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\hline
field &
define a specific field &
axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref,
id, level, long\_name, name, operation, prec, standard\_name, unit &
field\_definition, field\_group, file &
none \\
\hline
\end{tabularx}
\caption{XIOS: field tags ("\texttt{field\_*}")}
\end{table}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|X|X|l|}
\hline
tag name &
description &
accepted attribute &
child of &
parent of \\
\hline
\hline
file\_definition &
encapsulates the definition of all the files that will be outputted &
enabled, min\_digits, name, name\_suffix, output\_level,
split\_freq\_format, split\_freq, sync\_freq, type, src &
context &
file or file\_group \\
\hline
file\_group &
encapsulates a group of files that will be outputted &
enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level,
split\_freq\_format, split\_freq, sync\_freq, type, src &
file\_definition, file\_group &
file or file\_group \\
\hline
file &
define the contents of a file to be outputted &
enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level,
split\_freq\_format, split\_freq, sync\_freq, type, src &
file\_definition, file\_group &
field \\
\hline
\end{tabularx}
\caption{XIOS: file tags ("\texttt{file\_*}")}
\end{table}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|X|X|X|}
\hline
tag name &
description &
accepted attribute &
child of &
parent of \\
\hline
\hline
axis\_definition &
define all the vertical axis potentially used by the variables &
src &
context &
axis\_group, axis \\
\hline
axis\_group &
encapsulates a group of vertical axis &
id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
axis\_definition, axis\_group &
axis\_group, axis \\
\hline
axis &
define a vertical axis &
id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
axis\_definition, axis\_group &
none \\
\hline
\end{tabularx}
\caption{XIOS: axis tags ("\texttt{axis\_*}")}
\end{table}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|X|X|X|}
\hline
tag name &
description &
accepted attribute &
child of &
parent of \\
\hline
\hline
domain\_\-definition &
define all the horizontal domains potentially used by the variables &
src &
context &
domain\_\-group, domain \\
\hline
domain\_group &
encapsulates a group of horizontal domains &
id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj &
domain\_\-definition, domain\_group &
domain\_\-group, domain \\
\hline
domain &
define an horizontal domain &
id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj &
domain\_\-definition, domain\_group &
none \\
\hline
\end{tabularx}
\caption{XIOS: domain tags ("\texttt{domain\_*)}"}
\end{table}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|X|X|X|}
\hline
tag name &
description &
accepted attribute &
child of &
parent of \\
\hline
\hline
grid\_definition &
define all the grid (association of a domain and/or an axis) potentially used by the variables &
src &
context &
grid\_group, grid \\
\hline
grid\_group &
encapsulates a group of grids &
id, domain\_ref,axis\_ref &
grid\_definition, grid\_group &
grid\_group, grid \\
\hline
grid &
define a grid &
id, domain\_ref,axis\_ref &
grid\_definition, grid\_group &
none \\
\hline
\end{tabularx}
\caption{XIOS: grid tags ("\texttt{grid\_*}")}
\end{table}
%% =================================================================================================
\subsubsection{Attributes list per family}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|l|l|}
\hline
attribute name &
description &
example &
accepted by \\
\hline
\hline
axis\_ref &
refers to the id of a vertical axis &
axis\_ref="deptht" &
field, grid families \\
\hline
domain\_ref &
refers to the id of a domain &
domain\_ref="grid\_T" &
field or grid families \\
\hline
field\_ref &
id of the field we want to add in a file &
field\_ref="toce" &
field \\
\hline
grid\_ref &
refers to the id of a grid &
grid\_ref="grid\_T\_2D" &
field family \\
\hline
group\_ref &
refer to a group of variables &
group\_ref="mooring" &
field\_group \\
\hline
\end{tabularx}
\caption{XIOS: reference attributes ("\texttt{*\_ref}")}
\end{table}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|l|l|}
\hline
attribute name &
description &
example &
accepted by \\
\hline
\hline
zoom\_ibegin &
starting point along x direction of the zoom.
Automatically defined for TAO/RAMA/PIRATA moorings &
zoom\_ibegin="1" &
domain family \\
\hline
zoom\_jbegin &
starting point along y direction of the zoom.
Automatically defined for TAO/RAMA/PIRATA moorings &
zoom\_jbegin="1" &
domain family \\
\hline
zoom\_ni &
zoom extent along x direction &
zoom\_ni="1" &
domain family \\
\hline
zoom\_nj &
zoom extent along y direction &
zoom\_nj="1" &
domain family \\
\hline
\end{tabularx}
\caption{XIOS: domain attributes ("\texttt{zoom\_*}")}
\end{table}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|l|l|}
\hline
attribute name &
description &
example &
accepted by \\
\hline
\hline
min\_digits &
specify the minimum of digits used in the core number in the name of the NetCDF file &
min\_digits="4" &
file family \\
\hline
name\_suffix &
suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file &
name\_suffix="\_myzoom" &
file family \\
\hline
output\_level &
output priority of variables in a file: 0 (high) to 10 (low).
All variables listed in the file with a level smaller or equal to output\_level will be output.
Other variables won't be output even if they are listed in the file. &
output\_level="10" &
file family \\
\hline
split\_freq &
frequency at which to temporally split output files.
Units can be ts (timestep), y, mo, d, h, mi, s.
Useful for long runs to prevent over-sized output files. &
split\_freq="1mo" &
file family \\
\hline
split\_freq\-\_format &
date format used in the name of temporally split output files.
Can be specified using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s &
split\_freq\_format= "\%y\%mo\%d" &
file family \\
\hline
sync\_freq &
NetCDF file synchronization frequency (update of the time\_counter).
Units can be ts (timestep), y, mo, d, h, mi, s. &
sync\_freq="10d" &
file family \\
\hline
type (1) &
specify if the output files are to be split spatially (multiple\_file) or not (one\_file) &
type="multiple\_file" &
file familly \\
\hline
\end{tabularx}
\caption{XIOS: file attributes}
\end{table}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|l|l|}
\hline
attribute name &
description &
example &
accepted by \\
\hline
\hline
default\_value &
missing\_value definition &
default\_value="1.e20" &
field family \\
\hline
level &
output priority of a field: 0 (high) to 10 (low) &
level="1" &
field family \\
\hline
operation &
type of temporal operation: average, accumulate, instantaneous, min, max and once &
operation="average" &
field family \\
\hline
output\_freq &
operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. &
output\_freq="1d12h" &
field family \\
\hline
prec &
output precision: real 4 or real 8 &
prec="4" &
field family \\
\hline
long\_name &
define the long\_name attribute in the NetCDF file &
long\_name="Vertical T levels" &
field \\
\hline
standard\_name &
define the standard\_name attribute in the NetCDF file &
standard\_name= "Eastward\_Sea\_Ice\_Transport" &
field \\
\hline
\end{tabularx}
\caption{XIOS: field attributes}
\end{table}
\begin{table}
\begin{tabularx}{\textwidth}{|l|X|X|X|}
\hline
attribute name &
description &
example &
accepted by \\
\hline
\hline
enabled &
switch on/off the output of a field or a file &
enabled=".true." &
field, file families \\
\hline
description &
just for information, not used &
description="ocean T grid variables" &
all tags \\
\hline
id &
allow to identify a tag &
id="nemo" &
accepted by all tags except simulation \\
\hline
name &
name of a variable or a file. If the name of a file is undefined, its id is used as a name &
name="tos" &
field or file families \\
\hline
positive &
convention used for the orientation of vertival axis (positive downward in \NEMO). &
positive="down" &
axis family \\
\hline
src &
allow to include a file &
src="./field\_def.xml" &
accepted by all tags except simulation \\
\hline
time\_origin &
specify the origin of the time counter &
time\_origin="1900-01-01 00:00:00" &
context \\
\hline
type (2) &
define the type of a variable tag &
type="boolean" &
variable \\
\hline
unit &
unit of a variable or the vertical axis &
unit="m" &
field and axis families \\
\hline
\end{tabularx}
\caption{XIOS: miscellaneous attributes}
\end{table}
%% =================================================================================================
\subsection{CF metadata standard compliance}
Output from the XIOS IO server is compliant with
\href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of
the CF metadata standard.
Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of
section \autoref{subsec:DIA_IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard.
Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by
the namelist parameter \np{ln_cfmeta}{ln\_cfmeta} in the \nam{run}{run} namelist.
This must be set to true if these metadata are to be included in the output files.
%% =================================================================================================
\subsection{Enabling NetCDF4 compression with XIOS}
XIOS supports the use of gzip compression when compiled with NetCDF4 libraries but is subject to the
same restrictions as the underlying HDF5 component. That is, compression is not availiable when the
IO servers are writing in parallel to shared output files. Thus, compression can only be applied in
multiple\_file mode only or with two-levels of servers with multiple servers feeding a single server.
The XML tag to activate compression is:
\begin{xmllines}
compression_level="n"
\end{xmllines}
where n is an integer between 0 and 9. A value of 2 is normally recommended as a suitable trade-off between
algorithm performance and compression levels. This tag can be applied either at file level or to indivdual
fields, e.g.:
\begin{xmllines}
<file_definition>
<file name="output" output_freq="1ts" compression_level="2">
<field id="field_A" grid_ref="grid_A" operation="average" compression_level=" 4" />
<field id="field_B" grid_ref="grid_A" operation="average" compression_level=" 0" />
<field id="field_C" grid_ref="grid_A" operation="average" />
</file>
</file_definition>
\end{xmllines}
It is unclear how XIOS decides on suitable chunking parameters before applying compression so it may
be necessary to rechunk data whilst combining multiple\_file output. \forcode{REBUILD_NEMO} is capable
of doing this.
\section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})]{NetCDF4 support (\protect\key{netcdf4})}
\label{sec:DIA_nc4}
Since version 3.3, support for NetCDF4 chunking and (loss-less) compression has been
included. These options build on the standard NetCDF output and allow the user control
over the size of the chunks via namelist settings. Chunking and compression can lead to
significant reductions in file sizes for a small runtime overhead. For a fuller
discussion on chunking and other performance issues the reader is referred to the NetCDF4
documentation found
\href{https://www.unidata.ucar.edu/software/netcdf/docs/netcdf_perf_chunking.html}{here}.
This section only applies to the NetCDF output written directly by \NEMO; i.e. restart
files and mean files produced via the old IOIPSL interface when \key{xios} is not being
used. As such it has limited use since chunking and compression can be applied at the
rebuilding phase of such output.
The features are only available when the code has been linked with a NetCDF4 library
(version 4.1 onwards, recommended) which has been built with HDF5 support (version 1.8.4
onwards, recommended). Datasets created with chunking and compression are not backwards
compatible with NetCDF3 "classic" format but most analysis codes can be relinked simply
with the new libraries and will then read both NetCDF3 and NetCDF4 files. \NEMO\
executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by setting
the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4}{nc4} namelist:
\begin{listing}
\nlst{namnc4}
\caption{\forcode{&namnc4}}
\label{lst:namnc4}
\end{listing}
If \key{netcdf4} has not been defined, these namelist parameters are not read. In this
case, \np{ln_nc4zip}{ln\_nc4zip} is set false and dummy routines for a few
NetCDF4-specific functions are defined. These functions will not be used but need to be
included so that compilation is possible with NetCDF3 libraries.
When using NetCDF4 libraries, \key{netcdf4} should be defined even if the intention is to
create only NetCDF3-compatible files. This is necessary to avoid duplication between the
dummy routines and the actual routines present in the library. Most compilers will fail
at compile time when faced with such duplication. Thus when linking with NetCDF4
libraries the user must define \key{netcdf4} and control the type of NetCDF file produced
via the namelist parameter.
Chunking and compression is applied only to 4D fields and there is no advantage in
chunking across more than one time dimension since previously written chunks would have to
be read back and decompressed before being added to. Therefore, user control over chunk
sizes is provided only for the three space dimensions. The user sets an approximate
number of chunks along each spatial axis. The actual size of the chunks will depend on
global domain size for mono-processors or, more likely, the local processor domain size
for distributed processing. The derived values are subject to practical minimum values
(to avoid wastefully small chunk sizes) and cannot be greater than the domain size in any
dimension. The algorithm used is:
\begin{forlines}
ichunksz(1) = MIN(idomain_size, MAX((idomain_size-1) / nn_nchunks_i + 1 ,16 ))
ichunksz(2) = MIN(jdomain_size, MAX((jdomain_size-1) / nn_nchunks_j + 1 ,16 ))
ichunksz(3) = MIN(kdomain_size, MAX((kdomain_size-1) / nn_nchunks_k + 1 , 1 ))
ichunksz(4) = 1
\end{forlines}
\noindent As an example, setting:
\begin{forlines}
nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31
\end{forlines}
\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\texttt 46x38x1} respectively in
the mono-processor case (\ie\ global domain of {\small\texttt 182x149x31}).
An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in
table \autoref{tab:DIA_NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with
a 4x2 mpi partitioning.
Note the variation in the compression ratio achieved which reflects chiefly the dry to wet volume ratio of
each processing region.
\begin{table}
\centering
\begin{tabular}{lrrr}
Filename & NetCDF3 & NetCDF4 & Reduction \\
& filesize & filesize & \% \\
& (KB) & (KB) & \\
ORCA2\_restart\_0000.nc & 16420 & 8860 & 47\% \\
ORCA2\_restart\_0001.nc & 16064 & 11456 & 29\% \\
ORCA2\_restart\_0002.nc & 16064 & 9744 & 40\% \\
ORCA2\_restart\_0003.nc & 16420 & 9404 & 43\% \\
ORCA2\_restart\_0004.nc & 16200 & 5844 & 64\% \\
ORCA2\_restart\_0005.nc & 15848 & 8172 & 49\% \\
ORCA2\_restart\_0006.nc & 15848 & 8012 & 50\% \\
ORCA2\_restart\_0007.nc & 16200 & 5148 & 69\% \\
ORCA2\_2d\_grid\_T\_0000.nc & 2200 & 1504 & 32\% \\
ORCA2\_2d\_grid\_T\_0001.nc & 2200 & 1748 & 21\% \\
ORCA2\_2d\_grid\_T\_0002.nc & 2200 & 1592 & 28\% \\
ORCA2\_2d\_grid\_T\_0003.nc & 2200 & 1540 & 30\% \\
ORCA2\_2d\_grid\_T\_0004.nc & 2200 & 1204 & 46\% \\
ORCA2\_2d\_grid\_T\_0005.nc & 2200 & 1444 & 35\% \\
ORCA2\_2d\_grid\_T\_0006.nc & 2200 & 1428 & 36\% \\
ORCA2\_2d\_grid\_T\_0007.nc & 2200 & 1148 & 48\% \\
... & ... & ... & ... \\
ORCA2\_2d\_grid\_W\_0000.nc & 4416 & 2240 & 50\% \\
ORCA2\_2d\_grid\_W\_0001.nc & 4416 & 2924 & 34\% \\
ORCA2\_2d\_grid\_W\_0002.nc & 4416 & 2512 & 44\% \\
ORCA2\_2d\_grid\_W\_0003.nc & 4416 & 2368 & 47\% \\
ORCA2\_2d\_grid\_W\_0004.nc & 4416 & 1432 & 68\% \\
ORCA2\_2d\_grid\_W\_0005.nc & 4416 & 1972 & 56\% \\
ORCA2\_2d\_grid\_W\_0006.nc & 4416 & 2028 & 55\% \\
ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\% \\
\end{tabular}
\caption{Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression}
\label{tab:DIA_NC4}
\end{table}
%% =================================================================================================
\section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd}{trd})}
\label{sec:DIA_trd}
\begin{listing}
\nlst{namtrd}
\caption{\forcode{&namtrd}}
\label{lst:namtrd}
\end{listing}
Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to
\mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation
(\ie\ at the end of each \textit{dyn....F90} and/or \textit{tra....F90} routines).
This capability is controlled by options offered in \nam{trd}{trd} namelist.
Note that the output are done with XIOS, and therefore the \key{xios} is required.
What is done depends on the \nam{trd}{trd} logical set to \forcode{.true.}:
\begin{description}
\item [{\np{ln_glo_trd}{ln\_glo\_trd}}]: at each \np{nn_trd}{nn\_trd} time-step a check of the basin averaged properties of
the momentum and tracer equations is performed.
This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$,
and potential energy time evolution equations properties;
\item [{\np{ln_dyn_trd}{ln\_dyn\_trd}}]: each 3D trend of the evolution of the two momentum components is output;
\item [{\np{ln_dyn_mxl}{ln\_dyn\_mxl}}]: each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output;
\item [{\np{ln_vor_trd}{ln\_vor\_trd}}]: a vertical summation of the moment tendencies is performed,
then the curl is computed to obtain the barotropic vorticity tendencies which are output;
\item [{\np{ln_KE_trd}{ln\_KE\_trd}}] : each 3D trend of the Kinetic Energy equation is output;
\item [{\np{ln_tra_trd}{ln\_tra\_trd}}]: each 3D trend of the evolution of temperature and salinity is output;
\item [{\np{ln_tra_mxl}{ln\_tra\_mxl}}]: each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output;
\end{description}
Note that the mixed layer tendency diagnostic can also be used on biogeochemical models via
the \key{trdtrc} and \key{trdmxl\_trc} CPP keys.
\textbf{Note that} in the current version, many changes has been introduced but not fully tested.
In particular, options associated with \np{ln_dyn_mxl}{ln\_dyn\_mxl}, \np{ln_vor_trd}{ln\_vor\_trd}, and \np{ln_tra_mxl}{ln\_tra\_mxl} are not working,
and none of the options have been tested with variable volume (\ie\ \np[=.true.]{ln_linssh}{ln\_linssh}).
%% =================================================================================================
\section[FLO: On-Line Floats trajectories]{FLO: On-Line Floats trajectories}
\label{sec:DIA_FLO}
\begin{listing}
\nlst{namflo}
\caption{\forcode{&namflo}}
\label{lst:namflo}
\end{listing}
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 and the interface is activated by setting \np[=.true.]{ln_float}{ln\_float}.
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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
are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry.
%% =================================================================================================
\subsubsection{Input data: initial coordinates}
Initial coordinates can be given with Ariane Tools convention
(IJK coordinates, (\np[=.true.]{ln_ariane}{ln\_ariane}) ) or with longitude and latitude.
In case of Ariane convention, input filename is \textit{init\_float\_ariane}.
Its format is: \\
{ \texttt{I J K nisobfl itrash}}
\noindent with:
- I,J,K : indexes of initial position
- nisobfl: 0 for an isobar float, 1 for a float following the w velocity
- itrash : set to zero; it is a dummy variable to respect Ariane Tools convention
\noindent Example: \\
\noindent
{
\texttt{
100.00000 90.00000 -1.50000 1.00000 0.00000 \\
102.00000 90.00000 -1.50000 1.00000 0.00000 \\
104.00000 90.00000 -1.50000 1.00000 0.00000 \\
106.00000 90.00000 -1.50000 1.00000 0.00000 \\
108.00000 90.00000 -1.50000 1.00000 0.00000}
} \\
In the other case (longitude and latitude), input filename is init\_float.
Its format is: \\
{ \texttt{Long Lat depth nisobfl ngrpfl itrash}}
\noindent with:
- Long, Lat, depth : Longitude, latitude, depth
- nisobfl: 0 for an isobar float, 1 for a float following the w velocity
- ngrpfl : number to identify searcher group
- itrash :set to 1; it is a dummy variable.
\noindent Example: \\
\noindent
{
\texttt{
20.0 0.0 0.0 0 1 1 \\
-21.0 0.0 0.0 0 1 1 \\
-22.0 0.0 0.0 0 1 1 \\
-23.0 0.0 0.0 0 1 1 \\
-24.0 0.0 0.0 0 1 1 }
} \\
\np{jpnfl}{jpnfl} is the total number of floats during the run.
When initial positions are read in a restart file (\np[=.true.]{ln_rstflo}{ln\_rstflo} ),
\np{jpnflnewflo}{jpnflnewflo} can be added in the initialization file.
%% =================================================================================================
\subsubsection{Output data}
\np{nn_writefl}{nn\_writefl} is the frequency of writing in float output file and \np{nn_stockfl}{nn\_stockfl} is the frequency of
creation of the float restart file.
Output data can be written in ascii files (\np[=.true.]{ln_flo_ascii}{ln\_flo\_ascii}).
In that case, output filename is trajec\_float.
Another possiblity of writing format is Netcdf (\np[=.false.]{ln_flo_ascii}{ln\_flo\_ascii}) with
\key{xios} and outputs selected in iodef.xml.
Here it is an example of specification to put in files description section:
\begin{xmllines}
<group id="1d_grid_T" name="auto" description="ocean T grid variables" >
<file id="floats" description="floats variables">
<field ref="traj_lon" name="floats_longitude" freq_op="86400" />
<field ref="traj_lat" name="floats_latitude" freq_op="86400" />
<field ref="traj_dep" name="floats_depth" freq_op="86400" />
<field ref="traj_temp" name="floats_temperature" freq_op="86400" />
<field ref="traj_salt" name="floats_salinity" freq_op="86400" />
<field ref="traj_dens" name="floats_density" freq_op="86400" />
<field ref="traj_group" name="floats_group" freq_op="86400" />
</file>
</group>
\end{xmllines}
%% =================================================================================================
\section[Transports across sections]{Transports across sections}
\label{sec:DIA_diag_dct}
\begin{listing}
\nlst{nam_diadct}
\caption{\forcode{&nam_diadct}}
\label{lst:nam_diadct}
\end{listing}
A module is available to compute the transport of volume, heat and salt through sections.
This diagnostic is actived with \np[=.true.]{ln_diadct}{ln\_diadct}.
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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}
and are written in a binary file \texttt{section\_ijglobal.diadct} which is later read in by
\NEMO\ to compute on-line transports.
The on-line transports module creates three output ascii files:
- \texttt{volume\_transport} for volume transports (unit: $10^{6} m^{3} s^{-1}$)
- \texttt{heat\_transport} for heat transports (unit: $10^{15} W$)
- \texttt{salt\_transport} for salt transports (unit: $10^{9}Kg s^{-1}$) \\
Namelist variables in \nam{_diadct}{\_diadct} control how frequently the flows are summed and the time scales over which
they are averaged, as well as the level of output for debugging:
\np{nn_dct}{nn\_dct} : frequency of instantaneous transports computing
\np{nn_dctwri}{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
\np{nn_debug}{nn\_debug} : debugging of the section
%% =================================================================================================
\subsubsection{Creating a binary file containing the pathway of each section}
In \texttt{tools/SECTIONS\_DIADCT/run},
the file \textit{{list\_sections.ascii\_global}} contains a list of all the sections that are to be computed
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(this list of sections is based on MERSEA project metrics).
Another file is available for the GYRE configuration (\texttt{ {list\_sections.ascii\_GYRE}}).
Each section is defined by: \\
\noindent { \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\
with:
- \texttt{long1 lat1}, coordinates of the first extremity of the section;
- \texttt{long2 lat2}, coordinates of the second extremity of the section;
- \texttt{nclass} the number of bounds of your classes (\eg\ bounds for 2 classes);
- \texttt{okstrpond} to compute heat and salt transports, \texttt{nostrpond} if no;
- \texttt{ice} to compute surface and volume ice transports, \texttt{noice} if no. \\
\noindent The results of the computing of transports, and the directions of positive and
negative flow do not depend on the order of the 2 extremities in this file. \\
\noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\
{
\texttt{
long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\
classtype \\
zbound1 \\
zbound2 \\
. \\
. \\
nclass-1 \\
nclass}
}
\noindent where \texttt{classtype} can be:
- \texttt{zsal} for salinity classes
- \texttt{ztem} for temperature classes
- \texttt{zlay} for depth classes
- \texttt{zsigi} for insitu density classes
- \texttt{zsigp} for potential density classes \\
The script \texttt{job.ksh} computes the pathway for each section and creates a binary file
\texttt{section\_ijglobal.diadct} which is read by \NEMO. \\
It is possible to use this tools for new configuations: \texttt{job.ksh} has to be updated with
the coordinates file name and path. \\
Examples of two sections, the ACC\_Drake\_Passage with no classes,
and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\
\noindent
{
\texttt{
-68. -54.5 -60. -64.7 00 okstrpond noice ACC\_Drake\_Passage \\
-80.5 22.5 -80.5 25.5 05 nostrpond noice ATL\_Cuba\_Florida \\
ztem \\
-2.0 \\
4.5 \\
7.0 \\
12.0 \\
40.0}
}
%% =================================================================================================
\subsubsection{To read the output files}
The output format is: \\
{
\texttt{
date, time-step number, section number, \\
section name, section slope coefficient, class number, \\
class name, class bound 1 , classe bound2, \\
transport\_direction1, transport\_direction2, \\
transport\_total}
} \\
For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class and
the last line corresponds to the total transport summed over all classes.
For sections with no classes, class number \texttt{1} corresponds to \texttt{total class} and
this class is called \texttt{N}, meaning \texttt{none}.
- \texttt{transport\_direction1} is the positive part of the transport ($\geq$ 0).
- \texttt{transport\_direction2} is the negative part of the transport ($\leq$ 0). \\
\noindent The \texttt{section slope coefficient} gives information about the significance of transports signs and
direction: \\
\begin{table}
\begin{tabular}{|l|l|l|l|l|}
\hline
section slope coefficient & section type & direction 1 & direction 2 & total transport \\
\hline
0. & horizontal & northward & southward & postive: northward \\
\hline
1000. & vertical & eastward & westward & postive: eastward \\
\hline
\texttt{$\neq$ 0, $\neq$ 1000.} & diagonal & eastward & westward & postive: eastward \\
\hline
\end{tabular}
\end{table}
%% =================================================================================================
\section{Diagnosing the steric effect in sea surface height}
\label{sec:DIA_steric}
Changes in steric sea level are caused when changes in the density of the water column imply an expansion or
contraction of the column.
It is essentially produced through surface heating/cooling and to a lesser extent through non-linear effects of
the equation of state (cabbeling, thermobaricity...).
Non-Boussinesq models contain all ocean effects within the ocean acting on the sea level.
In particular, they include the steric effect.
In contrast, Boussinesq models, such as \NEMO, conserve volume, rather than mass,
and so do not properly represent expansion or contraction.
The steric effect is therefore not explicitely represented.
This approximation does not represent a serious error with respect to the flow field calculated by the model
\citep{greatbatch_JGR94}, but extra attention is required when investigating sea level,
as steric changes are an important contribution to local changes in sea level on seasonal and climatic time scales.
This is especially true for investigation into sea level rise due to global warming.
Fortunately, the steric contribution to the sea level consists of a spatially uniform component that
can be diagnosed by considering the mass budget of the world ocean \citep{greatbatch_JGR94}.
In order to better understand how global mean sea level evolves and thus how the steric sea level can be diagnosed,
we compare, in the following, the non-Boussinesq and Boussinesq cases.
Let denote
$\mathcal{M}$ the total mass of liquid seawater ($\mathcal{M} = \int_D \rho dv$),
$\mathcal{V}$ the total volume of seawater ($\mathcal{V} = \int_D dv$),
$\mathcal{A}$ the total surface of the ocean ($\mathcal{A} = \int_S ds$),
$\bar{\rho}$ the global mean seawater (\textit{in situ}) density
($\bar{\rho} = 1/\mathcal{V} \int_D \rho \,dv$), and
$\bar{\eta}$ the global mean sea level
($\bar{\eta} = 1/\mathcal{A} \int_S \eta \,ds$).
A non-Boussinesq fluid conserves mass. It satisfies the following relations:
\begin{equation}
\begin{split}
\mathcal{M} &= \mathcal{V} \;\bar{\rho} \\
\mathcal{V} &= \mathcal{A} \;\bar{\eta}
\end{split}
\label{eq:DIA_MV_nBq}
\end{equation}
Temporal changes in total mass is obtained from the density conservation equation:
\begin{equation}
\frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} )
= \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface}
\label{eq:DIA_Co_nBq}
\end{equation}
where $\rho$ is the \textit{in situ} density, and \textit{emp} the surface mass exchanges with the other media of
the Earth system (atmosphere, sea-ice, land).
Its global averaged leads to the total mass change
\begin{equation}
\partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}}
\label{eq:DIA_Mass_nBq}
\end{equation}
where $\overline{\textit{emp}} = \int_S \textit{emp}\,ds$ is the net mass flux through the ocean surface.
Bringing \autoref{eq:DIA_Mass_nBq} and the time derivative of \autoref{eq:DIA_MV_nBq} together leads to
the evolution equation of the mean sea level
\begin{equation}
\partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}}
- \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}}
\label{eq:DIA_ssh_nBq}
\end{equation}
The first term in equation \autoref{eq:DIA_ssh_nBq} alters sea level by adding or subtracting mass from the ocean.
The second term arises from temporal changes in the global mean density; \ie\ from steric effects.
In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ appears multiplied by
the gravity (\ie\ in the hydrostatic balance of the primitive Equations).
In particular, the mass conservation equation, \autoref{eq:DIA_Co_nBq}, degenerates into the incompressibility equation:
\[
\frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface}
% \label{eq:DIA_Co_Bq}
\]
and the global average of this equation now gives the temporal change of the total volume,
\[
\partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o}
% \label{eq:DIA_V_Bq}
\]
Only the volume is conserved, not mass, or, more precisely, the mass which is conserved is the Boussinesq mass,
$\mathcal{M}_o = \rho_o \mathcal{V}$.
The total volume (or equivalently the global mean sea level) is altered only by net volume fluxes across
the ocean surface, not by changes in mean mass of the ocean: the steric effect is missing in a Boussinesq fluid.
Nevertheless, following \citep{greatbatch_JGR94}, the steric effect on the volume can be diagnosed by
considering the mass budget of the ocean.
The apparent changes in $\mathcal{M}$, mass of the ocean, which are not induced by surface mass flux
must be compensated by a spatially uniform change in the mean sea level due to expansion/contraction of the ocean
\citep{greatbatch_JGR94}.
In others words, the Boussinesq mass, $\mathcal{M}_o$, can be related to $\mathcal{M}$,
the total mass of the ocean seen by the Boussinesq model, via the steric contribution to the sea level,
$\eta_s$, a spatially uniform variable, as follows:
\begin{equation}
\mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A}
\label{eq:DIA_M_Bq}
\end{equation}
Any change in $\mathcal{M}$ which cannot be explained by the net mass flux through the ocean surface
is converted into a mean change in sea level.
Introducing the total density anomaly, $\mathcal{D}= \int_D d_a \,dv$,
where $d_a = (\rho -\rho_o ) / \rho_o$ is the density anomaly used in \NEMO\ (cf. \autoref{subsec:TRA_eos})
in \autoref{eq:DIA_M_Bq} leads to a very simple form for the steric height:
\begin{equation}
\eta_s = - \frac{1}{\mathcal{A}} \mathcal{D}
\label{eq:DIA_steric_Bq}
\end{equation}
The above formulation of the steric height of a Boussinesq ocean requires four remarks.
First, one can be tempted to define $\rho_o$ as the initial value of $\mathcal{M}/\mathcal{V}$,
\ie\ set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero.
We do not recommend that.
Indeed, in this case $\rho_o$ depends on the initial state of the ocean.
Since $\rho_o$ has a direct effect on the dynamics of the ocean
(it appears in the pressure gradient term of the momentum equation)
it is definitively not a good idea when inter-comparing experiments.
We better recommend to fixe once for all $\rho_o$ to $1035\;Kg\,m^{-3}$.
This value is a sensible choice for the reference density used in a Boussinesq ocean climate model since,
with the exception of only a small percentage of the ocean, density in the World Ocean varies by no more than
2$\%$ from this value (\cite{gill_bk82}, page 47).
Second, we have assumed here that the total ocean surface, $\mathcal{A}$,
does not change when the sea level is changing as it is the case in all global ocean GCMs
(wetting and drying of grid point is not allowed).
Third, the discretisation of \autoref{eq:DIA_steric_Bq} depends on the type of free surface which is considered.
In the non linear free surface case, \ie\ \np[=.true.]{ln_linssh}{ln\_linssh}, it is given by
\[
\eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} }{ \sum_{i,\,j,\,k} e_{1t} e_{2t} e_{3t} }
% \label{eq:DIA_discrete_steric_Bq_nfs}
\]
whereas in the linear free surface,
the volume above the \textit{z=0} surface must be explicitly taken into account to
better approximate the total ocean mass and thus the steric sea level:
\[
\eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta }
{ \sum_{i,\,j,\,k} e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} e_{1t}e_{2t} \eta }
% \label{eq:DIA_discrete_steric_Bq_fs}
\]
The fourth and last remark concerns the effective sea level and the presence of sea-ice.
In the real ocean, sea ice (and snow above it) depresses the liquid seawater through its mass loading.
This depression is a result of the mass of sea ice/snow system acting on the liquid ocean.
There is, however, no dynamical effect associated with these depressions in the liquid ocean sea level,
so that there are no associated ocean currents.
Hence, the dynamically relevant sea level is the effective sea level,
\ie\ the sea level as if sea ice (and snow) were converted to liquid seawater \citep{campin.marshall.ea_OM08}.
However, in the current version of \NEMO\ the sea-ice is levitating above the ocean without mass exchanges between
ice and ocean.
Therefore the model effective sea level is always given by $\eta + \eta_s$, whether or not there is sea ice present.
In AR5 outputs, the thermosteric sea level is demanded.
It is steric sea level due to changes in ocean density arising just from changes in temperature.
It is given by:
\[
\eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv
% \label{eq:DIA_thermosteric_Bq}
\]
where $S_o$ and $p_o$ are the initial salinity and pressure, respectively.
Both steric and thermosteric sea level are computed in \mdl{diaar5}.
%% =================================================================================================
\section{Other diagnostics}
\label{sec:DIA_diag_others}
Aside from the standard model variables, other diagnostics can be computed on-line.