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doc/latex/NEMO/subfiles/chap_DIA.tex
View file @ 478dca63
......@@ -1464,7 +1464,7 @@ In particular, options associated with \np{ln_dyn_mxl}{ln\_dyn\_mxl}, \np{ln_vor
and none of the options have been tested with variable volume (\ie\ \np[=.true.]{ln_linssh}{ln\_linssh}).
%% =================================================================================================
\section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})]{FLO: On-Line Floats trajectories (\protect\key{floats})}
\section[FLO: On-Line Floats trajectories]{FLO: On-Line Floats trajectories}
\label{sec:DIA_FLO}
\begin{listing}
......@@ -1475,7 +1475,8 @@ and none of the options have been tested with variable volume (\ie\ \np[=.true.]
The on-line computation of floats advected either by the three dimensional velocity field or constraint to
remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project.
Options are defined by \nam{flo}{flo} namelist variables.
Options are defined by \nam{flo}{flo} namelist variables and the interface is activated by setting \np{ln_float = .true.}.
The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option),
or on a $4^th$ Runge-Hutta algorithm (\np[=.true.]{ln_flork4}{ln\_flork4}).
Note that the \cite{blanke.raynaud_JPO97} algorithm have the advantage of providing trajectories which
......@@ -1567,7 +1568,7 @@ Here it is an example of specification to put in files description section:
\end{xmllines}
%% =================================================================================================
\section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})}
\section[Transports across sections]{Transports across sections}
\label{sec:DIA_diag_dct}
\begin{listing}
......@@ -1577,7 +1578,7 @@ Here it is an example of specification to put in files description section:
\end{listing}
A module is available to compute the transport of volume, heat and salt through sections.
This diagnostic is actived with \key{diadct}.
This diagnostic is actived with \np{ln_diadct = .true.}.
Each section is defined by the coordinates of its 2 extremities.
The pathways between them are contructed using tools which can be found in \texttt{tools/SECTIONS\_DIADCT}
......
doc/latex/NEMO/subfiles/chap_DYN.tex
View file @ 478dca63
......@@ -1057,32 +1057,6 @@ the filter \autoref{eq:DYN_spg_ts_sshf} was found to be more conservative, and s
} %%end gm comment (copy of griffies book)
%% =================================================================================================
\subsection{Filtered free surface (\forcode{dynspg_flt?})}
\label{subsec:DYN_spg_fltp}
The filtered formulation follows the \citet{roullet.madec_JGR00} implementation.
The extra term introduced in the equations (see \autoref{subsec:MB_free_surface}) is solved implicitly.
The elliptic solvers available in the code are documented in \autoref{chap:MISC}.
%% gm %%======>>>> given here the discrete eqs provided to the solver
\cmtgm{ %%% copy from chap-model basics
\[
% \label{eq:DYN_spg_flt}
\frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= {\mathrm {\mathbf M}}
- g \nabla \left( \tilde{\rho} \ \eta \right)
- g \ T_c \nabla \left( \widetilde{\rho} \ \partial_t \eta \right)
\]
where $T_c$, is a parameter with dimensions of time which characterizes the force,
$\widetilde{\rho} = \rho / \rho_o$ is the dimensionless density,
and $\mathrm {\mathbf M}$ represents the collected contributions of the Coriolis, hydrostatic pressure gradient,
non-linear and viscous terms in \autoref{eq:MB_dyn}.
} %end cmtgm
Note that in the linear free surface formulation (\texttt{vvl?} not defined),
the ocean depth is time-independent and so is the matrix to be inverted.
It is computed once and for all and applies to all ocean time steps.
%% =================================================================================================
\section[Lateral diffusion term and operators (\textit{dynldf.F90})]{Lateral diffusion term and operators (\protect\mdl{dynldf})}
\label{sec:DYN_ldf}
......
doc/latex/NEMO/subfiles/chap_SBC.tex
View file @ 478dca63
......@@ -1004,7 +1004,7 @@ When an external wave model (see \autoref{sec:SBC_wave}) is used in the coupled
The namelist above allows control of various aspects of the coupling fields (particularly for vectors) and
now allows for any coupling fields to have multiple sea ice categories (as required by LIM3 and CICE).
now allows for any coupling fields to have multiple sea ice categories (as required by SI3).
When indicating a multi-category coupling field in \nam{sbc_cpl}{sbc\_cpl}, the number of categories will be determined by
the number used in the sea ice model.
In some limited cases, it may be possible to specify single category coupling fields even when
......@@ -2034,45 +2034,11 @@ the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc}{sbc}
This model computes the ice-ocean fluxes,
that are combined with the air-sea fluxes using the ice fraction of each model cell to
provide the surface averaged ocean fluxes.
Note that the activation of a sea-ice model is done by defining a CPP key (\key{si3} or \key{cice}).
Note that the activation of a sea-ice model is done by defining a CPP key (\key{si3}).
The activation automatically overwrites the read value of nn\_ice to its appropriate value
(\ie\ $2$ for SI3 or $3$ for CICE).
(\ie\ $2$ for SI3).
\end{description}
% {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?}
%GS: ocean-ice (SI3) interface is not located in SBC directory anymore, so it should be included in SI3 doc
%% =================================================================================================
\subsection[Interface to CICE (\textit{sbcice\_cice.F90})]{Interface to CICE (\protect\mdl{sbcice\_cice})}
\label{subsec:SBC_cice}
It is possible to couple a regional or global \NEMO\ configuration (without AGRIF)
to the CICE sea-ice model by using \key{cice}.
The CICE code can be obtained from \href{http://oceans11.lanl.gov/trac/CICE/}{LANL} and
the additional 'hadgem3' drivers will be required, even with the latest code release.
Input grid files consistent with those used in \NEMO\ will also be needed,
and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used
(seek advice from UKMO if necessary).
Currently, the code is only designed to work when using the NCAR forcing option for \NEMO\ %GS: still true ?
(with \textit{calc\_strair}\forcode{=.true.} and \textit{calc\_Tsfc}\forcode{=.true.} in the CICE name-list),
or alternatively when \NEMO\ is coupled to the HadGAM3 atmosphere model
(with \textit{calc\_strair}\forcode{=.false.} and \textit{calc\_Tsfc}\forcode{=false}).
The code is intended to be used with \np{nn_fsbc}{nn\_fsbc} set to 1
(although coupling ocean and ice less frequently should work,
it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly -
the user should check that results are not significantly different to the standard case).
There are two options for the technical coupling between \NEMO\ and CICE.
The standard version allows complete flexibility for the domain decompositions in the individual models,
but this is at the expense of global gather and scatter operations in the coupling which
become very expensive on larger numbers of processors.
The alternative option (using \key{nemocice\_decomp} for both \NEMO\ and CICE) ensures that
the domain decomposition is identical in both models (provided domain parameters are set appropriately,
and \textit{processor\_shape~=~square-ice} and \textit{distribution\_wght~=~block} in the CICE name-list) and
allows much more efficient direct coupling on individual processors.
This solution scales much better although it is at the expense of having more idle CICE processors in areas where
there is no sea ice.
%% =================================================================================================
\subsection[Freshwater budget control (\textit{sbcfwb.F90})]{Freshwater budget control (\protect\mdl{sbcfwb})}
\label{subsec:SBC_fwb}
......
doc/latex/NEMO/subfiles/chap_cfgs.tex
View file @ 478dca63
......@@ -41,13 +41,13 @@ Configuration is defined manually through the \nam{cfg}{cfg} namelist variables.
\end{listing}
%% =================================================================================================
\section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})]{C1D: 1D Water column model (\protect\key{c1d})}
\section[C1D: 1D Water column model]{C1D: 1D Water column model}
\label{sec:CFGS_c1d}
The 1D model option simulates a stand alone water column within the 3D \NEMO\ system.
It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model.
It is set up by defining the position of the 1D water column in the grid
(see \path{./cfgs/SHARED/namelist\_ref}).
(see \path{./cfgs/SHARED/namelist_ref}).
The 1D model is a very useful tool
\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes;
\textit{(b)} to investigate suitable parameterisations of unresolved turbulence
......@@ -61,7 +61,7 @@ a 3x3 domain with 75 vertical levels.
The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
and second, the two components of the velocity are moved on a $T$-point.
Therefore, defining \key{c1d} changes some things in the code behaviour:
Therefore, defining \np{ln_c1d = .true.} changes some things in the code behaviour:
\begin{enumerate}
\item a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
both lateral tendancy terms and lateral physics are not called;
......@@ -84,7 +84,7 @@ the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE
An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
The domain of ORCA2 configuration is defined in \textit{ORCA\_R2\_zps\_domcfg.nc} file,
this file is available in tar file on the \NEMO\ community zenodo platform: \\
https://doi.org/10.5281/zenodo.2640723
https://doi.org/10.5281/zenodo.3767939
In this namelist\_cfg the name of domain input file is set in \nam{cfg}{cfg} block of namelist.
......@@ -202,11 +202,10 @@ This \citet{large.yeager_trpt04} dataset is available through
the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
The "normal year" of \citet{large.yeager_trpt04} has been chosen of the \NEMO\ distribution since release v3.3.
ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined).
This is available as the AGRIF\_DEMO configuration that can be found in the \path{./cfgs/AGRIF_DEMO/} directory.
A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
sponge layers at open boundaries.
ORCA\_R2 pre-defined configuration can also be run with multiple online nested zooms, \ie\ using AGRIF with \key{agrif} defined.
This is available in the AGRIF\_DEMO configuration (located in \path{./cfgs/AGRIF_DEMO/} directory) that
accounts for two nested refinements over the Arctic region and a third zoom over the central Pacific area
using a two-ways coupling procedure.
%% =================================================================================================
\section{GYRE family: double gyre basin}
......@@ -289,7 +288,7 @@ namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
a regular lat-lon grid at approximately 12km horizontal resolution.
The appropriate \textit{\&namcfg} namelist is available in \path{./cfgs/AMM12/EXPREF/namelist\_cfg}.
The appropriate \textit{\&namcfg} namelist is available in \path{./cfgs/AMM12/EXPREF/namelist_cfg}.
It is used to build the correct dimensions of the AMM domain.
This configuration tests several features of \NEMO\ functionality specific to the shelf seas.
......
doc/latex/NEMO/subfiles/chap_misc.tex
View file @ 478dca63
......@@ -198,8 +198,8 @@ open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran
then the formally correct setting for \np{open_ocean_jstart}{open\_ocean\_jstart} is 41. Using this value as
the first row to be read will result in a 362x292 domain which is the same size as the
original ORCA1 domain. Thus the extended domain configuration file can be used with all
the original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav =
.false.}). Full instructions for achieving this are:
the original input files for ORCA1 if the ice cavities are not active (\np{ln_isfcav =
.false.}). Full instructions for achieving this are:
\begin{itemize}
\item Add the new attribute to any input files requiring a j-row offset, i.e:
......
doc/latex/TOP/main/abstract.tex
View file @ 478dca63
......@@ -9,7 +9,7 @@ It is intended to be a flexible tool for studying the on/offline oceanic tracers
the biogeochemical processes (``green ocean''),
as well as its interactions with the other components of the Earth climate system over
a wide range of space and time scales.
\TOP\ is interfaced with the \NEMO\ ocean engine, and,
\TOP\ is directly interfaced with the \NEMO\ ocean engine, and,
via the \href{http://portal.enes.org/oasis}{OASIS} coupler,
with several atmospheric general circulation models.
%It also supports two-way grid embedding by means of the \href{http://agrif.imag.fr}{AGRIF} software.
......
doc/latex/TOP/main/bibliography.bib
View file @ 478dca63
......@@ -305,18 +305,17 @@
}
@Manual{ nemo_manual,
author = {Madec Gurvan and NEMO System Team},
author = {{NEMO System Team}},
title = {NEMO ocean engine},
organization = {NEMO Consortium},
journal = {Notes du Pôle de modélisation de l\'Institut
Pierre-Simon Laplace (IPSL)},
journal = {Scientific Notes of Climate Modelling Center},
institution = {Institut Pierre-Simon Laplace (IPSL)},
issn = {1288-1619},
number = {27},
publisher = {Zenodo},
doi = {10.5281/zenodo.1464816},
url = {https://zenodo.org/record/1464816},
edition = {TBD},
year = {TBD}
year = {2022}
}
@Article{ meunier_2014,
......@@ -679,4 +678,45 @@
publisher = {Elsevier BV}
}
@Article{ bfm_nemo_coupling,
author = {Lovato, T. and Vichi, M. and Butenschön, M.},
title = {Coupling BFM with Ocean models: the NEMO model V3.6
(Nucleus for the European Modelling of the Ocean)},
journal = {BFM Report series},
number = 2,
year = 2020,
url = {https://bfm-community.github.io/www.bfm-community.eu/files/bfm-nemo-manual_r1.1_202006.pdf}
}
@article{ morel_1988,
author = {Morel, Andr{\'e}},
title = {Optical modeling of the upper ocean in relation to its biogenous matter content (case I waters)},
journal = {Journal of geophysical research: oceans},
volume = {93},
number = {C9},
pages = {10749--10768},
year = {1988},
publisher = {Wiley Online Library}
}
@article{ lengaigne_2007,
author = {Lengaigne, Matthieu and Menkes, Christophe and Aumont, Olivier and Gorgues, Thomas and Bopp, Laurent and Andr{\'e}, Jean-Michel and Madec, Gurvan},
title = {Influence of the oceanic biology on the tropical Pacific climate in a coupled general circulation model},
journal = {Climate Dynamics},
volume = {28},
number = {5},
pages = {503--516},
year = {2007},
publisher = {Springer}
}
@article{ morel_2001,
author = {Morel, Andr{\'e} and Maritorena, St{\'e}phane},
title = {Bio-optical properties of oceanic waters: A reappraisal},
journal = {Journal of Geophysical Research: Oceans},
volume = {106},
number = {C4},
pages = {7163--7180},
year = {2001},
publisher = {Wiley Online Library}
}
doc/latex/TOP/main/chapters.tex
View file @ 478dca63
\subfile{../subfiles/model_structure}
\subfile{../subfiles/model_description}
\subfile{../subfiles/model_setup}
\subfile{../subfiles/miscellaneous}
doc/latex/TOP/main/introduction.tex
View file @ 478dca63
......@@ -12,13 +12,13 @@ It includes three independent components :
\item a transport code TRP sharing 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
\item sources and sinks - SMS - models that can be typically biogeochemical, biological or radioactive
\item an offline option which is a simplified OPA 9 model using fields of physical variables that were previously stored on disk
\item an offline transport interface, which is a simplified version of the NEMO core workflow that read a set of physical fields previously stored on disk
\end{itemize}
There are two ways of coupling TOP to the dynamics :
\begin{itemize}
\item \textit{online coupling} : the evolution of passive tracers is computed along with the dynamics
\item \textit{online coupling} : the evolution of passive tracers is computed along with the ocean physical dynamics
\item \textit{offline coupling} : the physical variable fields are read from files and interpolated at each model time step, with no constraints on the temporal sampling in the input files
\end{itemize}
......@@ -28,14 +28,5 @@ TOP is designed to handle multiple oceanic tracers through a modular approach an
\item the ocean water age module (AGE) tracks down the time-dependent spread of surface waters into the ocean interior
\item inorganic (\eg, CFCs, SF6) and radiocarbon (C14) passive tracers can be modeled to assess ocean absorption timescales of anthropogenic emissions and further address water masses ventilation
\item a built-in biogeochemical model (PISCES) to simulate lower trophic levels ecosystem dynamics in the global ocean
\item a prototype tracer module (MY\_TRC) to enable user-defined cases or the coupling with alternative biogeochemical models (\eg, BFM, MEDUSA, ERSEM, BFM, ECO3M)
\item a prototype tracer module (MY\_TRC) to enable user-defined cases or the coupling with alternative biogeochemical models (\eg, BFM, MEDUSA, ERSEM, ECO3M)
\end{itemize}
\begin{figure}[ht]
\begin{center}
\vspace{0cm}
\includegraphics[width=0.80\textwidth]{Fig_TOP_design}
\caption{Schematic view of the NEMO-TOP component}
\label{topdesign}
\end{center}
\end{figure}
doc/latex/TOP/namelists/nam_trc_age 0 → 100644
View file @ 478dca63
! Variable setting
ctrcnm (jp_age) = 'Age'
ctrcln (jp_age) = 'Sea water age since surface contact'
ctrcun (jp_age) = 'year'
ln_trc_ini(jp_age) = .false.
ln_trc_sbc(jp_age) = .false.
ln_trc_cbc(jp_age) = .false.
ln_trc_obc(jp_age) = .false.
doc/latex/TOP/namelists/namdta_dyn_linssh 0 → 100644
View file @ 478dca63
!-----------------------------------------------------------------------
&namdta_dyn ! offline ocean input files (OFF_SRC only)
!-----------------------------------------------------------------------
cn_dir = './' ! root directory for the ocean data location
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_tem = 'dyna_grid_T' , 120. , 'votemper' , .true. , .true. , 'yearly'
sn_sal = 'dyna_grid_T' , 120. , 'vosaline' , .true. , .true. , 'yearly'
sn_mld = 'dyna_grid_T' , 120. , 'somixhgt' , .true. , .true. , 'yearly'
sn_emp = 'dyna_grid_T' , 120. , 'sowaflup' , .true. , .true. , 'yearly'
sn_fmf = 'dyna_grid_T' , 120. , 'iowaflup' , .true. , .true. , 'yearly'
sn_ice = 'dyna_grid_T' , 120. , 'soicecov' , .true. , .true. , 'yearly'
sn_qsr = 'dyna_grid_T' , 120. , 'soshfldo' , .true. , .true. , 'yearly'
sn_wnd = 'dyna_grid_T' , 120. , 'sowindsp' , .true. , .true. , 'yearly'
sn_uwd = 'dyna_grid_U' , 120. , 'uocetr_eff', .true. , .true. , 'yearly'
sn_vwd = 'dyna_grid_V' , 120. , 'vocetr_eff', .true. , .true. , 'yearly'
sn_wwd = 'dyna_grid_W' , 120. , 'wocetr_eff', .true. , .true. , 'yearly'
sn_avt = 'dyna_grid_W' , 120. , 'voddmavs' , .true. , .true. , 'yearly'
sn_ubl = 'dyna_grid_U' , 120. , 'sobblcox' , .true. , .true. , 'yearly'
sn_vbl = 'dyna_grid_V' , 120. , 'sobblcoy' , .true. , .true. , 'yearly'
/
doc/latex/TOP/namelists/namdta_dyn_nolinssh 0 → 100644
View file @ 478dca63
!-----------------------------------------------------------------------
&namdta_dyn ! offline ocean input files (OFF_SRC only)
!-----------------------------------------------------------------------
ln_dynrnf = .true. ! runoffs option enabled (T) or not (F)
ln_dynrnf_depth = .false. ! runoffs is spread in vertical (T) or not (F)
!
cn_dir = './' ! root directory for the ocean data location
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_tem = 'dyna_grid_T' , 120. , 'thetao' , .true. , .true. , 'yearly'
sn_sal = 'dyna_grid_T' , 120. , 'so' , .true. , .true. , 'yearly'
sn_div = 'dyna_grid_T' , 120. , 'hdivtr' , .true. , .true. , 'yearly'
sn_mld = 'dyna_grid_T' , 120. , 'mldr10_1' , .true. , .true. , 'yearly'
sn_emp = 'dyna_grid_T' , 120. , 'wfo' , .true. , .true. , 'yearly'
sn_empb = 'dyna_grid_T' , 120. , 'wfob' , .true. , .true. , 'yearly'
sn_fmf = 'dyna_grid_T' , 120. , 'fmmflx' , .true. , .true. , 'yearly'
sn_rnf = 'dyna_grid_T' , 120. , 'runoffs' , .true. , .true. , 'yearly'
sn_ice = 'dyna_grid_T' , 120. , 'siconc' , .true. , .true. , 'yearly'
sn_qsr = 'dyna_grid_T' , 120. , 'rsntds' , .true. , .true. , 'yearly'
sn_wnd = 'dyna_grid_T' , 120. , 'windsp' , .true. , .true. , 'yearly'
sn_uwd = 'dyna_grid_U' , 120. , 'uocetr_eff', .true. , .true. , 'yearly'
sn_vwd = 'dyna_grid_V' , 120. , 'vocetr_eff', .true. , .true. , 'yearly'
sn_wwd = 'dyna_grid_W' , 120. , 'wocetr_eff', .true. , .true. , 'yearly'
sn_avt = 'dyna_grid_W' , 120. , 'difvsolog' , .true. , .true. , 'yearly'
sn_ubl = 'dyna_grid_U' , 120. , 'ahu_bbl' , .true. , .true. , 'yearly'
sn_vbl = 'dyna_grid_V' , 120. , 'ahv_bbl' , .true. , .true. , 'yearly'
/
doc/latex/TOP/namelists/namisf_cfg_eORCA1 0 → 100644
View file @ 478dca63
!-----------------------------------------------------------------------
&namisf ! Top boundary layer (ISF) (default: OFF)
!-----------------------------------------------------------------------
!
! ---------------- ice shelf melt formulation -------------------------------
!
ln_isf = .true. ! activate ice shelf module
!
! ---------------- cavities opened -------------------------------
!
ln_isfcav_mlt = .false. ! ice shelf melting into the cavity (need ln_isfcav = .true. in domain_cfg.nc)
cn_isfcav_mlt = '3eq' ! ice shelf melting formulation (spe/2eq/3eq/oasis)
! ! spe = fwfisf is read from a forcing field
! ! 2eq = ISOMIP like: 2 equations formulation (Hunter et al., 2006 for a short description)
! ! 3eq = ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2016 for a short description
rn_htbl = 30. ! thickness of the top boundary layer (Losh et al. 2008)
! ! 0 => thickness of the tbl = thickness of the first wet cell
!
!* 'spe' and 'oasis' case
!---------------------------------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_isfcav_fwf = 'isfmlt_cav', -12. , 'fwflisf' , .false. , .true. , 'yearly'
!
! ---------------- cavities parametrised -------------------------------
!
ln_isfpar_mlt = .true. ! ice shelf melting parametrised
cn_isfpar_mlt = 'spe' ! ice shelf melting parametrisation (spe/bg03/oasis)
! ! spe = fwfisf is read from a forcing field
!
!---------------------------------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_isfpar_zmax = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sodepmax_isf' , .false. , .true. , 'yearly'
sn_isfpar_zmin = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sodepmin_isf' , .false. , .true. , 'yearly'
!* 'spe' and 'oasis' case
sn_isfpar_fwf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sornfisf', .false. , .true. , 'yearly'
doc/latex/TOP/namelists/namsbc_rnf_cfg_eORCA1 0 → 100644
View file @ 478dca63
!-----------------------------------------------------------------------
&namsbc_rnf ! runoffs (ln_rnf =T)
!-----------------------------------------------------------------------
ln_rnf_mouth = .false. ! specific treatment at rivers mouths
rn_hrnf = 15.e0 ! depth over which enhanced vertical mixing is used (ln_rnf_mouth=T)
rn_avt_rnf = 1.e-3 ! value of the additional vertical mixing coef. [m2/s] (ln_rnf_mouth=T)
rn_rfact = 1.e0 ! multiplicative factor for runoff
ln_rnf_icb = .true. ! read iceberg flux
cn_dir = './' ! root directory for the location of the runoff files
!---------------------------------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_rnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', -1 , 'sorunoff', .true. , .true. , 'yearly'
sn_i_rnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', -1 , 'Icb_flux', .true. , .true. , 'yearly'
sn_cnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', 0 , 'socoefr' , .false. , .true. , 'yearly'
sn_s_rnf = 'runoffs' , 24. , 'rosaline', .true. , .true. , 'yearly'
sn_t_rnf = 'runoffs' , 24. , 'rotemper', .true. , .true. , 'yearly'
sn_dep_rnf = 'runoffs' , 0. , 'rodepth' , .false. , .true. , 'yearly'
doc/latex/TOP/namelists/namtrc_ais_cfg 0 → 100644
View file @ 478dca63
!-----------------------------------------------------------------------
&namtrc_ais ! Representation of Antarctic Ice Sheet tracers supply
!-----------------------------------------------------------------------
rn_trafac(3) = 4.476e-07 ! ( 0.5e-3 / 55.85 * 0.05 )
!
nn_ais_tr = 1 ! tracer concentration in iceberg and ice shelf
! = 0 (null concentrations)
! = 1 prescribed concentrations
rn_icbdep = 120. ! Mean underwater depth of iceberg (m)
doc/latex/TOP/namelists/namtrc_bc_cfg 0 → 100644
View file @ 478dca63
!----------------------------------------------------------------------
&namtrc_bc ! data for boundary conditions
!-----------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_trcsbc(2) = 'dust.orca.new' , -1 , 'dustfer' , .true. , .true. , 'yearly'
sn_trcsbc(3) = 'ndeposition.orca', -12 , 'ndep' , .false. , .true. , 'yearly'
rn_trsfac(2) = 6.266e-04 ! Multiplicative factor
rn_trsfac(3) = 5.4464e-01 !
!
sn_trccbc(1) = 'river.orca' , -12 , 'riverdic' , .true. , .true. , 'yearly'
sn_trccbc(2) = 'river.orca' , -12 , 'riverdfe' , .true. , .true. , 'yearly'
sn_trccbc(3) = 'river.orca' , -12 , 'riverdin' , .true. , .true. , 'yearly'
rn_trcfac(1) = 1.0 ! Multiplicative factor
rn_trcfac(2) = 1.0 !
rn_trcfac(3) = 1.0 !
rn_cbc_time = 3.1536e+7 ! Time scaling factor for CBC data (seconds in a year)
doc/latex/TOP/namelists/namtrc_cfg 0 → 100644
View file @ 478dca63
!-----------------------------------------------------------------------
&namtrc ! tracers definition
!-----------------------------------------------------------------------
jp_bgc = 24
!
ln_pisces = .true.
ln_my_trc = .false.
ln_age = .false.
ln_cfc11 = .false.
ln_cfc12 = .false.
ln_c14 = .false.
!
!
ln_trcdta = .true. ! Initialisation from data input file (T) or not (F)
ln_trcdmp = .false. ! add a damping termn (T) or not (F)
ln_trcdmp_clo = .false. ! damping term (T) or not (F) on closed seas
ln_trcbc = .true. ! Surface, Lateral or Open Boundaries conditions
ln_trcais = .true. ! Antarctic Ice Sheet nutrient supply
! ! ! ! ! !
! ! name ! title of the field ! units ! init ! sbc ! cbc ! obc ! ais
sn_tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mol-C/L' , .true. , .false., .true. , .false. , .false.
sn_tracer(2) = 'Fer ' , 'Dissolved Iron Concentration ', 'mol-C/L' , .true. , .true. , .true. , .false. , .true.
sn_tracer(3) = 'NO3 ' , 'Nitrates Concentration ', 'mol-C/L' , .true. , .true. , .true. , .false. , .false.
sn_tracer(4) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false.
doc/latex/TOP/namelists/namtrc_dta_cfg 0 → 100644
View file @ 478dca63
!-----------------------------------------------------------------------
&namtrc_dta ! Initialisation from data input file
!-----------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_trcdta(1) = 'data_DIC_nomask.nc', -12 , 'PiDIC' , .false. , .true. , 'yearly' ,
sn_trcdta(2) = 'data_FER_nomask.nc', -1 , 'Fer' , .true. , .true. , 'yearly' ,
sn_trcdta(3) = 'data_NO3_nomask.nc', -1 , 'NO3' , .true. , .true. , 'yearly' ,
!
rn_trfac(1) = 1.028e-06 ! multiplicative factor
rn_trfac(2) = 1.0e-06 ! - - - -
rn_trfac(3) = 7.6e-06 ! - - - -
doc/latex/TOP/subfiles/miscellaneous.tex deleted 100644 → 0
View file @ 2c2c8a48
\documentclass[../main/TOP_manual]{subfiles}
\begin{document}
\chapter{Miscellaneous}
\section{TOP synthetic Workflow}
A synthetic description of the TOP interface workflow is given below to summarize the steps involved in the computation of biogeochemical and physical trends and their time integration and outputs, by reporting also the principal Fortran subroutine herein involved.
%\begin{figure}[!h]
% \centering
% \includegraphics[width=0.80\textwidth]{Top_FlowChart}
% \caption{Schematic view of NEMO-TOP flowchart}
% \label{img_cfcatm}
%\end{figure}
\begin{minted}{bash}
nemogcm
!
nemo_init ! NEMO General Initialisations
!
trc_init ! TOP Initialisations
!
stp() ! NEMO Time-stepping
!
trc_stp() ! TOP time-stepping
!
trc_wri() ! I/O manager : Output of passive tracers
trc_sms() ! Sinks and sources program manager
trc_trp() ! Transport of passive tracers
trc_rst_wri() ! Write tracer restart file
trd_mxl_trc() ! trends: Mixed-layer
\end{minted}
\subsection{Model initialization (./src/TOP/trcini.F90)}
This module consists on inital set up of passive tracers variables and parameters : read the namelist, set initial tracer fields (either read restart or read data or analytical formulation and specific initailisation in each SMS module ( analytical initialisation of tracers or constant values )
\begin{minted}{bash}
trc_init ! TOP Initialisations
!
IF( PISCES ) trc_ini_pisces() ! PISCES bio model
IF( MY_TRC) trc_ini_my_trc() ! MY_TRC model
IF( CFCs ) trc_ini_cfc () ! CFCs
IF( C14 ) trc_ini_c14 () ! C14 model
IF( AGE ) trc_ini_age () ! AGE tracer
!
IF( REST ) trc_rst_read() ! Restart from a file
ELSE trc_dta() ! Initialisation from data
\end{minted}
\subsection{BGC trends computation (./src/TOP/trcsms.F90)}
This is the main module where the passive tracers source minus sinks of each TOP sub-module is managed.
\begin{minted}{bash}
trc_sms() ! Sinks and sources prooram manager
!
IF( PISCES ) trc_sms_pisces() ! main program of PISCES
IF( CFCs ) trc_sms_cfc() ! surface fluxes of CFC
IF( C14 ) trc_sms_c14() ! surface fluxes of C14
IF( AGE ) trc_sms_age() ! Age tracer
IF( MY_TRC) trc_sms_my_trc() ! MY_TRC tracers
\end{minted}
\subsection{Physical trends computation (./src/TOP/TRP/trctrp.F90)}
This is the main module where the passive tracers transport is managed. All the physical trends is calculated ( advective \& diffusive trends, surface BC from freshwater or external inputs )
\begin{minted}{bash}
trc_trp() ! Transport of passive tracers
!
trc_sbc() ! Surface boundary condition of freshwater flux
trc_bc() ! Surface and lateral Boundary Conditions
trc_ais() ! Tracers from Antarctic Ice Sheet (icb, isf)
trc_bbl() ! Advective (and/or diffusive) bottom boundary layer scheme
trc_dmp() ! Internal damping trends
trc_bdy() ! BDY damping trends
trc_adv() ! Horizontal & Vertical advection
trc_ldf() ! Lateral mixing
trc_zdf() ! Vert. mixing & after tracer
trc_atf() ! Time filtering of "now" tracer fields
trc_rad() ! Correct artificial negative concentrations
\end{minted}
\subsection{Outputs (./src/TOP/TRP/trcwri.F90)}
This is the main module where the passive tracer outputs of each TOP sub-module is managed using the I/O library XIOS.
\begin{minted}{bash}
trc_wri() ! I/O manager : Output of passive tracers
!
IF( PISCES ) trc_wri_pisces() ! Output of PISCES diagnostics
IF( CFCs ) trc_wri_cfc() ! Output of Cfcs diagnostics
IF( C14 ) trc_wri_c14() ! surface fluxes of C14
IF( AGE ) trc_wri_age() ! Age tracer
IF( MY_TRC ) trc_wri_my_trc() ! MY_TRC tracers
\end{minted}
\section{Coupling an external BGC model using NEMO framework}
The coupling with an external BGC model through the NEMO compilation framework can be achieved in different ways according to the degree of coding complexity of the Biogeochemical model, like e.g., the whole code is made only by one file or it has multiple modules and interfaces spread across several subfolders.\\ \\
Beside the 6 core files of MY\_TRC module, see (see \label{Mytrc}, let's assume an external BGC model named \textit{"MYBGC"} and constituted by a rather essential coding structure, likely few Fortran files. The new coupled configuration name is NEMO\_MYBGC. \\ \\
The best solution is to have all files (the modified MY\_TRC routines and the BGC model ones) placed in a unique folder with root \path{<MYBGCPATH>} and to use the \textit{makenemo} external readdressing of MY\_SRC folder. \\ \\
The coupled configuration listed in \textbf{cfg.txt} will look like
\begin{minted}{bash}
NEMO_MYBGC OPA_SRC TOP_SRC
\end{minted}
and the related cpp\_MYBGC.fcm content will be
%
\begin{minted}{bash}
bld::tool::fppkeys key_xios key_top
\end{minted}
The compilation with \textit{makenemo} will be executed through the following syntax
\begin{minted}{bash}
makenemo -n NEMO_MYBGC -m <arch_my_machine> -j 8 -e <MYBGCPATH>
\end{minted}
The makenemo feature \textit{-e} was introduced to readdress at compilation time the standard MY\_SRC folder (usually found in NEMO configurations) with a user defined external one. \\ \\
The compilation of more articulated BGC model code \& infrastructure, like in the case of BFM (BFM-NEMO coupling manual), requires some additional features. \\ \\
As before, let's assume a coupled configuration name NEMO\_MYBGC, but in this case MYBGC model root becomes <MYBGCPATH> that contains 4 different subfolders for biogeochemistry, named initialization, pelagic, and benthic, and a separate one named nemo\_coupling including the modified MY\_SRC routines. The latter folder containing the modified NEMO coupling interface will be still linked using the makenemo \textit{-e} option. \\ \\
In order to include the BGC model subfolders in the compilation of NEMO code, it will be necessary to extend the configuration \textit{cpp\_NEMO\_MYBGC.fcm} file to include the specific paths of MYBGC folders, as in the following example
\begin{minted}{bash}
bld::tool::fppkeys key_xios key_top
src::MYBGC::initialization <MYBGCPATH>/initialization
src::MYBGC::pelagic <MYBGCPATH>/pelagic
src::MYBGC::benthic <MYBGCPATH>/benthic
bld::pp::MYBGC 1
bld::tool::fppflags::MYBGC \%FPPFLAGS
bld::tool::fppkeys \%bld::tool::fppkeys MYBGC_MACROS
\end{minted}
where MYBGC\_MACROS is the space delimited list of macros used in MYBGC model for selecting/excluding specific parts of the code. The BGC model code will be preprocessed in the configuration BLD folder as for NEMO, but with an independent path, like NEMO\_MYBGC/BLD/MYBGC/<subfolders>.\\
The compilation will be performed similarly to in the previous case with the following
\begin{minted}{bash}
makenemo -n NEMO_MYBGC -m <arch_my_machine> -j 8 -e <MYBGCPATH>/nemo_coupling
\end{minted}
Note that, the additional lines specific for the BGC model source and build paths, can be written into a separate file, e.g. named MYBGC.fcm, and then simply included in the cpp\_NEMO\_MYBGC.fcm as follow:
\begin{minted}{bash}
bld::tool::fppkeys key_zdftke key_dynspg_ts key_xios key_top
inc <MYBGCPATH>/MYBGC.fcm
\end{minted}
This will enable a more portable compilation structure for all MYBGC related configurations. \\ \\
Important: the coupling interface contained in nemo\_coupling cannot be added using the FCM syntax, as the same files already exists in NEMO and they are overridden only with the readdressing of MY\_SRC contents to avoid compilation conflicts due to duplicate routines. \\ \\
All modifications illustrated above, can be easily implemented using shell or python scripting to edit the NEMO configuration cpp.fcm file and to create the BGC model specific FCM compilation file with code paths.
\end{document}
doc/latex/TOP/subfiles/model_description.tex
View file @ 478dca63
......@@ -11,9 +11,9 @@
\chapter{Model Description}
\label{chap:ModDes}
\chaptertoc
%\chaptertoc
\section{Basics}
\section{The transport-reaction equation}
\label{sec:Bas}
The time evolution of any passive tracer $C$ is given by the transport equation, which is similar to that of active tracer - temperature or salinity :
......@@ -23,17 +23,17 @@ The time evolution of any passive tracer $C$ is given by the transport equation,
\label{Eq_tracer}
\end{equation}
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 \cite{nemo_manual}).
where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations (see sections 4.2 and 4.3 in NEMO manual).
{S(C)}, the first term on the right hand side of \autoref{Eq_tracer}, is the SMS - Sources Minus Sinks - inherent to the tracer.
In the case of a biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its loss 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 biogeochemical processes.
In the case of a radioactive tracer, {S(C)} is simply the loss due to radioactive decay.
The second term (within brackets) represents the advection of the tracer in the three directions.
The second term (within brackets) represents the advection of the tracer in three dimensions.
It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$
The third term represents the change due to lateral diffusion.
The third term represents the change due to lateral diffusion.
The fourth term denotes the change due to vertical diffusion, parameterized as eddy diffusion to represent vertical turbulent fluxes :
......@@ -44,103 +44,123 @@ D^{vC} = \frac{1}{e_{3t}} \frac{\partial}{\partial k} \left[ A^{vT} \frac{\par
where $A^{vT}$ is the vertical eddy diffusivity coefficient of active tracers.
\section{The NEMO-TOP interface}
\label{sec:TopInt}
\section{Physical transport component (TRP)}
TOP is the NEMO hardwired interface toward biogeochemical models, which provides 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.
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 to simulate marine biogeochemical cycles.
TOP interface has the following location in the code repository : \path{<repository>/src/TOP/}
and the following modules are available:
% ----------- tableau ------------------------------------
\begin{itemize}
\item \textbf{TRP} : Interface to NEMO physical core for computing tracers transport
\item \textbf{CFC} : Inert tracers (CFC11,CFC12, SF6)
\item \textbf{C14} : Radiocarbon passive tracer
\item \textbf{AGE} : Water age tracking
\item \textbf{MY\_TRC} : Template for creation of new modules and external BGC models coupling
\item \textbf{PISCES} : Built in BGC model. See \cite{aumont_2015} for a complete description
\end{itemize}
% ----------------------------------------------------------
\section{The transport component : TRP}
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.
The passive tracer transport component shares the same advection/diffusion routines with the dynamics, with specific treatment of some features like the damping or the positivity of passive tracers concentrations.
\subsection{Advection}
The advection schemes used for the passive tracers are the same as those used for $T$ and $S$. They are described in section 5.1 of \cite{nemo_manual}.
The advection schemes used for the passive tracers are the same as those used for $T$ and $S$. They are described in section 4.1 of the 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 \textit{namelist\_to}p (ref or cfg) in the namelist block \textit{namtrc\_adv}, 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.
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 artificial extrema are permitted. Their use is not recommended for passive tracers.
This choice is made in \textit{namelist\_top} (ref or cfg) in the namelist block \textit{namtrc\_adv}, by setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, as it is done for the active tracers counterparts.
Note that Centred (cen), Flux Corrected Transport (fct), Upstream-Biased (ubs), and QuiCKest (qck) parameterizations are not \textit{positive} schemes meaning that negative values can appear in an initially strictly positive tracer field which is advected, implying that artificial extrema are permitted. Their use is not recommended for passive tracers.
%------------------------------------------namtrc_adv----------------------------------------------------
\nlst{namtrc_adv}
%----------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
\subsection{Lateral diffusion}
In NEMO v4.0, diffusion of passive tracers has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same.
After NEMO v4.0, the lateral diffusion of passive tracers uses exactly the same form of active tracers, meaning that the numerical scheme is inherited from the physical setup and forced to 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 the numerical scheme is then set in the \forcode{&namtra_ldf} namelist section for the dynamic described in section 5.2 of \cite{nemo_manual}.
The choice of the numerical scheme is then set in the \forcode{&namtra_ldf} namelist section for the dynamic described in section 4.2 of NEMO manual.
rn\_fact\_lap is a factor used to increase zonal equatorial diffusion for depths beyond 200 m. It can be useful to achieve a better representation of Oxygen Minimum Zone (OMZ) in some biogeochemical models, especially at coarse resolution \citep{getzlaff_2013}.
\textit{rn\_fact\_lap} is a factor used to increase zonal equatorial diffusion for depths beyond 200 m. It can be useful to achieve a better representation of Oxygen Minimum Zone (OMZ) in some biogeochemical models, especially at coarse resolution \citep{getzlaff_2013}.
%------------------------------------------namtrc_ldf----------------------------------------------------
\nlst{namtrc_ldf}
%---------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
%-----------------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 :
%-----------------The code allows also 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 :
%-----------------\begin{equation} \label{eq:traqsr_iradiance}
%-----------------Aht = Aht * rn_fact_lap * \exp( - \max( 0., z -1000 ) / 1000} \quad \text{for $L=1$ to $N$}
%-----------------\end{equation}
\subsection{Vertical sinking of particles}
The module \textit{trc\_sink} computes the vertical flux of tracers that undergo to gravitational sinking (e.g., particulated matter). It also offers a temporary solution for the problem that may arise in specific situation where the CFL criterion is broken for vertical sedimentation of particles. To avoid this, a time splitting algorithm has been coded. The number of iterations (niter) necessary to respect the CFL criterion is dynamically computed. A specific maximum number of iterations (\textit{nitermax}) can be specified in the namelist. This allows to avoid a very large number of iterations when explicit free surface is used, for instance. If niter is larger than the prescribed nitermax, sinking speeds are clipped so that the CFL criterion is respected. The numerical scheme used to compute sedimentation is based on the MUSCL advection scheme.
%------------------------------------------namtrc_bdy----------------------------------------------------
\nlst{namtrc_snk}
%--------------------------------------------------------------------------------------------------------
\subsection{Tracer damping}
The use of newtonian damping to climatological fields or observations is also coded, sharing the same routine as that of active tracers.
Boolean variables are defined in the namelist\_top\_ref to select the tracers on which restoring is applied.
Boolean variables are defined in \textit{namelist\_top\_ref} to specify which tracers are affected by the restoring procedure.
Options are defined through the \textit{\&namtrc\_dmp} namelist variables.
The restoring term is added when the namelist parameter \textit{ln\_trcdmp} is set to \textit{true}.
The restoring coefficient is a three-dimensional array read in a file, whose name is specified by the namelist variable \textit{cn\_resto\_tr}.
This netcdf file can be generated using the DMP\_TOOLS tool.
This netcdf file can be generated using the \textit{DMP\_TOOLS} tool.
%------------------------------------------namtrc_dmp----------------------------------------------------
\nlst{namtrc_dmp}
%-----------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
\subsection{Tracer positivity}
Some numerical schemes can generate negative values of passive tracers concentration, which is obviously unrealistic.
For example, isopycnal diffusion can created local extrema, meaning that negative concentrations can be generated.
The trcrad routine artificially corrects negative concentrations with a very crude solution that either sets negative concentrations to zero without adjusting the tracer budget (CFCs or C14 chemical coumpounds), or by removing negative concentrations while computing the corresponding tracer content that is added and then, adjusting the tracer concentration using a multiplicative factor so that the total tracer concentration is preserved (PISCES model).
The treatment of negative concentrations is an option and can be selected in the namelist \textit{\&namtrc\_rad} by setting the parameter \textit{ln\_trcrad} to true.
Some numerical schemes can generate negative values of passive tracers concentration, thus leading to unrealistic features.
For example, isopycnal diffusion can created local extrema, meaning that negative concentrations are allowed to generate.
The trcrad routine artificially corrects negative concentrations with a very crude solution that either sets negative concentrations to zero without adjusting the tracer budget (CFCs or C14 chemical coumpounds), or by removing negative concentrations while computing the corresponding tracer content that is added and then, adjusting the tracer concentration using a multiplicative factor so that the total tracer concentration is preserved (e.g., in PISCES).
The treatment of negative concentrations is an option and can be selected in the namelist \textit{\&namtrc\_rad} by setting the parameter \textit{ln\_trcrad} to \textit{true}.
%------------------------------------------namtrc_rad----------------------------------------------------
\nlst{namtrc_rad}
%----------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
\subsection{Offline transport mode}
\label{Offline}
Coupling passive tracers offline with NEMO requires a set of physical fields computed in a previous ocean simulation.
Those fields are read in files and interpolated on-the-fly at each model time step.
There are two sets of fields to perform offline simulations :
\begin{itemize}
\item linear free surface ( ln\_linssh = .true. ) where the vertical scale factor is constant with time. At least, the following dynamical parameters should be absolutely passed
to transport : the effective ocean transport velocities (eulerian plus the eddy induced plus all others parameterizations), vertical diffusion coefficient and the freshwater flux
.
%------------------------------------------namtrc_sms----------------------------------------------------
\nlstlocal{namdta_dyn_linssh}
%-----------------------------------------------------------------------------------------------------------
\item non linear free surface ( ln\_linssh = .false. or key\_qco ): the same fields than the ones in the linear free surface case. In addition, the horizontal divergence transport is needed to recompute the time evolution of the sea surface heigth and the vertical scale factor and depth, and thus the time evolution of the vertical transport velocity.
%------------------------------------------namtrc_sms----------------------------------------------------
\nlstlocal{namdta_dyn_nolinssh}
%-----------------------------------------------------------------------------------------------------------
\end{itemize}
Additionally, temperature, salinity, and mixed layer depth are needed to compute slopes for isopycnal diffusion. Some ecosystem models like PISCES need sea ice concentration, short-wave radiation at the ocean surface, and wind speed (or at least, wind stress).
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 CO$_{2}$ sinks for climate-carbon studies.
The offline interface is located in the code repository : <repository>/src/OFF/. It is activated by adding the\textit{ key\_offline} CPP key to the CPP keys list.
There are two specifics routines for the offline code :
\begin{itemize}
\item dtadyn.F90 : this module reads and computes the dynamical fields at
each model time-step
\item nemogcm.F90 : a degraded version of the main nemogcm.F90 code of NEMO to
manage the time-stepping
\end{itemize}
\section{Forcing and Boundary conditions (BC)}
\subsection{Tracer boundary conditions}
In NEMO, different types of boundary conditions can be specified for biogeochemical tracers. For every single variable, it is possible to define a field of surface boundary conditions, such as deposition of dust or nitrogen, which is then interpolated to the grid and timestep using the fld\_read function. The same facility is available to include river inputs or coastal erosion (coastal boundary conditions) and the treatment of open boundary conditions. For lateral boundary conditions, spatial interpolation should not be activated.
In TOP, different types of boundary conditions can be specified for biogeochemical tracers. For every single variable, it is possible to define a field of surface boundary conditions, such as deposition of dust or nitrogen, which is then interpolated to the grid and timestep using the fld\_read function (see also Sec. 6.2 of NEMO manual). Through the same facility one can apply coastal inputs/loads (coastal boundary conditions) and to specify the treatment of lateral open boundary conditions. For the latter, the spatial interpolation functionality should not be activated.
%------------------------------------------namtrc_bc----------------------------------------------------
\nlst{namtrc_cfg}
%---------------------------------------------------------------------------------------------------------
The entire set of boundary conditions is activated with the paramter \forcode{ln_trcbc = .true.} in namtrc\_cfg (more details in Model Setup section).
\subsubsection{Surface and lateral boundaries}
\subsection*{Surface and lateral boundaries}
The namelist \textit{\&namtrc\_bc} is in file \textit{namelist\_top\_cfg} and allows to specify the name of the files, the frequency of the input and the time and space interpolation as done for any other field using the fld\_read interface.
%------------------------------------------namtrc_bc----------------------------------------------------
\nlst{namtrc_bc}
%---------------------------------------------------------------------------------------------------------
\subsubsection{Open boundaries}
%-------------------------------------------------------------------------------------------------------
\subsection*{Lateral open boundaries}
The BDY for passive tracer are set together with the physical oceanic variables (lnbdy =.true.). Boundary conditions are set in the structure used to define the passive tracer properties in the « cbc » column. These boundary conditions are applied on the segments defined for the physical core of NEMO (see BDY description in the User Manual).
The BDY for passive tracer are set together with the physical oceanic variables (ln?bdy =.true.). Boundary conditions are set in the structure used to define the passive tracer properties in the « obc » column. These boundary conditions are applied on the segments defined for the physical system, as described in the BDY section of NEMO manual.
\begin{itemize}
\item cn\_trc\_dflt : the type of OBC applied to all the tracers
\item cn\_trc : the boundary condition used for tracers with data file
......@@ -148,29 +168,23 @@ The BDY for passive tracer are set together with the physical oceanic variables
%------------------------------------------namtrc_bdy----------------------------------------------------
\nlst{namtrc_bdy}
%----------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
\subsubsection{Sedimentation of particles}
\subsection{Sea-ice interface}
This module computes the vertical flux of particulate matter due to gravitational sinking. It also offers a temporary solution for the problem that may arise in specific situation where the CFL criterion is broken for vertical sedimentation of particles. To avoid this, a time splitting algorithm has been coded. The number of iterations niter necessary to respect the CFL criterion is dynamically computed. A specific maximum number of iterations nitermax may be specified in the namelist. This is to avoid a very large number of iterations when explicit free surface is used, for instance. If niter is larger than the prescribed nitermax, sinking speeds are clipped so that the CFL criterion is respected. The numerical scheme used to compute sedimentation is based on the MUSCL advection scheme.
%------------------------------------------namtrc_bdy----------------------------------------------------
\nlst{namtrc_snk}
%----------------------------------------------------------------------------------------------------------
\subsubsection{Sea-ice growth and melt effect}
\subsection*{Sea-ice growth and melt effect}
NEMO provides three options for the specification of tracer concentrations in sea ice: (-1) identical tracer concentrations in sea ice and ocean, which corresponds to no concentration/dilution effect upon ice growth and melt; (0) zero concentrations in sea ice, which gives the largest concentration-dilution effect upon ice growth and melt; (1) specified concentrations in sea ice, which gives a possibly more realistic effect of sea ice on tracers. Option (-1) and (0) work for all tracers, but (1) is currently only available for PISCES.
%------------------------------------------namtrc_ice----------------------------------------------------
\nlst{namtrc_ice}
%---------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
\subsubsection{Antartic Ice Sheet tracer supply}
\subsection*{Antarctic Ice Sheet tracer supply}
The external input of biogeochemical tracers from the Antarctic Ice Sheet (AIS) is represented by associating a tracer content with the freshwater flux from icebergs and ice shelves \citep{person_sensitivity_2019}. This supply is currently implemented only for dissolved Fe (\autoref{img_icbisf}) and is effective in model configurations with south-extended grids (eORCA1 and eORCA025). As the ORCA2 grid does not extend south into Antarctica, the external source of tracers from the AIS cannot be enabled in this configuration.
The external input of biogeochemical tracers from the Antarctic Ice Sheet (AIS) is represented by associating a tracer content with the freshwater flux from icebergs and ice shelves \citep{person_sensitivity_2019}. This supply is currently implemented only for dissolved Fe (\autoref{img_icbisf}) and is effective in model configurations with south-extended grids (e.g., eORCA1 and eORCA025). As the ORCA2 grid does not extend south into Antarctica, the external source of tracers from the AIS cannot be enabled in this configuration.
For icebergs, a homogeneous distribution of biogeochemical tracers is applied from the surface to a depth that can be defined in \textit{\&namtrc\_ais}, currently set at 120 m. It should be noted that the freshwater flux from icebergs affects only the ocean properties at the surface. For ice shelves, biogeochemical tracers follow the explicit or parameterized representation of freshwater flux distribution modeled in NEMO. The AIS tracer supply is activated by setting \textit{ln\_trcais} to \textit{true} in the \textit{\&namtrc} section.
For icebergs, a homogeneous distribution of biogeochemical tracers is applied from the surface to a depth that can be defined in \textit{\&namtrc\_ais}, with a default values of 120 m. It should be noted that the freshwater flux from icebergs affects only the ocean properties at the surface. For ice shelves, biogeochemical tracers follow the explicit or parameterized representation of freshwater flux distribution modeled by the NEMO physical core. The AIS tracer supply is activated by setting \textit{ln\_trcais} to \textit{true} in the \textit{\&namtrc} section.
\begin{figure}[!h]
\centering
......@@ -181,19 +195,39 @@ For icebergs, a homogeneous distribution of biogeochemical tracers is applied fr
%------------------------------------------namtrc_ais----------------------------------------------------
\nlst{namtrc_ais}
%---------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
\subsection{Light vertical attenuation}
A dedicated module (\forcode{trcopt}) allows to compute form the sea surface solar radiation the amount of light that penetrate into the ocean interior depending on the chlorophyll field.
The visible part of solar radiation is used to derive the photosynthetic available radiation (PAR) using a simplified version of the model by \cite{morel_1988}, as described in \cite{lengaigne_2007}.
\section{The SMS modules}
In a nutshell, visible light is split into three wavebands (blue: 400–500 nm, green: 500–600 nm, red: 600–700 nm) and for each one the chlorophyll-dependent attenuation coefficients are fitted
to the coefficients computed from the full spectral model of \cite{morel_1988} (as modified in \cite{morel_2001}) assuming the same power-law expression.
The available light is then converted to PAR using a time-space constant value (\forcode{parlux}) or
by prescribing a spatially variable distribution of the fraction of the downwelling shortwave radiation (\forcode{sn_par}),
as specified with the logical parameter \forcode{ln_varpar}.
The \forcode{light_loc} parameter allows to select the way that light is computed within the gridcell volume, namely as the mean value at the cell center (\forcode{'center'}) or integrated within the cell (\forcode{'integral'}).
%--------------------------------------------namopt------------------------------------------------------
\nlst{namopt}
%--------------------------------------------------------------------------------------------------------
\section{“Source minus Sinks” modules (SMS)}
\label{SMS_models}
%------------------------------------------namtrc_sms----------------------------------------------------
%\nlst{namtrc}
%-------------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
\subsection{Ideal Age}
%------------------------------------------namage----------------------------------------------------
%---------------------------------------------namage-----------------------------------------------------
\nlst{namage}
%----------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
An `ideal age' tracer is integrated online in TOP when \textit{ln\_age} = \texttt{.true.} in namelist \textit{namtrc}.
This tracer marks the duration in units of years that fluid has spent in the interior of the ocean, insulated from exposure to the atmosphere (\autoref{img_ageatl} and \autoref{img_age200}).
......@@ -232,7 +266,7 @@ Since this relaxation is applied explicitly, the relaxation rate should in princ
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 age tracer module 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 is computed as:
To ensure that the forcing is independent from 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 is computed as:
\begin{equation}
\label{eq:TOP-age-mixed}
......@@ -255,7 +289,7 @@ This implementation was first used in the CORE-II intercomparison runs described
\nlst{namcfc}
%----------------------------------------------------------------------------------------------------------
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.
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.
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,
and additionally as an aerosol propellant.
......@@ -267,16 +301,6 @@ These declines have been driven by the Montreal Protocol (effective since August
stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. All three chemicals are also significantly more potent greenhouse gases
than CO$_{2}$ (especially SF6), although their relatively low atmospheric concentrations limit their role in climate change. \\
% Chlorofluorocarbons 11 and 12 (CFC-11 and CFC-12), and sulfur hexafluoride (SF6),
% are greenhouse gases that have been released into the atmosphere by human activities.
% In the case of CFC-11 and CFC-12, this release began in the 1930s, and atmospheric
% concentrations increased until around the late 1990s afterwhich they began to decline in
% response to the Montreal Protocol.
% In the case of SF6, release began in the 1950s
% This release began in the 1930s for CFC-11 and CFC-12, and the 1950s for SF6, and
% regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12,
% and is still increasing, and SF6 (see Figure \autoref{img_cfcatm}). \\
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
valuable in oceanography. % for tracking interior ventilation and mixing.
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 ventilation of the latter via transport and mixing.
......@@ -346,8 +370,7 @@ Sc = a0 + (a1 \, \cdot \, T) + (a2 \, \cdot \, T^2) + (a3 \, \cdot \, T^3) + (
The solubility, $Sol$, used in Equation \autoref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$,
and is specific for each gas.
It has been experimentally estimated by \citet{warner_1985} as a function of temperature
and salinity:
It has been experimentally estimated by \citet{warner_1985} as a function of temperature and salinity:
% AXY: this equation looks both weird and possibly wrong; it doesn't look like the one in the
% code version that I have to hand, although this might be out of date; in any case, I'dag
......@@ -381,13 +404,13 @@ This property, when divided by the surface CFC concentration, estimates the loca
% The standard outputs of the CFC module are the CFCs concentration in the sea water, and the records of the outputs-frequency-averaged as well as the total air-sea fluxes.
% Using XIOS, it is also possible to ask for the CFCs vertical inventory in the output file (see Figure cfc inventory example ?).
\subsubsection{Notes}
\subsubsection*{Notes}
In comparison to the OMIP protocol, the CFC module in NEMO has several differences:
% AXY: consider an itemized list here if you've got a list of differences
For instance, C$_{sat}$ is calculated for a fixed surface pressure of 1atm. This may be corrected in a future version of the module.
For instance, C$_{sat}$ is calculated for a fixed surface pressure of 1atm. This may be corrected in a future version of the module.\\
\begin{table}[!t]
......@@ -430,21 +453,21 @@ SF6 & & 3177.5 & -200.57 & 6.8865 & -0.13335 & 0.0010877 \\
\begin{figure}[!h]
\centering
\includegraphics[width=0.80\textwidth]{CFC-atm-evol}
\includegraphics[width=0.70\textwidth]{CFC-atm-evol}
\caption{Atmospheric CFC11, CFC12 and SF6 partial pressure evolution in both hemispheres.}
\label{img_cfcatm}
\end{figure}
\begin{figure}[!h]
\centering
\includegraphics[width=0.80\textwidth]{CFC_solub}
\includegraphics[width=0.70\textwidth]{CFC_solub}
\caption{CFC11 solubility in mol m$^{-3}$ pptv$^{-1}$, calculated from the World Ocean Atlas 2013 temperature and salinity annual climatology.}
\label{img_cfcsol}
\end{figure}
\begin{figure}[!h]
\centering
\includegraphics[width=0.80\textwidth]{CFC_inventory}
\includegraphics[width=0.70\textwidth]{CFC_inventory}
\caption{CFC11 vertical inventory in $\mu$mol m$^{-2}$, from one of the UK Earth System Model 1 model (UKESM1 - which uses NEMO as ocean component, with TOP for the passive tracers) historical run at year 2000.}
\label{img_cfcinv}
\end{figure}
......@@ -462,7 +485,7 @@ SF6 & & 3177.5 & -200.57 & 6.8865 & -0.13335 & 0.0010877 \\
The C14 package has been implemented in NEMO by Anne Mouchet $\Dcq$.
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.
\subsubsection{Method}
\subsection*{Method}
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:
......@@ -551,7 +574,7 @@ The following parameters intervening in the air-sea exchange rate are set in \te
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}.
%The sensitivity to this parametrization is discussed in section \autoref{sec:result}.
%
\item Chemical enhancement (term $b$ in Eq. \autoref{eq:wanchem}) may be set on/off by means of the logical variable \forcode{ln\_chemh}.
\item Chemical enhancement (term $b$ in Eq. \autoref{eq:wanchem}) may be set on/off by means of the logical variable \forcode{ln_chemh}.
\end{itemize}
%
......@@ -597,7 +620,7 @@ Time on x-axis is in simulation year.\label{fig:drift} }
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}
\end{figure}
Performing this type of experiment requires that a pre-industrial equilibrium run has been performed beforehand (\forcode{ln\_rsttr} should be set to \texttt{.TRUE.}).
Performing this type of experiment requires that a pre-industrial equilibrium run has been performed beforehand (\forcode{ln_rsttr} should be set to \texttt{.TRUE.}).
An exception to this rule is when performing 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.
......@@ -613,13 +636,13 @@ Dates in these forcing files are expressed as yr AD.
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:
\begin{itemize}
\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).
\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).
\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).
\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).
\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).
\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).
\end{itemize}
If the experiment date is outside the data time span, the first or last atmospheric concentrations are then prescribed depending on whether the date is earlier or later.
Note that \forcode{tyrc14\_beg} (\texttt{namelist\_c14}) is not used in this context.
Note that \forcode{tyrc14_beg} (\texttt{namelist\_c14}) is not used in this context.
%
\textbf{Transient: Past}
......@@ -646,9 +669,9 @@ These atmospheric values are reproduced in Fig. \autoref{fig:paleo}.
Dates in these files are expressed as yr BP.
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.
The true experiment starting date is given by \forcode{tyrc14\_beg} (in yr BP) in \texttt{namelist\_c14}.
In consequence, \forcode{nn\_date0} in \texttt{namelist} MUST be set to 00010101.\\
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).
The true experiment starting date is given by \forcode{tyrc14_beg} (in yr BP) in \texttt{namelist\_c14}.
In consequence, \forcode{nn_date0} in \texttt{namelist} MUST be set to 00010101.\\
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).
These two parameters have then to be set to 2 for the following years (read the date in the restart file). \\
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.
......@@ -709,7 +732,7 @@ N_A \Rq_\mathrm{oxa} \overline{\Ct} \left( \int_\Omega \Rq d\Omega \right) /10^{
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 \autoref{eq:inv}.
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. }.
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. }.
The global transfer velocities represent time-averaged\footnote{the actual duration is set in \texttt{iodef.xml}} global integrals of the transfer rates:
......@@ -775,43 +798,9 @@ Be aware that lateral boundary conditions are applied in trcnxt routine.
IMPORTANT: the routines to compute 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.
\item \textit{trcice\_my\_trc.F90} : Here it is possible to prescribe the tracers concentrations in sea ice that will be used as boundary conditions when ice formation and melting occurs (nn\_ice\_tr =1 in namtrc\_ice).
See e.g. the correspondent PISCES subroutine.
\item \textit{trcwri\_my\_trc.F90} : This routine performs the output of the model tracers using IOM module (see Manual Chapter Output and Diagnostics).
\item \textit{trcwri\_my\_trc.F90} : This routine performs the output of the model tracers using IOM module (see NEMO manual Chapter on 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}.
\end{itemize}
\section{The Offline Option}
\label{Offline}
Coupling passive tracers offline with NEMO requires precomputed physical fields
from OGCM. Those fields are read in files and interpolated on-the-fly at each model
time step. There are two sets of fields to perform offline simulations :
\begin{itemize}
\item linear free surface ( ln\_linssh = .true. ) where the vertical scale factor is constant with time. At least, the following dynamical parameters should be absolutely passed
to transport : the effective ocean transport velocities (eulerian plus the eddy induced plus all others parameterizations), vertical diffusion coefficient and the freshwater flux
.
%------------------------------------------namtrc_sms----------------------------------------------------
\nlst{namdta_dyn_linssh}
%-----------------------------------------------------------------------------------------------------------
\item non linear free surface ( ln\_linssh = .false. or key\_qco ) : the same fields than the ones in the linear free surface case. In addition, the horizontal divergence transport is needed to recompute the time evolution of the sea surface heigth and the vertical scale factor and depth, and thus the time evolution of the vertical transport velocity.
%------------------------------------------namtrc_sms----------------------------------------------------
\nlst{namdta_dyn_nolinssh}
%-----------------------------------------------------------------------------------------------------------
\end{itemize}
Additionally, temperature, salinity, and mixed layer depth are needed to compute slopes for isopycnal diffusion. Some ecosystem models like PISCES need sea ice concentration, short-wave radiation at the ocean surface, and wind speed (or at least, wind stress).
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 CO$_{2}$ sinks for climate-carbon studies.
The offline interface is located in the code repository : <repository>/src/OFF/. It is activated by adding the\textit{ key\_offline} CPP key to the CPP keys list.
There are
two specifics routines for the offline code :
\begin{itemize}
\item dtadyn.F90 : this module reads and computes the dynamical fields at
each model time-step
\item nemogcm.F90 : a degraded version of the main nemogcm.F90 code of NEMO to
manage the time-stepping
\end{itemize}
\end{document}