{kortzinger_2001}. 667 No silicified zooplankton is assumed. 668 The bacterial pool is not yet explicitly modeled. 669 670 There are three non-living compartments: Semi-labile dissolved organic matter, small sinking particles, and large sinking particles. 671 As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCES-v2. 672 Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. 673 The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{honjo_1996,armstrong_2001}). 674 The latter particles are assumed to sink at the same speed as the large organic matter particles. 675 All the non-living compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM. 572 676 573 677 \subsection{MY\_TRC interface for coupling external BGC models} 574 678 \label{Mytrc} 575 679 576 The NEMO-TOP has only one built-in biogeochemical model - PISCES - but there are several BGC models - MEDUSA, ERSEM, BFM or ECO3M - which are meant to be coupled with the NEMO dynamics. Therefore it was necessary to provide to the users a framework for easily add their own BGCM model, that can be a single passive tracer. 577 The generalized interface is pivoted on MY\_TRC module that contains template files to build the coupling between NEMO and any external BGC model. The call to MY\_TRC is activated by setting \textit{ln\_my\_trc} = \texttt{.true.} in namelist \textit{namtrc} 680 The NEMO-TOP has only one built-in biogeochemical model - PISCES - but there are several BGC models - MEDUSA, ERSEM, BFM or ECO3M - which are meant to be coupled with the NEMO dynamics. 681 Therefore it was necessary to provide to the users a framework for easily add their own BGCM model, that can be a single passive tracer. 682 The generalized interface is pivoted on MY\_TRC module that contains template files to build the coupling between NEMO and any external BGC model. 683 The call to MY\_TRC is activated by setting \textit{ln\_my\_trc} = \texttt{.true.} in namelist \textit{namtrc} 578 684 579 685 The following 6 fortran files are available in MY\_TRC with the specific purposes here described. … … 581 687 \begin{itemize} 582 688 \item \textit{par\_my\_trc.F90} : This module allows to define additional arrays and public variables to be used within the MY\_TRC interface 583 \item \textit{trcini\_my\_trc.F90} : Here are initialized user defined namelists and the call to the external BGC model initialization procedures to populate general tracer array (trn and trb). Here are also likely to be defined suport arrays related to system metrics that could be needed by the BGC model. 689 \item \textit{trcini\_my\_trc.F90} : Here are initialized user defined namelists and the call to the external BGC model initialization procedures to populate general tracer array (trn and trb). 690 Here are also likely to be defined suport arrays related to system metrics that could be needed by the BGC model. 584 691 \item \textit{trcnam\_my\_trc.F90} : This routine is called at the beginning of trcini\_my\_trc and should contain the initialization of additional namelists for the BGC model or user-defined code. 585 \item \textit{trcsms\_my\_trc.F90} : The routine performs the call to Boundary Conditions and its main purpose is to contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model. Be aware that lateral boundary conditions are applied in trcnxt routine. IMPORTANT: the routines to compute the light penetration along the water column and the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in the code. 586 \item \textit{trcice\_my\_trc.F90} : Here it is possible to prescribe the tracers concentrations in the seaice that will be used as boundary conditions when ice melting occurs (nn\_ice\_tr =1 in namtrc\_ice). See e.g. the correspondent PISCES subroutine. 587 \item \textit{trcwri\_my\_trc.F90} : This routine performs the output of the model tracers using IOM module (see Manual Chapter Output and Diagnostics). It is possible to place here the output of additional variables produced by the model, if not done elsewhere in the code, using the call to \textit{iom\_put}. 692 \item \textit{trcsms\_my\_trc.F90} : The routine performs the call to Boundary Conditions and its main purpose is to contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model. 693 Be aware that lateral boundary conditions are applied in trcnxt routine. 694 IMPORTANT: the routines to compute the light penetration along the water column and the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in the code. 695 \item \textit{trcice\_my\_trc.F90} : Here it is possible to prescribe the tracers concentrations in the seaice that will be used as boundary conditions when ice melting occurs (nn\_ice\_tr =1 in namtrc\_ice). 696 See e.g. the correspondent PISCES subroutine. 697 \item \textit{trcwri\_my\_trc.F90} : This routine performs the output of the model tracers using IOM module (see Manual Chapter Output and Diagnostics). 698 It is possible to place here the output of additional variables produced by the model, if not done elsewhere in the code, using the call to \textit{iom\_put}. 588 699 \end{itemize} 589 590 700 591 701 \section{The Offline Option} … … 596 706 %------------------------------------------------------------------------------------------------------------- 597 707 598 Coupling passive tracers offline with NEMO requires precomputed physical fields from OGCM. Those fields are read from files and interpolated on-the-fly at each model time step 708 Coupling passive tracers offline with NEMO requires precomputed physical fields from OGCM. 709 Those fields are read from files and interpolated on-the-fly at each model time step 599 710 At least the following dynamical parameters should be absolutely passed to the transport : ocean velocities, temperature, salinity, mixed layer depth and for ecosystem models like PISCES, sea ice concentration, short wave radiation at the ocean surface, wind speed (or at least, wind stress). 600 711 The so-called offline mode is useful since it has lower computational costs for example to perform very longer simulations - about 3000 years - to reach equilibrium of CO2 sinks for climate-carbon studies. 601 712 602 The offline interface is located in the code repository : \path{<repository>/src/OFF/}. It is activated by adding the CPP key \textit{key\_offline} to the CPP keys list. There are two specifics routines for the Offline code : 713 The offline interface is located in the code repository : \path{<repository>/src/OFF/}. 714 It is activated by adding the CPP key \textit{key\_offline} to the CPP keys list. 715 There are two specifics routines for the Offline code : 603 716 604 717 \begin{itemize} … … 606 719 \item \textit{nemogcm.F90} : a degraded version of the main nemogcm.F90 code of NEMO to manage the time-stepping 607 720 \end{itemize} 608 609 721 610 722 %- -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/global/document.tex
r14328 r14676 7 7 8 8 %% Layout 9 %\documentclass[fontsize=10pt,twoside,abstract,draft]{scrreprt}10 \documentclass[fontsize=10pt,twoside,abstract ]{scrreprt}9 \documentclass[fontsize=10pt,twoside,abstract,draft]{scrreprt} 10 %\documentclass[fontsize=10pt,twoside,abstract ]{scrreprt} 11 11 12 12 %% Overall configuration -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/global/highlighting.tex
r14328 r14676 30 30 %% Namelists inclusion 31 31 \newcommand{\nlst}[1]{\forfile{../../../namelists/#1}} 32 %\newcommand{\nlst}[1]{ 33 % \begin{listing} 34 % \newmintedfile{fortran}{../../../namelists/#1} 35 % \caption{\forcode{}} 36 % \label{lst:#1} 37 % \end{listing} 38 %} 32 -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/global/latexmk.pl
r14328 r14676 9 9 10 10 ## Custom cmds 11 set_tex_cmds('-shell-escape -interaction=batchmode'); 12 #set_tex_cmds('-shell-escape'); 13 $makeindex = 'makeindex -s %R.ist %O -o %D %S'; 11 set_tex_cmds('-shell-escape -file-line-error -interaction=nonstopmode'); 12 #set_tex_cmds('-shell-escape -file-line-error'); 13 $makeindex = 'makeindex %O -s %R.ist -o %D %S'; 14 ## %D: Destination file (.ind for index) 15 ## %O: Options 16 ## %R: Root filename (${model}_manual) 17 ## %S: Source file (.idx for index) -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/global/new_cmds.tex
r14328 r14676 57 57 } 58 58 59 %% Workaround for \listoffigures issue 60 \DeclareRobustCommand{\triad}[6]{ 61 \ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}} 62 } 59 %% Custom aliases 60 \newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 61 \newcommand{\rML}[1][i]{\ensuremath{_{\mathrm{ML}\,#1}}} 62 \newcommand{\rMLt}[1][i]{\tilde{r}_{\mathrm{ML}\,#1}} 63 \newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 64 \newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}} 65 \newcommand{\triadt}[5]{\ensuremath{{}_{#1}^{#2}{\tilde{\mathbb{#3}}}_{#4}^{\,#5}}} 66 \newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}} 67 \newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 63 68 64 69 %% New command for ToC (?) -
NEMO/branches/2020/dev_14237_KERNEL-01_IMMERSE_SEAMOUNT/doc/latex/global/styles.tex
r14328 r14676 10 10 %% Cover page 11 11 \backgroundsetup{ 12 firstpage=true,scale =1, 13 angle =0 ,opacity=1, 12 firstpage=true,scale=1,angle=0,opacity=1, 14 13 contents ={ 15 14 \begin{tikzpicture}[remember picture,overlay] … … 22 21 %\pagestyle{scrheadings} 23 22 %\renewcommand{\chapterpagestyle}{empty} 24 \renewcommand{\chaptermark}[1]{ \markboth{#1}{}} %% Convert mark to lowercase23 \renewcommand{\chaptermark}[1]{\markboth{ #1}{}} %% Convert mark to lowercase 25 24 \renewcommand{\sectionmark}[1]{\markright{#1}{}} %% " "" "" " 26 25 \ohead{} %% Clear default headings … … 37 36 %% Cross-referencing 38 37 \hypersetup{ 39 pdftitle=\hdg , 40 pdfauthor=Gurvan Madec and NEMO System Team , 41 pdfsubject=Reference manual of NEMO modelling framework, 42 pdfkeywords=ocean circulation modelling , 43 colorlinks , 44 allcolors=manclr 38 pdftitle=\hdg,pdfauthor=Gurvan Madec and NEMO System Team, 39 pdfsubject=Reference manual of NEMO modelling framework,pdfkeywords=ocean circulation modelling, 40 colorlinks,allcolors=manclr 45 41 } 46 42 \renewcommand{\appendixautorefname}{appendix} %% `\autoref` uncapitalization … … 63 59 %% Catcodes (between `\makeatletter` and `\makeatother`) 64 60 \makeatletter 65 66 %\global\let\tikz@ensure@dollar@catcode=\relax %% Prevent error with tikz and namelist inclusion67 61 68 62 %% Apply manual color for chap. headings (original snippets from fncychap.sty) … … 93 87 } 94 88 95 %% Temporary fix?96 %\def\set@curr@file#1{97 % \begingroup98 % \escapechar\m@ne99 % \xdef\@curr@file{\expandafter\string\csname #1\endcsname}100 % \endgroup101 %}102 %\def\quote@name#1{"\quote@@name#1\@gobble""}103 %\def\quote@@name#1"{#1\quote@@name}104 %\def\unquote@name#1{\quote@@name#1\@gobble"}105 106 89 \makeatother
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