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doc/latex/NEMO/subfiles/chap_DIA.tex
View file @ 821dc71a
......@@ -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 @ 821dc71a
......@@ -793,11 +793,11 @@ so that the update of the next velocities is done in module \mdl{dynspg\_flt} an
The form of the surface pressure gradient term depends on how the user wants to
handle the fast external gravity waves that are a solution of the analytical equation (\autoref{sec:MB_hor_pg}).
Three formulations are available, all controlled by a CPP key (ln\_dynspg\_xxx):
Two formulations are available, all controlled by a CPP key (ln\_dynspg\_<method>):
an explicit formulation which requires a small time step;
a filtered free surface formulation which allows a larger time step by
adding a filtering term into the momentum equation;
and a split-explicit free surface formulation, described below, which also allows a larger time step.
%a filtered free surface formulation which allows a larger time step by
%adding a filtering term into the momentum equation;
a split-explicit free surface formulation which also allows a larger time step.
The extra term introduced in the filtered method is calculated implicitly, so that a solver is used to compute it.
As a consequence the update of the $next$ velocities is done in module \mdl{dynspg\_flt} and not in \mdl{dynnxt}.
......@@ -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_LDF.tex
View file @ 821dc71a
......@@ -485,8 +485,8 @@ the horizontal divergence for operators acting along model-surfaces are no longe
Except in global ORCA $0.5^{\circ}$ runs with \key{traldf\_eiv},
where $A_l$ is set like $A_e$ but with a minimum vale of $100\;\mathrm{m}^2\;\mathrm{s}^{-1}$
}.
In idealised setups with \key{traldf\_c2d}, $A_e$ is reduced similarly, but if \key{traldf\_eiv} is set in
the global configurations with \key{traldf\_c2d}, a horizontally varying $A_e$ is instead set from
In idealised setups with (\protect\np[=-20]{nn_aht_ijk_t}{nn\_aht\_ijk\_t}), $A_e$ is reduced similarly, but if \np[=.true.]{ln_ldfeiv}{ln\_ldfeiv} also is set in
the global configurations a horizontally varying $A_e$ is instead set from
the Held-Larichev parameterisation
\footnote{
In this case, $A_e$ at low latitudes $|\theta|<20^{\circ}$ is further reduced by a factor $|f/f_{20}|$,
......
doc/latex/NEMO/subfiles/chap_SBC.tex
View file @ 821dc71a
......@@ -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 @ 821dc71a
......@@ -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 @ 821dc71a
......@@ -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 @ 821dc71a
......@@ -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 @ 821dc71a
......@@ -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 @ 821dc71a
\subfile{../subfiles/model_structure}
\subfile{../subfiles/model_description}
\subfile{../subfiles/model_setup}
\subfile{../subfiles/miscellaneous}
doc/latex/TOP/main/introduction.tex
View file @ 821dc71a
......@@ -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 @ 821dc71a
! 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 @ 821dc71a
!-----------------------------------------------------------------------
&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 @ 821dc71a
!-----------------------------------------------------------------------
&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 @ 821dc71a
!-----------------------------------------------------------------------
&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'
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!-----------------------------------------------------------------------
&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'
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!-----------------------------------------------------------------------
&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)
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!----------------------------------------------------------------------
&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)
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!-----------------------------------------------------------------------
&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.
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!-----------------------------------------------------------------------
&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
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\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}