CDFTOOLS - diagnostics in Fortran 90 for NEMO model outputs
CDFTOOLS is a diagnostic package written in fortran 90 for the analysis of NEMO model output, initialized in the frame of the DRAKKAR project (https://www.drakkar-ocean.eu/). It is now available on GitHub under the CeCILL license (http://www.cecill.info/licences/Licence_CeCILL_V2-en.html).
NEMO web site : http://www.nemo-ocean.eu/
CDFTOOLS is a collection of fortran program. Each program belonging to this collection is designed to perform some specific actions on NEMO output files, and generally provides another netcdf file as output. Output files follow the same CDF format as NEMO file, thus allowing for the building of a secondary data base (assuming that the primary data base is just the raw model output).
This documentation is automatically produced by the concatenation of the USAGE messages produced by each particular program when invoked without any argument. (Standard behaviour of all cdftools). In the documentation, we use a rather classical formalism, where mandatory arguments are just indicated on the command line and options are indicated between squared brackets [..].
Each program name starts with the 3 letters 'cdf' followed by a word related to the action performed by the tools. Example: cdfw Ufile.nc Vfile.nc is used to compute the vertical velocity using the horizontal velocity field represented by its two components Ufile.nc and Vfile.nc.
Better than a long speech, the following paragraphs describes each of the existing cdftools. CDFTOOLS have been sorted out by classes in order to have a consistent documentation.
usage : cdfbn2 -t T-file [-W] [-full] [-o OUT-file] [-nc4] [-vvl W-file]
PURPOSE :
Compute the Brunt-Vaissala frequency (N2) according to temperature and
salinity given in the input file.
ARGUMENTS :
-t T-file : netcdf input gridT file for temperature and salinity.
OPTIONS :
[-W ] : keep N2 at W points. Default is to interpolate N2 at T point on
the vertical.
[-full ] : indicate a full step configuration instead of the default
partial steps.
[-o OUT-file ] : specify output file name instead of bn2.nc.
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl W-file ] : use time-varying vertical metrics, W-file is a file
holding e3w(t) for vvl.
OPENMP SUPPORT : yes
REQUIRED FILES :
mesh_zgr.nc is needed for this program.
OUTPUT :
netcdf file : bn2.nc unless -o option specified
variables : vobn2
SEE ALSO :
cdfsig0, cdfsigi, cdfsiginsitu, cdfsigntr usage : cdfsig0 -t T-file [-sal SAL-name] [-tem TEM-name] [-nc4] [-o OUT-file]
PURPOSE :
Compute potential density (sigma-0) refered to the surface.
ARGUMENTS :
-t T-file : netcdf file with temperature and salinity.
OPTIONS :
[-sal SAL-name] : name of salinity variable
[-tem TEM-name] : name of temperature variable
[-nc4] : enable chunking and compression
[-o OUT-file] : specify output filename instead of sig0.nc
OPENMP SUPPORT : yes
REQUIRED FILES :
none
OUTPUT :
netcdf file : sig0.nc
variables : vosigma0 ( kg/m3 - 1000 )
SEE ALSO :
cdfsigi, cdfsigintu, signtr usage : cdfsigi -t T-file -r REF-dep(m) [-o OUT-file] [-nc4]
PURPOSE :
Compute potential density referred to the depth given in arguments.
ARGUMENTS :
-t T-file : netcdf file with temperature and salinity.
-r REF-dep : reference depth in meter.
OPTIONS :
[-o OUT-file ] : Specify output file name instead of sigi.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : sigi.nc
variables : vosigmai (kg/m3 -1000 )
SEE ALSO :
cdfsig0, cdfsiginintu
usage : cdfsiginsitu -t T-file [-sal SAL-name] [-tem TEM-name ] ...
[-dep depth] [-o OUT-file ] [-nc4 ]
PURPOSE :
Compute in situ density from temperature and salinity. Depths are taken
from input file.
ARGUMENTS :
-t T-file : netcdf file with temperature and salinity.
OPTIONS :
[-sal SAL-name] : name of salinity variable
[-tem TEM-name] : name of temperature variable
[-dep depth ] : depth to be used in case of 2D input file (only)
[-nc4] : enable chunking and compression
[-o OUT-file] : specify output filename instead of siginsitu.nc
OPENMP SUPPORT : yes
REQUIRED FILES :
none
OUTPUT :
netcdf file : siginsitu.nc or the file name specified
with -o option
variables : vosigmainsitu (kg/m3 -1000 )
SEE ALSO :
cdfsig0, cdfsigi, cdfsigntr
usage : cdfsigntr -t T-file [-o OUT-file] [-nc4]
PURPOSE :
Compute neutral volumic mass (kg/m3) from temperature and salinity.
ARGUMENTS :
-t T-file : netcdf file with temperature and salinity.
OPTIONS :
[-o OUT-file ] : Specify output file name instead of signtr.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
OPENMP SUPPORT : yes
REQUIRED FILES :
none
OUTPUT :
netcdf file : signtr.nc unless option -o is used.
variables : vosigntr ( kg/m3 )
SEE ALSO :
cdfsig0, cdfsigi, cdfsiginsitu, cdfspice usage : cdfspice -t T-file [-sal SAL-name] [-tem TEM-name] ...
... [-o OUT-file] [-nc4]
PURPOSE :
Compute the spiceness corresponding to temperatures and salinities
given in the input file.
spiciness = sum(i=0,5)[sum(j=0,4)[b(i,j)*theta^i*(s-35)^j]]
with: b -> coefficients
theta -> potential temperature
s -> salinity
ARGUMENTS :
-t T-file : netcdf file with temperature and salinity (gridT)
OPTIONS :
[-sal SAL-name] : name of salinity variable
[-tem TEM-name] : name of temperature variable
[-o OUT-file] : specify output filename instead of spice.nc
[-nc4] : enable chunking and compression
OPENMP SUPPORT : yes
REQUIRED FILES :
none
OUTPUT :
netcdf file : spice.nc unless option -o is used.
variables : vospice
REFERENCE :
Flament (2002) "A state variable for characterizing
water masses and their diffusive stability: spiciness."
Progress in Oceanography Volume 54, 2002, Pages 493-501.
usage : cdfbotpressure -f T-file [-full] [-ssh] [-ssh2 ] [-xtra ] [-vvl ]
... [ -o OUT-file ] [-nc4]
PURPOSE :
Compute the bottom pressure (pa) from in situ density.
ARGUMENTS :
-f T-file : gridT file holding both temperature and salinity.
OPTIONS :
[-full] : for full step computation
[-ssh] : Also take SSH into account in the computation
In this case, use rau0= 1035.000 kg/m3 for
surface density (as in NEMO)
If you want to use 2d surface density from
the model, use option -ssh2
[-ssh2] : as option -ssh but surface density is taken from
the model instead of a constant
[-xtra] : Using this option, the output file also contains the ssh,
and the pressure contribution of ssh to bottom pressure.
Require either -ssh or -ssh2 option. Botpressure is still
the total pressure, including ssh effect.
[-vvl] : Use time-varying vertical metrics e3t
[-o OUT-file] : specify output file instead of botpressure.nc
[-nc4] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
OPENMP SUPPORT : yes
REQUIRED FILES :
mask.nc and mesh_zgr.nc
OUTPUT :
netcdf file : botpressure.nc unless -o option is used.
variables : sobotpres, [sossheig sosshpre ]
SEE ALSO :
cdfvint
usage : cdfbottom -f IN-file [-p C-type] [-o OUT-file] [-nc4]
PURPOSE :
Create a 2D file with bottom most values for all the variables which
are in the input 3D file.
ARGUMENTS :
-f IN-file : input netcdf 3D file.
OPTIONS :
[-p C-type] : specify the type of grid point on the C-grid (T|U|V|F).
If not given, assume that land points are values with 0.
[-o OUT-file ]: specify output filename instead of bottom.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mask.nc file is required if the grid point is specified or if
the land value is not 0.
OUTPUT :
netcdf file : bottom.nc unless -o option is used.
variables : same names than input file, long_name attribute is
prefixed by Bottom
usage : cdfbottomsig -t T-file [-r REF-depth ] [-ntr] [-o OUT-file] [-nc4]
PURPOSE :
Create a 2D file with bottom density. In case a depth reference is
given, the density is referred to this depth. By default sigma-0 is
used. Bottom most point is determined from the last non zero salinity
point in the water column.
ARGUMENTS :
-t T-file : input file with temperature and salinity.
OPTIONS :
[-r REF-depth] : depth reference for potential density.
Without -r nor -ntr options sigma-0 is assumed.
[-ntr ]: Will use neutral density.
Without -r nor -ntr options sigma-0 is assumed.
[-o OUT-file] : Specify output file name instead of botsig.nc
[-nc4]: Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
OPENMP SUPPORT : yes
REQUIRED FILES :
none
OUTPUT :
netcdf file : botsig.nc unless -o option is used.
variables : sobotsig0 or sobotsigi ( kg/m3 - 1000 )
or sobotsigntr (kg/m3)
usage : cdf16bit -f 32BIT-file [-check] [-verbose] [-o OUT-file] [-nc4]
PURPOSE :
Convert input 32 bit precision file into 16 bit precision file using
add_offset and scale_factor.
Note that predifined values for these two parameters are defined
according to the variable name. If variable name is not supported,
no conversion is performed.
ARGUMENTS :
-f 32BIT-file : input 32 bit file to be converted
OPTIONS :
[-check ] : control than the scale factors are adequate.
[-verbose ] : give information level by level.
[-o OUT-file] : Specify output file name instead of cdf16bit.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : cdf16bit.nc
variables : same names than in input file usage : cdf2levitusgrid2d -f IN-file -o OUT-file -v VAR-name2D
PURPOSE :
Remaps (by binning) 2D high resolution (i.e. finer than 1x1 deg)
fields on Levitus 2D 1x1 deg grid. This program does not work for
vector fields.
It assumes that the southwestern-most grid cell of the target grid
(Levitus 1 deg) is centered at (0.5W,89.5S).
ARGUMENTS :
-f IN-file : netcdf input file
-o OUT-file : netcdf output file
-v VAR-name2D : input variable name for interpolation
OPTIONS :
REQUIRED FILES :
mesh_hgr.nc
mask.nc
levitus_mask.nc
OUTPUT :
netcdf file : name given as second argument
variables : 2d_var_name usage : cdf2matlab -f IN-file -v IN-var -k level [-o OUT-file] [-nc4]
PURPOSE :
Convert global nemo input file (ORCA configurations) into
a file with monotonically increasing longitudes.
ARGUMENTS :
-f IN-file : input model file.
-v IN-var : netcdf variable name to process.
-k level : level to process.
OPTIONS :
[-o OUT-file] : specify output file name instead of output.nc
[-nc4 ]: Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : output.nc
variables : same name than in input file. usage : cdf2regular -f IN-file -v VAR-name [-o OUT-file] [-360] ...
... [-r TGT-resolution] [-nc4]
PURPOSE :
Remap (by binnig) high resolution fields on a coarser regular grid,
keeping the same vertical grid as in the input file.
This program is not suitable for vector fields, as far as transport
conservation is concerned.
Default output grid resolution is 1/ 3 deg. It can be changed using
the -r option.
Note that output file is not masked.
ARGUMENTS :
-f IN-file : netcdf input file
-v VAR-name : input variable name to be remapped.
OPTIONS :
[-o OUT-file]: netcdf output file, instead of regular.nc
[-nc4 ]: Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-360 ]: Output file longitudes span [0 -> 360 deg.], instead of
the default [-180 -> 180 deg.].
[-r TGT-resolution ]: Target resolution (in degrees).
REQUIRED FILES :
mesh_hgr.nc
mask.nc
OUTPUT :
netcdf file : name given as second argument
variables : 3d_var_name
SEE ALSO :
cdf2levitus2d (a particular case)
usage : cdfbathy/cdfvar -f IN-file [options]
PURPOSE :
Allow manual modification of the input file. Very convenient for
bathymetric files, can also be used with any other model file.
Keep a log.f90 file of the modifications for automatic reprocessing
ARGUMENTS :
-f IN-file : original input file. The program works on a copy of the
original file (default)
OPTIONS :
-file (or -f ) : name of input file
-var (or -v ) : name of cdf variable [default: Bathymetry]
-lev (or -l ) : level to work with
-time (or -t ) : time to work with
-scale s : use s as a scale factor (divide when read the file)
-zoom (or -z ) : sub area of the bathy file to work with (imin imax jmin jmax)
-fillzone (or -fz ) : sub area will be filled with 0 up to the first coast line
-fillpool (or -fp ) [ icrit ] : the whole file is check and fill all the pool smaller than (icrit) cell by 0
-raz_zone (or -raz ) : sub area will be filled with 0 up
-raz_below depmin : any depth less than depmin in subarea will be replaced by 0
(or -rb depmin )
-set_below depmin : any depth less than depmin in subarea will be replaced by depmin
(or -sb depmin )
-fullstep depmin : sub area will be reshaped as full-step, below depmin
(or -fs depmin ) requires the presence of the file zgr_bat.txt (from ocean.output, eg )
-dumpzone (or -d ) : sub area will be output to an ascii file, which can be used by -replace
after manual editing
-nicedumpzone : sub area will be output to an ascii file (nice output)
(or -nd )
-replace (or -r ) : sub area defined by the file will replace the original bathy
-append (or -a ) : fortran log file (log.f90) will be append with actual modif
Standard behaviour is to overwrite/create log file
-overwrite (or -o ) : input bathy file will be used as output.
Standard behaviour is to use a work copy of the original file
(indexed from 01 to 99 if necessary )
-log logfile : log file for change (default is log.f90)
OUTPUT :
netcdf file : according to used options, if the original file is to be modified
a sequence number is added at the end of the input file name, to keep
modifications.
variables : same as input file usage : cdfcoloc -w ROOT-weight -t T-file -u U-file -v V-file [-h] ...
... [-l LST-fields] [-trc TRC-file] [-d DIAG-file] [-b ETOPO-file]
PURPOSE :
This program produces 3D colocalized model values for selected fields.
It is the final pass in the colocalization process initialized by
'cdfweight', in which the location of the points to be colocalized
is set. The 2 steps of the process are separated because weight files
are to be produced only once for a set of data-point and model config,
whereas 'cdfcoloc' is used for several model files corresponding to
different times.
This program was initially written to deal with G. Holloway topostrophy
works.
ARGUMENTS :
-w ROOT-weight : specify the root-name of the weight files (binary
files), to which the suffixes '_T.bin', '_U.bin' or '_V.bin'
are appended if necessary.
-t T-file : name of gridT model file, used for default fields.
-u U-file : name of gridU model file, used for default fields.
-v V-file : name of gridV model file, used for default fields.
OPTIONS :
[-h ] : Gives details on the available fields.
[-l LST-fields ] : Gives a comma-separated list of selected fields to be
colocalized, from a whole set of fields which are fully described
with the '-h' option. The default list is: U,V,Sx,Sy,H
According to the selected fields, specific model files are to be
passed to the program with corresponding option.
[-trc TRC-file]: name of ptrcT model file, used for when passive tracers
related fields are selected (CFCINV, CFCCINC or PENDEP).
[-d DIAG-file ] : name of specific diagnostic file. This file is used
when 'PENDEP' or 'ISOTHICK' are selected. It must have the
variables pendep or isothick, respectively produced by
'cdfpendep' and 'cdfsigintegr'.
[-b ETOPO-file ] : name of 'etopo-like' bathymetric file.
REQUIRED FILES :
mask.nc. If bathymetric slopes are needed, then
coordinates.nc and mesh_zgr.nc files are also required.
OUTPUT :
Output is a multi columns ASCII file with first 2 columns giving
'ID' and 'DEPTH'. Then the line is completed with colocated
field values. The output file looks pretty much as the input file
used in 'cdfweight' for building the weight files.
SEE ALSO :
cdfweight
usage : cdffixtime -f IN-file -i initial date [-t tag] [-dt freq] ...
... [-keep ] [-leap] [-noleap]
PURPOSE :
Change time_counter in file to set it according to drakkar rule,
time_counter attibutes 'units' and 'time_origin' are ajusted.
* units are 'seconds since yyyy-mm-dd hh:mm:ss'
* time_origin is set to 'yyyy-MMM-dd hh:mm:ss', MMM represents a
literal abbreviation for the month (eg: JAN FEB MAR ...)
Once fixed, the time_counter indicates the middle of the output
interval (in case of averaged output, of course).
ARGUMENTS :
-f IN-file : specify the file whose time_counter need adjustment
-i inital date : indicate the time origin in a fixed 2 words format
yyyy-mm-dd hh:mm:ss ( eg: 1956-05-16 04:30:00 )
OPTIONS :
[-t tag] : supply a time tag corresponding to the file. If not
supplied, tag is taken from the name of the input file
assuming DRAKKAR convention ( CONFIG-CASE_tag_xxxx.nc )
[-dt freq]: number of days between model output [ 5d ]
[-leap] : assume a calendar with leap years
[-noleap] : assume a calendar without leap years (default)
[-keep] : keep the actual value of time_counter, adjust time_counter
attributes only;
REQUIRED FILES :
none
OUTPUT :
netcdf file : Input file is modified (only attributes)
usage : cdfnorth_unfold -f IN-file -jatl jatl -jpacif jpacif -piv pivot ...
... -p C-type [-o OUT-file] [-nc4]
PURPOSE :
Unfolds the Artic Ocean in an ORCA configuration. Produce a netcdf
file with the Artic ocean as a whole. The area can be adjusted on
both Atlantic and Pacific sides.
ARGUMENTS :
-f IN-file : Input netcdf file to be unfolded.
-jatl jatl : J index to start the unfold process in the Atlantic.
-jpacif jpacif : J index to start the unfold process in the Pacific.
-piv pivot : type of pivot for the north fold condition ( T or F )
ORCA1, ORCA05 use F-pivot, ORCA2, ORCA025, ORCA12 use T-pivot.
-p C-type : one of T|U|V|W|F , indicating the grid point where the
variables in the input file are located. If all variables in a
single file are not on the same C-grid location, there might be
a problem ...
OPTIONS :
[-o OUT-file] : Specify output file name instead of unfold.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : unfold.nc unless -o option is used.
variables : same name and units than in the input file.
usage : cdfsmooth -f IN-file -c ncut [-t FLT-type] [-k LST-level] ...
[-anis ratio ] [-nc4 ]
PURPOSE :
Perform a spatial smoothing on the file using a particular filter as
specified in the '-t' option. Available filters are : Lanczos, Hanning,
Shapiro and Box car average. Default is Lanczos filter.
ARGUMENTS :
-f IN-file : input data file. All variables will be filtered
-c ncut : number of grid step to be filtered, or number
of iteration of the Shapiro filter.
OPTIONS :
[-t FLT-type] : Lanczos , L, l (default)
Hanning , H, h
Shapiro , S, s
Box , B, b
[-anis ratio ] : Specify an anisotropic ratio in case of Box-car filter.
With ratio=1, the box is a square 2.ncut x 2.ncut grid points.
In general, the box is then a rectangle 2.ncut*ratio x 2.ncut.
[-k LST-level ] : levels to be filtered (default = all levels)
LST-level is a comma-separated list of levels. For example,
the syntax 1-3,6,9-12 will select 1 2 3 6 9 10 11 12
[-nc4] : produce netcdf4 output file with chunking and deflation.
OUTPUT :
Output file name is build from input file name with indication
of the filter type (1 letter) and of ncut.
netcdf file : IN-file[LHSB]ncut
variables : same as input variables.
usage : cdfweight -f IN-file [-c COORD-file] [-p C-type] [-2d] [-v]
PURPOSE :
Produces a weight file for further bilinear colocalisation with
cdfcoloc program. It takes the position of the points to be
colocated into a simple ascii file.
ARGUMENTS :
-f IN-file : input file is a iyxz ASCII file, 1 line per point.
OPTIONS :
[-c COORD-file] : coordinate file [coordinates.nc]
[-p C-type ] : point type on C-grid (either T U V or F ) [F]
[-2d ] : tell cdfweight that only 2D weights will be computed.
[-v ] : Verbose mode for extra information (debug mode).
REQUIRED FILES :
coordinates.nc file if not passed as argument.
If working with 3D files, mesh_zgr.nc is required.
OUTPUT :
binary weight file : weight_point_type.bin
standard output : almost the same info that is saved in the binary file
When using -v option, even more informations !
SEE ALSO :
cdfcoloc
usage : cdfcurl -u U-file U-var -v V-file V-var -l LST-level [-T] [-8]...
... [-surf] [-overf] [-o OUT-file] [-nc4]
PURPOSE :
Compute the curl of a vector field, at a specified level. If level is
specified as 0, assume that the input files are forcing files, using
an A-grid. In this latter case, the vector field is interpolated on the
C-grid. In any case, curl is computed on F-point (unless '-T' option
is used).
ARGUMENTS :
-u U-file U-var : file and variable name for zonal component
-v V-file V-var : file and variable name for meridional component
-l LST-level : levels to be processed. If set to 0, assume forcing file
in input. Example of recognized syntax :
-l "1,10,30" or -l "1-20" or even -l "1-3,10-20,30-"
-l 1 . Note that -l "3-" set a level list from 3 to the bottom.
OPTIONS :
[-T] : compute curl at T point instead of default F-point
[-8] : save in double precision instead of standard simple precision.
[-surf] : work with single level C-grid (not forcing)
[-overf]: store the ratio curl/f where f is the coriolis parameter.
This option is not compatible with -T option.
[-o OUT-file] : specify output file name instead of curl.nc
[-nc4] : use netcdf4 output with chunking and deflation 1
REQUIRED FILES :
mesh_hgr.nc
OUTPUT :
netcdf file : curl.nc
variables : socurl or socurlt (if -T option), units : s^-1
or socurloverf, no units (if -overf option)
usage : cdfdiv -u U-file U-var -v V-file V-var -l LST-level [-8]...
... [-surf] [-overf] [-full] [-o OUT-file ] [-nc4]
... [-vvl T-file]
PURPOSE :
Compute the divergence of the flow from the U and V velocity components.
Divergence is computed at T point on the C-grid.
ARGUMENTS :
-u U-file U-var : file and variable name for zonal component
-v V-file V-var : file and variable name for meridional component
-l LST-level : levels to be processed. If set to 0, assume forcing file.
in input. Example of recognized syntax :
-l "1,10,30" or -l "1-20" or even -l "1-3,10-20,30-"
-l 1 . Note that -l "3-" set a level list from 3 to the bottom
OPTIONS :
[-8]: save in double precision instead of standard simple precision.
[-surf] : work with single level C-grid (not forcing)
[-overf]: store the ratio div/f where f is the coriolis parameter
[-full] : in case of full step configuration. Default is partial step.
[-o OUT-file] : specify output file name instead of div.nc
[-nc4] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl T-file] : use time-varying e3t, specify T-file for e3t.
REQUIRED FILES :
mesh_hgr.nc mesh_zgr.nc
OUTPUT :
netcdf file : div.nc unless -o option is used.
variables : div units : s^-1
or divoverf, no units (if -overf option)
usage : cdfdynh_anom -f T-file [-limit lev1 lev2] [-vvl] [-o OUT-file] [-nc4]
PURPOSE :
Compute dynamic height anomaly from T-file given as argument.
In this tool, the cumulated values (from top to bottom) are saved at
each model level.
If the -limit option is used, only the 2D integral of the dynamic
height anomaly between lev1 and lev2 is saved.
This program replace cdfhdy ( case using -limit option) and cdfhdy3d
in the standard case.
ARGUMENTS :
-f T-file : netcdf file with temperature and salinity.
OPTIONS :
[-limit lev1 lev2] : if specified, the program will only output the
dynamic height anomaly at lev1 with reference at lev2.
[-vvl] : use time-varying vertical metrics.
[-o OUT-file] : Specify output file name instead of cdfhdy3d.nc
[-nc4] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
OPENMP SUPPORT : yes
REQUIRED FILES :
mask.nc and mesh_zgr.nc
OUTPUT :
netcdf file : cdfhdy3d.nc unless -o option is used.
variables : vohdy ( m )
If -limit option is used :
netcdf file : cdfhdy2d.nc unless -o option is used.
variables : sohdy ( m )
SEE ALSO :
replace old tools cdfhdy and cdfhdy3d.
usage : cdfeke -u U-file [-u2 U2-file] -v V-file [-v2 V2-file] -t T-file ...
... [-mke] [-o OUT-file] [-nc4]
PURPOSE :
Compute the Eddy Kinetic Energy from previously computed mean values
and mean squared values of velocity components.
ARGUMENTS : both 'General Use' or 'Reduced Use' are acceptable
* General Use: 5 files are given in argument, and EKE is computed
-u U-file : gridU type file with mean U component.
-u2 U2-file : gridU2 type file with mean U2 component.
-v V-file : gridV type file with mean V component.
-v2 V2-file : gridV2 type file with mean V2 component.
-t T-file : any gridT or gridT2 (smaller) file, used for EKE header.
* Reduced Use: no U2/V2 file, only MKE is computed from U and V file.
-u U-file : gridU type file with mean U component.
-v V-file : gridV type file with mean V component.
-t T-file : any gridT or gridT2 (smaller) file, used for MKE header.
OPTION :
[-mke] : output MKE field together with EKE.
[-nc4] : allow netcdf4 output with compression and chunking.
[-o output file]: specify output file name instead of eke.nc
REQUIRED FILES :
none
OUTPUT :
netcdf file : eke.nc unless -o option in use.
variables : voeke (m2/s)
variables : vomke (m2/s) if required
usage : cdfgeo-uv -f T-file [-o UOUT-file VOUT-file ] [-nc4] [-C option]
PURPOSE :
Compute the geostrophic velocity components from the gradient of the
SSH read in the input file.
Without any -C option, the zonal component is located on a C-grid
V point, the meridional one is located on a C-grid U point. See the
use of the -C option in order to have (Ugeo, Vgeo) at (U,V) points on
the C-grid.
ARGUMENTS :
-f T-file : netcdf file with SSH (input).
OPTIONS :
[-o UOUT-file VOUT-file]: specify the names of the output files.
Default are: ugeo.nc vgeo.nc.
[-nc4]: Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-C option]: Using this option, the output velocity component are at the
correct (U,V) points on the C-grid. Two options are available :
option = 1 : SSH is interpolated on the F point prior derivation.
option = 2 : Ugeo and Vgeo are interpolated on the C-grid after
derivation.
Both options should give very similar results...
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
- netcdf file : ugeo.nc (default)
variables : vozocrtx
Unless -C option is used :
*** CAUTION: this variable is located on V-point ***
- netcdf file : vgeo.nc (default)
variables : vomecrty
Unless -C option is used :
*** CAUTION: this variable is located on U-point ***
usage : cdfgeostrophy -f T-file [-o OUT-ufile OUT-vfile] [-nc4] [-vvl]
PURPOSE :
Compute the geostrophic velocity components from the pressure gradient
induced by SSH and in-situ density (T,S of input file), using the
thermal wind equation.
WARNING : USE AT YOUR OWN RISKS.
ARGUMENTS :
-f T-file : netcdf file with SSH, T and S.
OPTIONS :
[-o OUT-ufile OUT-vfile] : Specify output files name's instead of
ugeo.nc and vgeo.nc
[-nc4 ]: Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl] : use time varying vertical metrics.
REQUIRED FILES :
mask.nc mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
- netcdf file : ugeo.nc
variables : vozocrtx
- netcdf file : vgeo.nc
variables : vomecrty
usage : cdfgradT -t T-file [-s S-file] [-o OUT-file] [-nc4] [-vvl W-file]
PURPOSE :
Compute horizontal and vertical gradient of temperature and salinity.
Results are saved at U point for zonal gradient, V point for meridional
gradient and W for vertical gradient.
ARGUMENTS :
-t T-file : File with votemper and vosaline variables
If vosaline not in T-file consider the use of -s option.
OPTIONS :
[-s S-file ] : File with vosaline variable if not in T file
[-o OUT-file] : specify output file name, instead of gradT.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl W-file ] : use time-varying vertical metrics. W-file is a file
where the time-varying vertical e3w metrics can be found.
REQUIRED FILES :
mesh_hgr.nc mask.nc and mesh_zgr.nc
OUTPUT :
netcdf file : gradT.nc
6 variables :
vozogradt, vomegradt, vovegradt : 3 component of the temperature
located respectively at U, V and W points
vozograds, vomegrads, vovegrads : 3 component of the salinity
located respectively at U, V and W points
SEE ALSO :
cdfhgradb
usage : cdfhgradb -t T-file [-s S-file] [-o OUT-file] [-nc4] ...
... [-sal SAL-name] [-tem TEMP-name]
PURPOSE :
Compute the norm of the horizontal buoyancy gradient. Results are
saved at T points.
ARGUMENTS :
-t T-file : File with votemper and vosaline variables
If vosaline not in T-file use -s option.
Note that salinity and/or temperature variables name can be changed
with -sal and/or -tem options, respectively.
OPTIONS :
[-s S-file ] : File with vosaline variable if not in T file.
[-o OUT-file] : specify the name of output file instead of
hgradb_gridT.nc
[-nc4] : use netcdf4 chunking and deflation on output.
[-sal SAL-name]: specify the name of salinity variable.
[-tem TEM-name]: specify the name of temperature variable.
REQUIRED FILES :
mesh_hgr.nc mask.nc and mesh_zgr.nc
OPENMP SUPPORTED : yes
OUTPUT :
netcdf file : hgradb_gridT.nc ( unless specified with -o option)
1 variables :
vohgradb: norm of the horizontal buoyancy gradient at t-point
SEE ALSO :
cdfbuoyflx
usage : cdflap -f IN-file -v IN-var -t IN-type [-overf2] [-nometric] ...
...[-o OUT-file] [-nc4]
PURPOSE :
Compute the Laplacian of the variable IN-var in file IN-file. Assume
that the data are on a C-grid model (as NEMO).
ARGUMENTS :
-f IN-file : netcdf file in input
-v IN-var : name of the variable to process
-t IN-TYPE : Position of the variable on the C-grid [ T U V F ]
OPTIONS :
[-overf2] : save laplacien/f/f*g (where f is the local coriolis
parameter, and g is the accelaration due to gravity --9.81 m/s2-- )
For the SSH field, this is a proxy for geostrophic vorticity
[-nometric] : compute laplacian without considering metrics
[-o OUT-file] : specify output file name instead of lap.nc
This option must be used after the -overf2 or -nometric option, as
output file name is redefined when using these options.
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1..
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_hgr.nc mesh_zgr.nc and mask.nc
OUTPUT :
netcdf file : lap.nc
variables : lap<var> (unit/m2)
if option -overf2 is used, netcdf file is lapoverf2.nc and
variable is lap<var>overf2 usage : cdfpvor -t T-file -u U-file -v V-file [-full] [-lspv] ...
... [-o OUT-file] [-nc4] [-vvl W-file]
PURPOSE :
Compute the Ertel potential vorticity and save the relative
vorticity, the stretching and the total potential vorticity.
Qtot = ( f + xsi ) . D(rho)/D(z) = Qstrech + Qrel
With -lspv option, compute only Qstretch or Large Scale P V
ARGUMENTS :
-t T-file : netcdf file for temperature and salinity.
-u U-file : netcdf file for zonal component of the velocity.
-v V-file : netcdf file for meridional component of the velocity.
OPTIONS :
[-full ] : indicate a full step configuration.
[-lspv ] : calculate only the large scale potential vorticity.
( replace the old cdflspv tool).
If used only T-file is required, no need for velocities.
[-nc4 ] : use netcdf4 with chunking and deflation
[-o OUT-file] : use output file instead of default pvor.nc
[-vvl W-file] : use time-varying vertical metrics. W-file holds the
time-varying e3w vertical metrics.
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
netcdf file : pvor.nc
variables : vorelvor (1.e-7 kg.m-4.s-1 ) relative vorticity
vostrvor (1.e-7 kg.m-4.s-1 ) stretching vorticity
vototvor (1.e-7 kg.m-4.s-1 ) total potential vorticity
Ertel PV are located at T points.
With option -lspv :
netcdf file : lspv.nc
variables : volspv (1.e-7 kg.m-4.s-1 ) large scale potential
vorticity. LSPV is located at W points.
SEE ALSO :
cdfcurl ( compute only the curl on 1 level)
usage : cdfrhoproj-v IN-var -s RHO-file -l LST-files [-p C-type] [-debug]...
... [-isodep] [-s0 sig0 | -s0 sigmin,sigstp,nsig] [-sig sigma_name]..
... [-noiso] [-rholev TXT-file] [-o OUT-isodep] [-nc4]
PURPOSE :
This program aims at projecting the model variable IN-var, from a list
of model files (LST-files) on some isopycnic surfaces, inferred from
a 3D density file, passed as one the arguments of the program.
The density values corresponding to the isopycnic surfaces can be
specified in three ways :
1. Using a predefined text file rho_lev with density
values. The format is straightforward: one value per line, first
line giving the number of isopycnic to consider. (The default
name of this text file can be changed using -rholev option).
2. Using the -s0 option, with 3 parameters, defining equally spaced
isopycnic surfaces.
3. Using the -s0 option with only one parameter, defining then a
single surface.
WARNING: This cdftool is one of the few using 3D arrays. Additional
development is required to work with vertical slabs instead.
ARGUMENTS :
-v IN-var : name of the input variable to be projected
-s RHO-file : netcdf file with potential density field. If not a sigma0
file, use -sig option to indicate the name of the density
variable.
-l LST-files: List of netcdf file with variable IN-var to process.
OPTIONS :
[-s0 sigma | -s0 sigmin,sigstp,nsig] : In the first form define a
single sigma surface, while in the 2nd form, it defines a set of
'nsig' density values, starting from 'sigmin' and spaced every
'sigstp'. This option prevails the use of rho_lev file.
[-rholev TXT-file] : Specify the name of the 'rholev' text file,
instead of rho_lev.
[-p C-type] : position of IN-var on the C-grid ( either T U V F W S ),
default is 'T'. 'S' special point is used in case of section
files created by cdf_xtract_brokenline.
[-sig sigma_name] : name of the density variable in RHO_file. Default is
vosigma0.
[-isodep ] : Only computes the isopycnic depth, then stops.
[-noiso] : Does not save isopycnic depth (suitable for big files).
[-debug] : Produces extra prints.
[-o OUT-isodep]: specify the name of isodep file (-isodep option),
instead of isopycdep.nc.
[ -nc4 ] : Use netcdf4 output with chunking and deflation level 1..
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
If not using -s0 option rho_levis required, unless
the default name is changed by -rholev option.
OPENMP SUPPORT : yes
OUTPUT :
There are as many output files than input files, with '.interp'
suffix added to the original name.
netcdf files : <IN-file>.interp
variables : VAR-in (unit is the same as input var)
vodepiso (m) : depth of isopycnic.
If option -isodep is used, only isopycnic depth is output on
netcdf file : isopycdep.nc (unless -o option is used).
variables : vodepiso (m)
SEE ALSO :
cdfmocsig
usage : cdfrichardson -t gridT -u gridU -v gridV [-W] [-full] ...
... [-o OUT-file] [-nc4] [-vvl W-file]
PURPOSE :
Compute the Richardson Number (Ri) according to temperature,
salinity and velocity components, given in the input files.
Richardson's number is the ratio N2/(Vertical Shear)^2, N being
the Brunt-Vaissala frequency.
ARGUMENTS :
-t gridT : input gridT file for temperature and salinity
-u gridU : input gridU file for zonal velocity component
-v gridV : input gridV file for meridional velocity component
OPTIONS :
[-W ] : keep N2 at W points. Default is to interpolate N2 at T points
on the vertical
[-full ] : indicate a full step configuration instead of the default
partial steps.
[-o OUT-file ]: specify output file instead of richardson.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl W-file ]: use time-varying vertical metrics. W-file holds the
time-varying e3w vertical metrics.
REQUIRED FILES :
mesh_zgr.nc is needed for this program.
OUTPUT :
netcdf file : richardson.nc unless option -o is used.
variables : voric
usage : cdfspeed -u U-file U-var -v V-file V-var [-t T-file] ...
... [-o OUT-file] [-nc4] [-lev LST-level] [-C]
PURPOSE :
Compute the speed of ocean currents or wind speed.
If the input files are 3D, the input is assumed to be a model
output on native C-grid. Speed is computed on the A-grid.
If the input file is 2D then we assume that this is a forcing
file already on the A-grid, unless -C option is used.
ARGUMENTS :
-u U-file U-var : netcdf file for U component and variable name.
-v V-file V-var : netcdf file for V componentt and variable name.
OPTIONS :
[-t T-file] : indicate any file on gridT for correct header of the
output file (needed for 3D files or if -C option is used).
[-lev LST-level] : indicate a list of levels to be processed.
If not used, all levels are processed.
[-C] : indicates that data are on a C-grid even if input files are 2D.
[-o OUT-file] : use specified output file instead of speed.nc
[-nc4] : use netcdf4 output with chunking and deflation.
OUTPUT :
Output on speed.nc unless -o option is used.
netcdf variable : U
SEE ALSO :
cdfvita also computes the speed.
usage : cdfvita -u U-file -v V-file -t T-file [-w W-file] [-geo] [-cubic]
... [-o OUT-file] [-nc4] [-lev LST-level]
PURPOSE :
Creates a file with velocity components, module and direction
at T points from file on C-grid. T-file is used only for
getting the header of the output file. Any file on T grid
can be used.
ARGUMENTS :
-u U-file : netcdf file with zonal component of velocity
-v V-file : netcdf file with meridional component of velocity
-t T-file : netcdf file with T points header OK.
OPTIONS :
[-w W-file ]: if used, also compute vertical velocities at T points.
[-geo ] : indicate that input velocity files are produced by
cdfgeo-uv, hence ugeo on V-point, vgeo on U-points.
[-cubic ] : Save the cube of the velocity module.
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-o OUT-file ] : Specify name of output file instead of vita.nc
[-lev LST-level] : specify a blank-separated list of levels to be used.
(default option is to use all input levels).
REQUIRED FILES :
none
OUTPUT :
netcdf file : vita.nc unless -o option is used
variables : sovitua, sovitva, sovitmod, sovitdir, [sovitmod3] and
[sovitwa]. Note that the direction is relative to the
model grid.
SEE ALSO :
cdfspeed only computes the speed (velocity module).
usage : cdfw -u U-file -v V-file [-var U-var V-var] [-full] [-o OUT-file] ...
... [-nc4] [-vvl T-file ]
PURPOSE :
Compute the vertical velocity from the vertical integration of
of the horizontal divergence of the velocity.
ARGUMENTS :
-u U-file : netcdf file with the zonal velocity component.
-v V-file : netcdf file with the meridional velocity component.
OPTIONS :
[-var U-var V-var] : names of the zonal and meridional velocity
components. Default are vozocrtx and vomecrty
[ -full ] : in case of full step configuration. Default is partial step.
[ -o OUT-file] : specify the output file name instead of w.nc
[ -nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[ -vvl T-file ] : Use time varying vertical metrics (e3t), provided
in T-file.
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
netcdf file : w.nc unless -o option is used.
variables : vovecrtz (m/s) usage : cdfzisot -t T-file -iso ISO-temp [-o OUT-file] [-nc4]
PURPOSE :
Compute the depth of an isotherm surface from the temperature file
and value of the isotherm given on the command line.
ARGUMENTS :
-t T-file : input netcdf file with the ocean temperature.
-iso ISO-temp : Indicates the temperature (Celsius) of the chosen
isotherm.
OPTIONS :
[-o OUT-file] : specify the output file name instead of zisot.nc
[-nc4] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_zgr.nc
In case of FULL STEP configuration, bathy_level.nc is also required.
OUTPUT :
netcdf file : zisot.nc unless option -o is used.
usage : cdfeddyscale -f PASS1-meanfile [-o OUT-file] [-nc4]
PURPOSE :
This program computes 3 quantities relative to the eddy scales,
from a file preprocessed by cdfeddyscale_pass1 :
-the Taylor scale or large scale eddy (lambda1)
-the small scale eddy (lambda2)
-and the inertial range (scar) on F-points
lambda1 = sqrt(mean Kinetic Energie / Enstrophy)
lambda2 = sqrt(Enstrophy / Palinstrophy)
Inertial Range = lambda1 / lambda2
Enstrophy = 1/2 * ( mean((RV)^2) )
Palenstrophy = 1/2 * ( mean((dx(RV))^2 + (dy(RV))^2) )
ARGUMENTS :
-f PASS1-meanfile : time average of cdfeddyscale_pass1 preprocessed
files.
OPTIONS :
[-o OUT-file ]: specify the output file name instead of lambda.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
OUTPUT :
netcdf file : lambda.nc unless -o option is used.
variables : solambda1 (m), solambda2 (m), soscar
SEE ALSO :
cdfeddyscale_pass1 usage : cdfeddyscale_pass1 -u U-file U-var -v -V-file V-var -l lev ...
... [-o OUT-file] [-nc4]
PURPOSE :
This program computes some elements whose temporal mean is required
in the determination of the eddyscales (cf cdfeddyscale). These
elements are :
- the curl and the square of curl on F-points,
- the gradient components of the curl and the
square of the gradient components on UV-points,
- the square of velocity components on UV-points,
They are computed for the set of U/V files given in arguments.
Therefore, for a particular experiment, the resulting files obtained
for a series of time-frames, need to be time-averaged (cdfmoy), before
using the final cdfeddyscale program, for the computation of the eddy
scales : Taylor scale (Large scale eddy --lambda1--), and small scale
eddy (lambda2).
ARGUMENTS :
-u U-file U-var: zonal component of the vector field:
filename and variable name
-v V-file V-var: meridional component of the vector field:
filename and variable name
-l lev : level to be processed.
OPTIONS :
[-o OUT-file] : specify output file instead of lambda_int.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_hgr.nc
OUTPUT :
netcdf file : lambda_int.nc
variables : socurl (s^-1), socurl2 (s^-2)
variables : sodxcurl, sodycurl (s^-1.m^-1)
variables : sodxcurl2, sodycurl2 (s^-2.m^-2)
variables : vozocrtx2, vomecrty2 (m^2.s^-2)
WARNING : variables in the output file are not located at the same
C-grid point.
SEE ALSO :
cdfmoy, cdfeddyscale usage : cdfets -f T-file [-o OUT-file] [-nc4] [-vvl W-file]
PURPOSE :
Compute the eddy time scale, and a proxy for rossby radius. The Rossby
radius is computed as the vertical integral of N2 (Brunt Vaissala
frequency), scaled by |f|*pi.
The Eddy Time Scale is the ratio N/|grad B| where N is the square root
of N2 and |grad B| is the module of the horizontal buoyancy gradient.
B is the buoyancy computed as B=-g rho/rho0.
ARGUMENTS :
-f T-file : netcdf input file for temperature and salinity (gridT).
OPTIONS :
[-o OUT-file] : specifiy the name of output file instead of ets.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl W-file] : use time varying vertical metrics. W-file holds the
time-varying e3w vertical metrics.
REQUIRED FILES :
mesh_hgr.nc, mesh_zgr.nc
OUTPUT :
netcdf file : ets.nc unless -o option is used.
variables : voets (days) and sorosrad (m) usage : cdfnrj_bci -f UVWT-file [-o OUT-file] [-nc4]
PURPOSE :
Compute elements (see variable list below) for analysing the baroclinic
instability.
Note : this program was formerly named cdfbci.
ARGUMENTS :
-f UVWT-file : input file is produced by cdfuvwt, and the mean
must be computed on a long-enough period for the statistics
to be meaningful. Points are on T grid.
OPTIONS :
[-o OUT-file] : specify output file name instead of bci.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
Need mesh_hgr.nc file
OUTPUT :
netcdf file : bci.nc
variables : 5 output variables
dTdx : zonal derivative of Tbar on T point (*1000)
dTdy : meridional derivative of Tbar on T point (*1000)
uT : anomaly of u times anomaly of T on T point
vT : anomaly of v times anomaly of T on T point
bci : transfert of energy for the baroclinic instability (*1000)
SEE ALSO :
cdfuvwt, cdfnrj_bti, cdfnrj_components, cdfnrj_transfert usage : cdfnrj_bti -f UVWT-file [-o OUT-file] [-nc4]
PURPOSE :
Compute the terms in the barotropic energy tranfert equation.
The transfert of energy for the barotropic instability is
bti= -[(u'bar)^2*dubar/dx ...
+(v'bar)^2*dvbar/dy ...
+(u'v'*(dubar/dy +dvbar/dx))]
Note : This program was formerly named cdfbti.
ARGUMENTS :
-f UVWT-file : netcdf file produced by cdfuvwt
OPTIONS :
[-o OUT-file] : specify the output file name instead of bti.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_hgr.nc
OUTPUT :
netcdf file : bti.nc
variables :
dudx : zonal derivate of ubar on T point
dvdx : zonal derivate of vbar on T point
dudy : meridional derivate of ubar on T point
dvdy : meridional derivate of vbar on T point
anousqrt : mean of (u-ubar)^2 on T point
anovsqrt : mean of (v-vbar)^2 on T point
anouv : mean of (u-ubar)*(v-vbar) on T point
bti : transfert of energy for the barotropic instability.
SEE ALSO :
cdfuvwt, cdfnrj_bci, cdfnrj_components, cdfnrj_transfert
usage : cdfnrj_components -f UVWT-file [-o OUT-file] [-nc4]
PURPOSE :
Compute contributing terms of the energy equation at T-points.
Input file contains mean values processed by cdfuvwt.
The means must have been computed on long enough period for the
statistics to be meaningful.
Note : this program was formerly named cdfnrjcomp. It needs some
additional cleaning and revision. Use with care!
ARGUMENTS :
-f UVWT-file: netcdf file produced by cdfuvwt.
OPTIONS :
[-o OUT-file]: specify output file name instead of nrjcomp.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : nrjcomp.nc
all variables are located at T point.
variables : tbar : mean temperature
ubar : mean zonal velocity
vbar : mean meridional velocity
anotsqrt : mean squared temperature anomaly
anousqrt : mean squared zonal velocity anomaly
anovsqrt : mean squared meridional velocity anomaly
SEE ALSO :
cdfuvwt, cdfnrj_bti, cdfnrj_bci, cdfnrj_transfert but also
cdfeke, cdfmoy, cdfstdevt etc...
usage : cdfnrj_transfert -f UVWT-file [-o OUT-file] [-nc4]
PURPOSE :
This program computes the energy transfert term from previously
computed high order moments (cdfuvwt). High order moments must
have been evaluated on a long enough period, in order to get
meaningfull statistics.
Note : this program was formerly named cdfkempemekeepe. (no idea of the
pronunciation :) ).
ARGUMENTS :
-f UVWT-file : Input file is the output of cdfuvwt, holding the required
high order moments.
OPTIONS :
[-o OUT-file] : Specify the output file name instead of trf_t1t3.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : trf_t1t3.nc unless option -o is used.
variables : WT : temporal mean of Wbar x Tbar at T point.
anoWT : temporal mean of W'xT' at T points.
units : 1000 x Celsius x m/s
SEE ALSO :
cdfuvwt, cdfnrj_bci, cdfnrj_bti, cdfnrj_components
usage : cdfokubow -u U-file U-var -v V-file V-var [-l lev] ...
... [-o OUT-file] [-nc4]
PURPOSE :
Compute Okubo-Weiss parameter of a vector field at all level or at
specified level (-l option).
This parameter represents the balance between strain and vorticity.
W = Sn^2 +Ss^2 - curl(V)^2. Sn and Ss are the non-symetrical and
symetrical components of the strain, respectively.
ARGUMENTS :
-u U-file U-var: zonal component of the vector field:
filename and variable name
-v V-file V-var: meridional component of the vector field:
filename and variable name
OPTIONS :
[-l lev]: level to be processed. Process all level by default.
[-o OUT-file] : specify output file instead of okubow.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_hgr.nc and mask.nc
OUTPUT :
netcdf file : okubow.nc
variables : sokubow (s^-2) usage : cdfenstat -l LST-mbr-files [-spval0] [-v4d] [-o OUT-file] [-nc4]
PURPOSE :
Compute an ensemble mean and standard deviation for a set of files
corresponding to different members from an ensemble run.
This program assumes that each of the member files have the same
variables, and the same number of time frames.
This program uses optimal algorithm for computing the mean and std dev,
in order to reduce truncation errors.
ARGUMENTS :
-l LST-mbr-files : A list of members model output files.
OPTIONS :
[ -spval0 ] : set missing_value attribute to 0 for all output
variables and take care of the input missing_value.
This option is usefull if missing_values differ from files
to files; it was formely done by cdfmoy_chsp).
[ -v4d ] : uses 4D arrays for improved performance (use more memory !)
[ -o OUT-file ] : specify a name for output file instead of cdfmoy.nc
[ -nc4 ] : output file will be in netcdf4, with chunking and deflation
REQUIRED FILES :
none
OUTPUT :
netcdf file : cdfmoy.ncunless -o option in use
variables : are the same than in the input files. Standard Dev are
named stdev_<variable> usage : cdfcensus -t T-file [-log nlog] [-zoom imin imax jmin jmax] ...
... [-klim kmin kmax] [-srange smin smax ds] ...
... [-trange tmin tmax dt] [-full] [-vvl] [-o OUT-file] [-nc4]
PURPOSE :
Compute the volumetric water mass census: the ocean is divided in
T,S bins; the program gives the volume of water for each bin.
A sub-area can be specified, both horizontaly and vertically.
Temperature and salinity ranges can be also adapted, as well as the
width of the bins. Default values are provided. In order to attenuate
the huge maximum values, a log10 operator can be applied many times,
the number of filter passes being set on the command line.
ARGUMENTS :
-t T-file : netcdf file name for temperature and salinity
OPTIONS :
[-log nlog] : number of log10 filter to perform. 0 by default.
[-zoom imin imax jmin jmax] : define a model sub-area, in model
coordinates
[-klim kmin kmax] : set limits on the vertical.
[-srange smin smax ds ] : define the size of the salinity bin
defaut is : 25.0 40.0 0.020
[-trange tmin tmax dt ] : define the size of the temperatude bin
defaut is : -2.0 38.0 0.050
[-full ] : use for full step computation
[-vvl ] : use time-varying vertical metrics.
[-o OUT-file] : specify output file name instead of census.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
- netcdf file : census.nc
variables : volcensus (10^15 m3 )
sigma0 (kg/m3 -1000 )
sigma2 (kg/m3 -1000 )
sigma3 (kg/m3 -1000 ) usage : cdffindij -w xmin xmax ymin ymax [-c COOR-file] [-p C-type]...
... [-f LST-file] [-d descriptor] [-o OUT-file] [-A] [-l]
PURPOSE :
Return the model limit (i,j space) of the geographical window given on
the input line. If using -f list_file option, then the output is just
a single point, not a window, and there are no need to define the
window with -w.
ARGUMENTS :
-w xmin xmax ymin ymax : geographical limits of the window, in lon/lat
(relevant only if -f option not used.)
OPTIONS :
[-c COOR-file ] : specify a particular coordinate file
default is coordinates.nc
[-p C-type] : specify the point on the C-grid (T U V F). Default is F.
[-f LST-file ] : LST-file is an ascii file describing the location
(one per line) of geographical points to be translated to
model (i,j) point. Unless specified with -d option, this list
file contains Longitude (X) Latitudes (Y) information.
[-d descriptor] : descriptor is a string indicating the position of
X and Y coordinates for the lines of list_file. Default value
of the descriptor is 'XY'. Any other field on the line is
indicated with any characterm except X or Y. Example of valid
descriptor : 'oXYooo' or 'ooYabcdfXooo'
[-A ] : With this option, output is similar to input with I,J appended
to the corresponding line.
[-l ] : With this option, also output the exact model longitude and
latitude of the I,J point.
[-o OUT-file]: write output in text OUT-file instead of standard output.
REQUIRED FILES :
coordinates.nc or the specified coordinates file.
OUTPUT :
Output is done on standard output.
SEE ALSO :
cdfwhereij
usage : cdfinfo -f MODEL-file [-dep dep]
PURPOSE :
Gives very basic information about the file given in arguments.
ARGUMENTS :
model output file in netcdf.
OPTIONS :
[-dep depth ] : return the nearest k index corresponding to depth
OUTPUT :
On standard ouput, gives the size of the domain, the depth
dimension name, the number of variables.
usage : cdfmax -f IN-file -v IN-var [-lev kmin kmax ] ...
... [-zoom imin imax jmin jmax] [-time tmin tmax ] ...
... [-fact multfact] [-xy ]
PURPOSE :
Find minimum and maximum of a file as well as their respective
location. Options allow to restrict the finding to a sub area in time
time and space. This program also deal with vertical slabs in a domain.
ARGUMENTS :
-f IN-file : input file
-v IN-var : input variable
OPTIONS :
[-lev kmin kmax ] : restrict to level between kmin and kmax.
[-zoom imin imax jmin jmax] : restrict to sub area specified by the
given limits. If the zoomed area is degenerated to a single
line, then the vertical slab is considered as the domain.
[-time tmin tmax ] : restrict to the indicated time windows.
[-fact multfact] : use a multiplicative factor for the output
[-xy ] : force horizontal slab even in the case of a degenerated
zoomed area.
REQUIRED FILES :
none
OUTPUT :
output is done on standard output. usage : cdfmsk MSK-file
PURPOSE :
Compute the number of ocean points, land points and displaysome
statistics: number and percentage of land points, number and
percentage of sea points.
ARGUMENTS :
MSK-file : input mask file (which contains tmask).
REQUIRED FILES :
none apart the mask file passed as argument.
OUTPUT :
Standard output usage : cdfnamelist [-i] [-p]
PURPOSE :
Give information [-i option] on the namelist mechanism implemented
since CDFTOOLS v3. Write a namelist template [-p option] to initialize
the mechanism.
Note also than since CDFTOOLS v4, the name of the mesh/mask files as
well as the name of the coordinates file can be modified from the
default, setting corresponding environment variable :
CDFT_MESH_HGR to change the default mesh_hgr.nc
CDFT_MESH_ZGR to change the default mesh_zgr.nc
CDFT_MASK to change the default mask.nc
CDFT_BASINS to change the default new_maskglo.nc
CDFT_COORD to change the default coordinates.nc
ARGUMENTS :
none
OPTIONS :
[ -i ] : print informations
[ -p ] : write a template namelist.
REQUIRED FILES :
none
OUTPUT :
with option -p, print a template namelist : PrintCdfNames.namlist
usage : cdfprobe -f IN-file -v IN-var -i ilook -j jlook [-k klook]
PURPOSE :
Displays a series of pair of values (time, value) corresponding to the
IN-var variable in IN-file, at location (ilook, jlook,[klook]). The
standard output can be piped to a graphical tool such as 'graph' to
easily plot the time evolution of IN-var.
ARGUMENTS :
-f IN-file : input file to look for
-i ilook : i position of the probe.
-j jlook : j position of the probe.
-v IN-var : name of the cdf variabled to be displayed
OPTIONS :
[-k klook] : Use the probe at level klook, instead of the first level.
REQUIRED FILES :
none
OUTPUT :
2 columns ( time , value ) ASCII output on display
time are given in days since the begining of the run. usage : cdfprofile -f IN-file -v IN-var -IJ I J [-dep depth ] [-o OUT-file]
PURPOSE :
Extracts a vertical profile at location I J, for the IN-var variable of
the IN-file. A depth can optionally be specified.
ARGUMENTS :
-f IN-file : input file to work with.
-v IN-var : variable name whose profile is requested.
-IJ I J : I, J position of the point to extract from file.
OPTIONS :
[-dep depth] : specify a depth where vertical value will be
interpolated.
[-o OUT-file]: specify output file name instead of profile.nc
REQUIRED FILES :
none
OUTPUT :
netcdf file : profile.nc unless -o option is used.
variable : name given as argument.
Profile is also written on standard output. usage : cdfwhereij -w imin imax jmin jmax [-c COOR-file] [-p C-type]
PURPOSE :
Return the geographical coordinates of a model sub-area specified
by a rectangular window in (i,j) space.
ARGUMENTS :
-w imin imax jmin jmax : (i,j) space window coordinates.
OPTIONS :
[-c COOR_file ] : specify a coordinates file instead of coordinates.nc
[-p C-type ] : specify a point type on the C-grid (T U V F),
default is T.
REQUIRED FILES :
coordinates.nc or COOR-file given in the -c option
OUTPUT :
Standard output
SEE ALSO :
cdffindij
usage : cdfzonalout -f ZONAL-file
PURPOSE :
This is a formatting program for zonal files, either mean or integral.
It displays results on the standard output from the input zonal file.
It only works with 1D zonal variables, skipping 2D variables, that
cannot be easily displayed !
ARGUMENTS :
-f ZONAL-file : input netcdf zonal file produced by one of the zonal
tools.
REQUIRED FILES :
none
OUTPUT :
- Standard output, structured in columns:
J LAT ( zonal mean, var = 1--> nvar)
SEE ALSO :
cdfzonalmean, cdfzonalmeanvT, cdfzonalsum
usage : cdfzoom -f IN-file -zoom imin imax jmin jmax -v IN-var ...
... [-lev kmin kmax ] [-time tmin tmax ] [-fact factor]
PURPOSE :
Displays the numerical values of a zoomed area. By default, all times
and levels are shown. If the zoomed area is degenerated to a single
line, then the vertical slab is displayed.
ARGUMENTS :
-f IN-file : name of input file
-zoom imin imax jmin jmax : spatial window definition
-v IN-var : cdf variable name to work with.
OPTIONS :
[-lev kmin kmax ] : vertical limits for display.
[-time tmin tmax ] : time limits for display.
[-fact factor ] : use a scaling factor for display.
Values are DIVIDED by factor
REQUIRED FILES :
none
OUTPUT :
display on standard output usage : cdfchgrid -f IN-file -r REF-file -var IN-var [-o OUT-file] [-nc4] [-d]
PURPOSE :
Builds a new file on a refined grid, from a coarser grid, assuming that
the two grids are embedded, with common points (hence an odd scaling
factor). Grid characteristics are hard wired in the code. Support for
ORCA025 --> ORCA12, eORCA025 --> eORCA12 is actually provided. Hooks
are ready in the code for adding new conversion.
No interpolation, only copying value of a coarse grid cell, onto
scale x scale cells of the output grid (scale is the refinement factor)
RESTRICTION :
Caution for mask coherence !
This tool is only adapted for drowned fields.
ARGUMENTS :
-f IN-file : input Coarser-grid file
-r REF-file : Reference file used for identification of the output grid
should be of same geometry than the output file.
-var IN-var : input coarser-grid variable to be converted
OPTIONS :
[-o OUT-file] : specify output file name instead of cdfchgrid.nc
[-nc4 ] : use netcdf4 chunking and deflation for the output file
[-d ] : Display some debugging information
REQUIRED FILES :
none
OUTPUT :
netcdf file : cdfchgrid.nc
variable : same name as in input file
SEE ALSO :
cdf2regular cdfdegrad
usage : cdfclip -f IN-file -zoom imin imax jmin jmax ...
...[-klim kmin kmax] [-o OUT-file] [-nc4]
PURPOSE :
Clips the input file according to the indices given in the zoom option.
If no vertical zoomed area is indicated, the whole water column is
considered.
This program is able to extract data for a region crossing the E-W
periodic boundary of a global configuration. It does so if imax < imin.
ARGUMENTS :
-f IN-file : specify the input file to be clipped
-zoom imin imax jmin jmax : specify the domain to be extracted.
If imin=imax, or jmin = jmax assume a vertical section either
meridional or zonal.
OPTIONS :
[-o OUT-file ] : use OUT-file instead of cdfclip.nc for output file
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-klim kmin kmax ] : specify vertical limits for the zoom, in order to
reduce the extracted area to some levels. Default is to take the
while water column.
REQUIRED FILES :
none
OUTPUT :
netcdf file : cdfclip.nc This can be changed using -o option
variables : same as input variables. usage : cdfcmp -f1 IN-file1 -f2 IN-file2 -v IN-var ...
... [-lev kmin kmax ] [-zoom imin imax jmin jmax] ...
PURPOSE :
Find where IN-var is different between IN-file1 and IN-file2
Options allow to restrict the finding to a sub area in space
ARGUMENTS :
-f1 IN-file1 : input file1
-f2 IN-file2 : input file2
-v IN-var : input variable
OPTIONS :
[-lev kmin kmax ] : restrict to level between kmin and kmax.
[-zoom imin imax jmin jmax] : restrict to sub area specified
by the given limits.
REQUIRED FILES :
none
OUTPUT :
output is done on standard output. usage : cdfconvert -t CLIPPER_tag -c CLIPPER_Confcase
PURPOSE :
Convert dimg files (CLIPPER like) to netcdf (DRAKKAR like).
With recent version of NEMO and XIOS this program is likely to become
obsolete soon. It is maintained for historical reasons.
ARGUMENTS :
CLIPPER_tag : a string such as y2000m01d15 for time identification.
CLIPPER_confcase : CONFIG-CASE of the files to be converted (eg ATL6-V6)
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
netcdf file : gridT, gridU, gridV files
variables : same as in standard NEMO output
SEE ALSO :
usage : cdfcsp -l LST-files [-v value]
PURPOSE :
Replace missing_values by 0 and update attribute.
This program is not working properly with NETCDF4/HDF5 files!
Even more : problem when **compiled** with NETCDF4.
CAUTION :
################################
# INPUT FILES ARE OVER-WRITTEN #
################################
ARGUMENTS :
-l LST-files : The list of cdf file to process, all variables will
be processed.
OPTIONS :
[-v value] : use value instead of 0 as the new missing_value
REQUIRED FILES :
none
OUTPUT :
netcdf file : same as input file (modified)
variables : same as input file
usage : cdfdegrad -f IN-file -v IN-var -r ri rj -p C-type [-start i0 j0]
... [-full] [-vvl] [-o OUT-file]
PURPOSE :
Degrad the horizontal resolution of a NEMO ouput file,
for each z-level and time step, with a ratio of ri along
x direction and rj along y direction. If specified, the input
grid is considered starting from the indices i0 and j0.
ARGUMENTS :
-f IN-file : netcdf input file on grid point corresponding to -p option.
-v IN-var : name of netcdf variable to work with
-r ri rj : degradation ratio for x-direction and y-direction.
-p C-type : position of variable on C-grid, one of T|U|V|W.
OPTIONS :
[-start i0 j0] : spatial indices from where the procedure of
degradation starts.
[-o OUT-file ]: output filename instead of 'degraded_<IN-var>.nc'
[-vvl ] : use time-varying vertical metrics.
[-full] : flag for full steps grid, instead of default partial
steps.
REQUIRED FILES :
Files mesh_hgr.nc, mesh_zgr.nc, mask.nc
OUTPUT :
netcdf file : degraded_<IN-var>.nc unless -o option is used
variables : degraded_<IN-VAR>
flsdc : fluid subdomain counter
usage : cdfdifmask -m mask1 mask2 [-o OUT-file] [-nc4]
PURPOSE :
Compute the difference between 2 NEMO mask files.
This difference is not easy to perform with nco.
ARGUMENTS :
-m mask1 mask2 : model mask files to be compared.
OPTIONS :
[-o OUT-file ]: specify output file name instead of mask_diff.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : mask_diff.nc unless -o option is used.
variables : tmask umask vmask fmask usage : cdfnan -l LST-files [-r value] [-absmax max]
PURPOSE :
Detect NaN values in the input files, and change them to either spval
(missing_value) or the value given with -r option.
When absolute value is larger than huge or that the value given with
the -absmax option, it is also replaced as NaN are replaced.
CAUTION :
################################
# INPUT FILES ARE OVER-WRITTEN #
################################
ARGUMENTS :
-l LST-files : A blank-separated list of the name of the files to
process. All files in the list must have the same geometry and
must contain the same variables.
CAUTION : input files are over-written!
OPTIONS :
[-r value] : use value instead of missing_value for replacing NaN.
[-absmax rabsmax ] : replace values whose absolute value is greater
than max.
OUTPUT :
netcdf file : input file is rewritten without NaN.
variables : same name as input.
usage : cdfscale -f INOUT-file -v IN-var -s SCAL-factor
PURPOSE :
Replace IN-var in INOUT-file by its values x SCAL-factor.
CAUTION :
#############################
# INPUT FILE IS OVERWRITTEN #
#############################
ARGUMENTS :
-f INOUT-file : netcdf input file (!overwritten!).
-v IN-var : netcdf variable to be scaled.
-s SCAL-factor : Scale value to be used (multiplication factor).
OUTPUT :
netcdf file : input file is rewritten
variables : same name as input. usage : cdfbuoyflx -t T-file [-r RNF-file] [-f FLX-file ] [-sss SSS-name]
... [-sst SST-name] [-nc4] [-o OUT-file] [-short ]
PURPOSE :
Compute (or read) the heat and water fluxes components.
Compute (or read) the net heat and water fluxes.
Compute the buoyancy heat and water fluxes components.
Compute the net buoyancy fluxes.
Save sss and sst.
ARGUMENTS :
-t T-file : netcdf file with temperature and salinity
OPTIONS :
[-r RNF-file ] : Specify a run-off file if runoff not in T-file
nor in FLX-file
[-f FLX-file ] : Use this option if fluxes are not saved in gridT files
[-sss SSS-name ] : Use this option if SSS variable name in T-file
differ from vosaline
[-sst SST-name ] : Use this option if SST variable name in T-file
differ from votemper
[-nc4 ] Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-o OUT-file ] Default is buoyflx.nc
[-short ] With this option only save the buoyancy flux without
all the components of the flux.
REQUIRED FILES :
none
OUTPUT :
netcdf file : buoyflx.nc
variables : 25 variables (2D) or 1 variable in case of -short option
SEE ALSO :
usage : cdfhflx -f T-file [-o OUTNC-file ] [-ot OUTTXT-file]
PURPOSE :
Compute the Meridional Heat Transport (MHT) from surface heat fluxes,
in function of the latitude.
If a sub-basin file is available, MHT is computed for each sub-basin.
Note that the latitude is in fact a line of constant J coordinate, not
a true parallel, if the model grid is distorted as in the northern most
part of ORCA configurations.
ARGUMENTS :
-f T-file : a file with heat fluxes (gridT).
OPTIONS :
[-o OUTNC-file ]: specify the name of the netcdf output file, instead of
cdfhflx.nc
[-ot OUTTXT-file ]: specify the name of the text output file, instead of
hflx.out
REQUIRED FILES :
Files mesh_hgr.nc, new_maskglo.nc and mask.nc.
If new_maskglo.nc is not available, only global MHT is computed.
OUTPUT :
ASCII file : hflx.out
netcdf file : cdfhflx.nc
variables : hflx_glo, [hflx_atl, hflx_inp, hflx_pac, hflx_ind] usage : cdfwflx -t T-file -r RNF-file [-f FLX-file] [-o OUT-file] [-nc4]
PURPOSE :
Compute the water fluxes components. Suitable for annual means files.
All output variables are in mm/days.
ARGUMENTS :
-t T-file : model output file with water fluxes (gridT).
-r RNF-file : file with the climatological runoff on the model grid.
OPTIONS :
[-f FLX-file]: model output file with water fluxes if not in T-file.
[-o OUT-file]: specify output file name instead of wflx.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : wflx.nc unless -o option is used.
variables : soevap, soprecip, sorunoff, sowadmp, sowaflux
usage : cdficediag -i ICE-file [-lim3] [-o OUT-file] [-maskfile MSK-file] ...
... [-maskvar MSK-var]
PURPOSE :
Compute the ice volume, area and extent for each hemisphere.
The extent is computed in a similar way to NSIDC for easy
comparison : the extent is the surface of the grid cells covered
by ice when the ice concentration is above 0.15
For compatibility with previous version, another estimate of
the extend is computed using grid cell surfaces weighted by the
ice concentration, but it will be deprecated soon.
ARGUMENTS :
-i ICE-file : netcdf icemod file (LIM2 by default)
OPTION :
[-lim3 ] : LIM3 variable name convention is used. Default is LIM2.
[-maskfile MSK-file] : specify name of mask file instead of mask.nc
[-maskvar MSK-var ] : specify name of mask variable instead of tmask
[-o OUT-file ] : specify output file instead of icediags.nc
REQUIRED FILES :
mesh_hgr.nc and mask.nc
OUTPUT :
netcdf file : icediags.nc
variables : [NS]Volume (10^9 m3 )
[NS]Area (10^9 m2 )
[NS]Extent (10^9 m2 ) -- obsolete --
[NS]Exnsidc (10^9 m2 )
N = northern hemisphere
S = southern hemisphere
standard output usage : cdfisf_fill -f ISF-file -v ISF-var -l ISF-list [-nc4 ] [-o OUT-file]
PURPOSE : Builds nc file with a single value for each pool around a list
of given point. A warning is given when neighbouring ice-shelves
cannot be discriminated (no gap in between). In this case, hand
edit on the ISF-file is required.
ARGUMENTS :
-f ISF-file : netcdf file which contains the ice shelf draft variable
(mesh_zgr is OK). It is used as a mask, only.
-v ISF-var : variable name corresponding to the ice shelf draft or
ice shelf level
-l ISF-list : text file containing at least the following information:
1 NAME LON LAT I J
...
i NAMEi LON LAT I J
...
EOF
No NAME X Y I J
OPTIONS :
-nc4 : use NetCDF4 chunking and deflation for the output
-o OUT-file : specify the name of the output file instead of fill.nc
This file will be one of the input file for cdfmkforcingisf
as the ISF-fill_file
OUTPUT :
netcdf file : fill.nc
variable : sofillvar contains for all points in ice shelf NAME
the value -i (negative value)
text file : <ISF-list>_zmin_zmax.txt
this output file is similar to <ISF-list> but updated
with the minimum and maximul value of ice-draft for
each shelf.
SEE ALSO :
cdfisf_forcing, cdfisf_rnf , cdfisf_poolchk
usage : cdfisf_forcing -f ISF-fill_file -v ISF-fill_var -l ISF-listfile
-m ISF-poolmask [-vm ISF-poolmask_variable] [-p PATTERN-file]
[-vp PATTERN-variable] [-nc4] [-o OUT-file ]
PURPOSE :
Build basal melting rate file used in NEMO ISF when nn_isf=4
ARGUMENTS :
-f ISF-fill_file : file built by cdfisf_fill (all the ice shelves
are tagged with an id)
-v ISF-fill_var : name of fill variable to use in ISF-fill_file
-l ISF-listfile : text file used to build the ISF-fill_file.
Only the last variable on each line is used (GT/y)
OPTIONS :
-p PATTERN-file : specify the file use for patterns.
[ default : isfpattern.nc ]
-vp PATTERN-variable : specify the name of the pattern variable.
[ default : sowflisf ]
-vm ISF-poolmask_variable : specify the name of the variable used
for masking the pools. [ default : isfpoolmask ]
-nc4 : use netcdf4 chunking and deflation
-o OUT-file : specify output filename. [ default : isfforcing.nc ]
REQUIRED FILES :
mesh_zgr.nc mesh_hgr.nc,
isfpattern.nc (ie reference file used to define the isf melting
pattern), unless -p option is used to give different name.
OUTPUT :
netcdf file : isfforcing.nc unless specified with -o option
variable : sofwfisf
SEE ALSO : cdfisf_fill, cdfisf_rnf, cdfisf_poolchk
usage : cdfisf_poolchk -m MASK-file -d ISFDRAFT-file [-v ISFDRAFT-variable]
[-nc4] [-o OUT-file]
PURPOSE :
Produces a netcdf mask file with 1 everywhere, except for points not
connected to the open ocean (frequent for cavities below ice-shelves),
which have 0 value. Both 3D and 2D variables are created, the 2D
variables being used for cdfisf_forcing.
ARGUMENTS :
-m MASK-file : name of the input NEMO mask file, with tmask variable.
-d ISFDRAFT-file : name of the file with ice shelf draft.
OPTIONS :
-v ISFDRAFT-variable: name of the variable for ice shelf draft.
-nc4 : use netcdf4 with chunking and deflation for the output.
-o OUT-file : name of the output file. [Default : poolmask.nc ]
REQUIRED FILES :
Only the mask file given as argument
OUTPUT :
netcdf file : poolmask.nc unless -o option is used.
variables : tmask_pool3d, tmask_pool2d
SEE ALSO :
cdfisf_fill, cdfisf_forcing, cdfisf_rnf
usage : cdfisf_rnf -f ISF-fill-file -v ISF-fill_var -l ISF-listfile -w width
[-b BATHY-file] [-vb BATHY-var] [-i ISFDRAFT-file] [-vi ISFDRAFT-variable]
[-nc4] [-o OUT-file ]
PURPOSE :
Build a netcdf file runoff file using the basal melting of the
ice-shelves. This netcdf file is intented to be used with NEMO when
nn_isf namelist parameter is set to 3.
ARGUMENTS :
-f ISF-fill_file : file built by cdffill (all the ice shelves are
tagged with an id)
-v ISF-fill_var : name of fill variable to use in ISF-fill_file
-l ISF-list : Text file with the melting rate (GT/y) given for
each ice shelf.
-w width : specify the width (in grid points) on which the run-off
will be applied.
OPTIONS :
-b BATHY-file : give name of bathy file.
[ default : bathy.nc ]
-vp BATHY-var : give name of bathy variable.
[ default : Bathymetry ]
-i ISFDRAFT-file : give name of isf_draft file.
[ default : isf_draft.nc ]
-vi ISFDRAFT-var : give name of isf_draft variable.
[ default : isf_draft ]
-nc4 : Use this option to have netcdf4 output file, with chunking
and deflation.
-o OUT-file : Specify the name of the output file instead of
the default name rnfisf.nc
REQUIRED FILES :
mesh_hgr.nc and all files specified on the command line
OUTPUT :
netcdf file : rnfisf.nc unless -o option used
variables : sozisfmax (m), sozisfmin(m), sofwfisf (kg/m2/s)
SEE ALSO :
cdfisf_fill, cdfisf_forcing, cdfisf_poolchk
usage : cdficb_clim -l LST-ICB-monthly-files [-o OUT-file] [-nc4]
PURPOSE :
Concatenates 12 monthly input files, into a 12 frames output file.
This is done for the 2 variables corresponding to mass and melt.
No process done in this tool.
ARGUMENTS :
-l LST-ICB-monthly-files : A list of 12 monthly-mean ICB files.
These files are likely produced by cdfmoy.
OPTIONS :
[-o OUT-file] : specify output file name instead of icbdiags.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : icbdiags.nc
variables : Mass (Kg/m2 )
Melt (Kg/m2/s ) usage : cdficb_diags -f ICB-file [-jperio jperio] [-o OUT-file]
PURPOSE :
Compute the spatially integrated icb mass and melt flux for
both hemispheres.
ARGUMENTS :
-f ICB-file : a single netcdf icb file
OPTIONS :
[-jperio jperio] : specify the NEMO jperio parameter for the north pole
folding condition. Default is 4
- ORCA2 ORCA025, ORCA12 uses 4
- ORCA1 ORCA05 uses 6
[-o OUT-file] : specifiy output file name instead of icbdiags.nc
REQUIRED FILES :
mesh_hgr.nc and mask.nc
OUTPUT :
netcdf file : icbdiags.ncwith single values.
variables : [NS]Mass (Kg )
[NS]Melt (Kg/s )
N = northern hemisphere
S = southern hemisphere
standard output
usage : cdffwc -t T-file -bv BASIN-var1,var2,.. [-o OUT-file] [-sref REFSAL]
[-full] [-accum] [-ssh] [-vvl]
PURPOSE :
Compute the freshwater content in a given basin from top to bottom
for each layer, using a reference salinity ( 34.7) that
can be changed with -sref option.
ARGUMENTS :
-t T-file : netcdf input file holding salinity (in general a gridT).
-bv BASIN-var1,var2,.. : Comma separated list of sub-basin variables
to process. E.g.: -bv tmaskatl,tmaskind
OPTIONS :
-full : for full step computation
-accum : compute accumulated content from top to bottom
-ssh : take ssh into account for surface layer
-sref REFSAL : reference salinity ( 34.7 by default)
-vvl : use time-varying vertical metrics
-o OUT-file : use specified output file instead of fwc.nc
-b SUBAS-file : use specified subbasin file instead of subbasins.nc
REQUIRED FILES :
mesh_zgr.nc, mesh_hgr.nc and subbasins.nc and mask.nc
OUTPUT :
netcdf file : fwc.nc (or specified with -o option)
variables : fwc_BASIN, where BASIN was set by argument BASIN-var*
(cAsE sensitive !)
usage : cdfheatc -f T-file [-mxloption option] -[mxlf MXL-file] ...
[-zoom imin imax jmin jmax kmin kmax] [-full] [-o OUT-file]
[-M MSK-file VAR-mask ] [-vvl ]
PURPOSE :
Compute the heat content in the specified 3D area (Joules)
ARGUMENTS :
-f T-file : name of the input file with temperature (and MLD if needed).
OPTIONS :
[-zoom imin imax jmin jmax kmin kmax] : limit of a sub domain where
the heat content will be calculated.
- if imin = 0 then ALL i are taken
- if jmin = 0 then ALL j are taken
- if kmin = 0 then ALL k are taken
[-full ] : assume full step model output instead of default
partial steps.
[-mxloption option]: option= 1 : compute only in the mixed layer,
option=-1 : exclude mixed layer in the computation
option= 0 : [Default], do not take care of mxl.
[-mxlf MXL-file ]: give name where MLD is found, if not in T-file.
Only usefull if mxl option is not 0.
[-o OUT-file ] : specify netcdf output filename instead of heatc.nc
[-M MSK-file VAR-mask] : Allow the use of a non standard mask file
with VAR-mask, instead of mask.nc and tmask
This option is a usefull alternative to -zoom option, when the
area of interest is not 'box-like'
[ -vvl ] : use time-varying e3t for integration
REQUIRED FILES :
Files mesh_hgr.nc, mesh_zgr.nc and mask.nc
OUTPUT :
netcdf file : heatc.nc unless -o option is used.
variables: heatc3d (Joules)
: heatc2d(dep) (Joules)
: heatc3dpervol (Joules/m3)
Standard output
SEE ALSO:
cdfpolymask usage : cdfmean -f IN-file -v IN-var -p C-point ...
... [-w imin imax jmin jmax kmin kmax] [-full] [-var] [-zeromean]...
... [-M MSK-file VAR-mask ] [-o OUT-file] [ -ot OUTASCII-file] ...
... [-oz ZEROMEAN-file] [-ov VAR-file] [ -vvl ]
PURPOSE :
Compute the mean value of the field (3D, weighted). For 3D fields,
a horizontal mean for each level is also given. If a spatial window
is specified, the mean value is computed only in this window.
ARGUMENTS :
-f IN-file : input netcdf file.
-v IN-var : name of netcdf variable to work with.
-p C-point : one of T|U|V|F|W indicating the position of IN-var on the
C-grid.
OPTIONS :
[-w imin imax jmin jmax kmin kmax] : spatial window where mean value
is computed:
if imin = 0 then ALL i are taken
if jmin = 0 then ALL j are taken
if kmin = 0 then ALL k are taken
[-M MSK-file VAR-mask] : Allow the use of a non standard mask file
with VAR-mask, instead of mask.nc and the variable
associated with the grid point set by -p argument.
This option is a usefull alternative to the -w option, when the
area of interest is not 'box-like'. However, for vertical
selection, both -w and -M can be used together.
[-full ] : compute the mean for full steps, instead of default
partial steps.
[-var ]: also compute the spatial variance of IN-var.
[-zeromean ] : create a file with cdfvar having a zero spatial mean.
[-o OUT-file]: specify the name of the output file instead of cdfmean.nc
[-ot OUTASCII-file] : specify the name of the output ASCII file instead
of cdfmean.txt
[-oz ZEROMEAN-file] : specify the name of the output netcdf file for
option -zeromean, instead of zeromean.nc
[-ov VAR-file] : specify the name of the output text file for option
-var, instead of cdfvar.txt
[-vvl ] : use time-varying vertical metrics.
REQUIRED FILES :
Files mesh_hgr.nc, mesh_zgr.nc, mask.nc
OUTPUT :
- netcdf file : cdfmean.nc
variables : mean_<IN-var>, mean_3D_<IN-var>
[var_<IN-VAR>, var_3D_<IN-var>, in case of -var]
- netcdf file : zeromean.nc [ in case of -zeromean option]
variables : <IN-var>
- ASCII files : cdfmean.txt
[ cdfvar.txt, in case of -var ]
- all output on ASCII files are also sent to standard output.
usage : cdfsigintegr -v IN-var -s RHO-file -l LST-files [-p C-type ] ...
... [-sig sigma_name] [-full] [-nc4] [-vvl]
PURPOSE :
Take a list of input files with specific IN-var variable, associated
with a reference density file. A set of isopycnal surfaces is defined
in an ASCII file (rho_lev by default), using same depth reference than
the input reference density file. This program computes the integral of
IN-var between the isopycnals defined in rho_lev. It also gives the
isopycnal depth and thickness of density layers.
Rho_lev file first line indicates the number of following isopycnals.
Then a list of the densities is given, one per line.
ARGUMENTS :
-v IN-var : input variable to be integrated
-s RHO-file : netcdf file with already computed density
-l LST-files : a blank separated list of model netcdf files
containing IN-var.
OPTIONS :
[-p C-type ] : one of T U V F W which defined the position of
IN-var in the model C-grid. Default is T
[-sig sigma_name ] : give the name of sigma variable in RHO-file.
Default is vosigma0
[-full ] : indicate a full step configuration.
[-rholev file] : indicates name of file defining the limits for
integration. Default is rho_lev
[-vvl ] : use time-varying vertical metrics.
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_zgr.nc and rho_lev
OPENMP SUPPORT : yes
OUTPUT :
netcdf file : IN-file.integr
variables : inv_<IN-var> : inventory of IN-var from input file.
vodepiso (m) : depth of isopycnal.
isothick (m) : thickness of isopycnal layer.
mean_<IN-var> (same unit as IN-var) : mean IN-var in the isopycnal
SEE ALSO :
cdfrhoproj, cdfsigtrp, cdfisopycdep
usage : cdfsum -f IN-file -v IN-var -p C-type ...
... [-w imin imax jmin jmax kmin kmax] [-full ] ...
... [-o OUT-file] [-nc4] [-M MSK-file VAR-mask ] [-vvl]
PURPOSE :
Compute the sum value of the field (3D, weighted). This sum can be
optionally limited to a 3D sub-area.
ARGUMENTS :
-f IN-file : netcdf input file.
-v IN-var : netcdf variable to work with.
-p C-type : one of T|U|V|F|W indicating rhe C-grid point where
IN-var is located.
OPTIONS :
[-w imin imax jmin jmax kmin kmax]: set the 3D window limiting sub area.
if imin=0 all i are taken
if jmin=0 all j are taken
if kmin=0 all k are taken
[-full ]: Use full steps instead of default partial steps
[-vvl ]: use time -varying vertical metrics
[-o OUT-file ] : name of the output file instead ofcdfsum.nc
[-nc4 ] : use netcdf4 chunking and deflation.
[-M MSK-file VAR-mask] : Allow the use of a non standard mask file
with VAR-mask, instead of mask.nc and the variable
associated with the grid point set by -p argument.
This option is a usefull alternative to the -w option, when the
area of interest is not 'box-like'. However, for vertical
selection, both -w and -M can be used together.
REQUIRED FILES :
mesh_hgr.nc, mesh_zgr.nc and mask.nc. If
-M option is used, the specified mask file is required instead
mask.nc
OUTPUT :
Standard output.
netcdf file : cdfsum.nc unless modified with -o option.
- 2 variables : vertical profile of sum and 3D sum.
names are sum_<varname> and sum3D_<varname>.
SEE ALSO:
cdfmean usage : cdfvertmean -f IN-file -l LST-var -p C-type -zlim dep1 dep2
... [-full] [-o OUT-file] [-nc4] [-vvl] [-debug]
PURPOSE :
Compute the vertical mean between dep1 and dep2 given in m, for the
list of variables LST-var, belonging to the input file.
ARGUMENTS :
-f IN-file : netcdf input file.
-l LST-var : Comma separated list of input variables to process.
-p C-type : one of T U V W indicating position of variable on C-grid
-zlim dep1 dep2 : depths limit for vertical integration (in meters),
from top to bottom, positive depths.
OPTIONS :
[-full ] : for full step configurations. Default is partial step.
[-debug ] : print some extra informations.
[-vvl ] : use time-varying vertical metrics.
[-o OUT-file ] : specify output file instead of vertmean.nc
[-nc4 ]: Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_zgr.nc and mask.nc
OUTPUT :
netcdf file : vertmean.nc
variables : varin_vertmean (same units as input variable)
usage : cdfvint -f T-file [-v IN-var] [-GSOP] [-OCCI] [-full] [-vvl] ...
... [-tmean] [-smean] [-o OUT-file] [-nc4]
PURPOSE :
Compute the vertical integral of the variable from top to bottom,
and save the cumulated valued, level by level. For temperature
(default variable), the integral is transformed to heat content,
(unit in 10^6 J/m2) hence for salinity, the units are PSU.m
ARGUMENTS :
-f T-file : gridT file holding either temperature or salinity
OPTIONS :
[-v IN-var ] : name of input variable to process. Default is votemper
Possible other choice is vosaline
[-GSOP] : Use 7 GSOP standard level for the output
Default is to take the model levels for the output
[-OCCI] : Use 3 levels for the output: 700m, 2000m and bottom
Default is to take the model levels for the output
[-full] : for full step computation
[-vvl] : use time-varying metrics for vertical integration
(still some details to fix for the last cell including the
target deptht).
[-tmean] : output mean temperature instead of heat content
[-smean] : output mean salinity instead of PSU.m
[-o OUT-file] : use specified output file instead of <IN-var>.nc
[-nc4] : use netcdf4 output with chunking and deflation
REQUIRED FILES :
mask.nc, mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
netcdf file : VAR-name.nc (or specified with -o option)
variables : either voheatc or vohsalt, unless -tmean or -smean used
In this latter case, variables are votemper and
vosaline
SEE ALSO :
cdfvertmean, cdfheatc, cdfmxlhcsc and cdfmxlheatc
usage : cdfzonalmean -f IN-file -p C-type [-b BASIN-file] ...
... [-l LST-var] [-max ] [-pdep] [-o OUT-file ] [-debug] ...
PURPOSE :
Compute the zonal mean of all the variables available in the input
file. This program assumes that all the variables are located on the
same C-grid point, specified on the command line. Using -l option
limits the variables to be processed to the listed variables.
Zonal mean is in fact the mean value computed along the I coordinate.
The result is a vertical slice, in the meridional direction.
REMARK : partial step and vvl output are not handled properly (but
probably minor impact on results), e3x not zonally constant.
ARGUMENTS :
-f IN-file : input netcdf file.
-p C-type : indicate the location on C-grid (T|U|V|F|W)
OPTIONS :
[-b BASIN-file] : netcdf file describing sub basins, similar to
new_maskglo.nc. If this name is not given as option,
only the global zonal mean is computed.
[-max ] : output the zonal maximum and minimum of the variable
[-l LST-var] : Comma separated list of selected variables
[-pdep ] : use positive depths in the output file. Default behaviour
is to have negative depths.
[-ndep_in ] : negative depths are used in the input file. Default
behaviour is to have positive depths.
[-o OUT-file ] : specify output file name instead of zonalmean.nc
[-debug ] : add some print for debug.
REQUIRED FILES :
mesh_hgr.nc, mesh_zgr.nc and mask.nc
OUTPUT :
netcdf file : zonalmean.nc unless option -o is used.
variables : output variable names are built with the following
convention: zoxxxx_bas
- where zo replace vo/so prefix of the input variable,
- where bas is a suffix for each sub-basins (or glo) if a
BASIN-file is used.
If option -max is used, then <IN-var>_max and <IN-var>_min
variables are created.
usage : cdfzonalmeanvT -c CONFIG-CASE -l LST-tags [-b BASIN-file] [-pdep] ...
... [-ndep_in] [-o OUT-file]
PURPOSE :
Compute the time average of zonal-mean(V) x zonal-mean(T/S) for the
set of files corresponding to the list of tags, passed as arguments.
This quantity is the mean-flow contribution to the heat/salt transport
overturning component. < > being the zonal average, we have:
Total = mean-flow + eddy.
time_mean(<V><T>) = time_mean(<V>)*time_mean(<T>)+time_mean(<V>'<T>')
Zonal mean is in fact the mean value computed along the I coordinate.
The result is a vertical slice, in the meridional direction.
REMARKS: Partial steps are not handled properly (but probably minor
impact on results) nor vvl case !.
ARGUMENTS :
-c CONFIG-CASE is the config name of a given experiment (eg ORCA025-G70)
The program will look for gridT, gridU and gridV files for this
config (grid_T, grid_U and grid_V are also accepted). In addition,
if gridS or grid_S file is found, it will be taken in place of
gridT for the salinity variable.
-l LST-tags : a blank-separated list of time tags that will be used
for time averaging. e.g. y2000m01d05 y2000m01d10 ...
OPTIONS :
[-b BASIN-file] : netcdf file describing sub basins, similar to
new_maskglo.nc. If this name is not given as option, only
the global zonal mean is computed.
[-pdep ] : use positive depths in the output file.
Default behaviour is to have negative depths.
[-ndep_in ] : negative depths are used in the input file.
Default behaviour is to have positive depths.
[-o OUT-file] : specify output file name instead of zonalmeanvt.nc
[-debug] : add some print for debug
REQUIRED FILES :
mesh_hgr.nc, mesh_zgr.nc and mask.nc
OUTPUT :
netcdf file : zonalmeanvt.nc
variables : zovzot : mean product of zonal_mean(V) x zonal_mean(T)
zovzot : mean product of zonal_mean(V) x zonal_mean(S)
A suffix _bas is append to variable name oin order to
indicate the basin (atl, inp, ind, pac) or glo for global
usage : cdfzonalsum -f IN-file -p C-type [-b BASIN-file] [-l LST-var] ...
... [-pdep] [-pdeg] [-o OUT-file] [-debug]
PURPOSE :
Compute the zonal sum of all the variables available in the input file.
This program assumes that all the variables are located at the same
C-grid point, specified on the command line. If a list of variables is
given with -l option, only the listed variables will be processed.
Zonal sum is in fact the integral value computed along the I coordinate.
The result is a vertical slice, in the meridional direction.
REMARK : partial step and vvl output are not handled properly (but
probably minor impact on results), e3x not zonally constant.
ARGUMENTS :
-f IN-file : input netcdf file.
-p C-type : indicate the location on C-grid (T|U|V|F|W)
OPTIONS :
[-b BASIN-file] : netcdf file describing sub basins, similar to
new_maskglo.nc. If this name is not given as option, only
the global zonal integral is computed.
[-l LST-var ] : Comma separated list of selected variables
[-pdep ] : use positive depths in the output file.
Default behaviour is to have negative depths.
[-pdeg ] : When using this option, the zonal integral is normalized per
degree of latitude. This was formerly done with cdfzonalintdeg.
Default behaviour is not to normalize.
[-o OUT-file ] : specify output file name instead of zonalsum.nc
[-debug ] : add some print for debug
REQUIRED FILES :
mesh_hgr.nc, mesh_zgr.nc and mask.nc
OPENMP SUPPORT : yes
OUTPUT :
netcdf file : zonalsum.nc or zonalintdeg.nc (-pdeg option)
variables : output variable names are built with the following
convention: zoixxxx_bas
where zoi replace vo/so prefix of the input variable
where bas is a suffix for each sub-basins (or glo)
if a BASIN-file is used.
Units are modified by adding '.m2' at the end. Can be improved !
In addition, '.degree-1' is append to unit with -pdeg option.
usage : cdfmeshmask -n NAMELIST-file -b BATHY-file -c COORD-file ...
... [-njbloc nbloc]
PURPOSE :
Create mesh_mask from bathymetry and namdom information (namelist)
ARGUMENTS :
-n NAMELIST-file : name of the namelist file (with NEMO namdom block)
-b BATHY-file : name of bathymetry (meters)
-c COORD-file : name of coordinates file
OPTIONS :
[-njbloc nbloc]: number of j-bloc of rows to treat together. Increasing
nbloc decreases memory usage but increases writing time.
default : nbloc = npjglo (worst condition)
REQUIRED FILES :
namelist, bathymetry and coordinated passed on the command line
OUTPUT :
netcdf files : cdf_mesh_zgr.nc cdf_mesh_hgr.nc and cdf_mask.nc
SEE ALSO :
usage : cdfmkmask -f T-file [-zoom lonmin lonmax latmin latmax] ...
... [-zoomij iimin iimax ijmin ijmax] ...
... [-zoombat bathymin bathymax] ...
... [-zoomvar varname varmin varmax] ...
... [-time ] [-o OUT-file]
PURPOSE :
Builds a mask file from vosaline array read from the input file.
It assumes that land salinity values are set to 0.
Additional criteria can be added such as geographical limits, model
limits, bathymetric limits and variable range limits.
Any combination of the criteria is valid.
ARGUMENTS :
-f T-file : netcdf file with salinity.
if T-file = -maskfile, we assume a reference file named mask.nc
with tmask variable.
if T-file = -mbathy, we assume a reference file named
bathylevel.nc with mbathy variable, giving the number of
levels in the ocean.
OPTIONS :
[-zoom lonmin lonmax latmin latmax] : geographical windows used to
limit the area where the mask is builded. Outside
this area, the mask is set to 0.
[-zoomij iimin iimax ijmin ijmax] : model grid windows used to
limit the area where the mask is builded. Outside
this area, the mask is set to 0.
[-zoombat bathymin bathymax] : depth windows used to
limit the area where the mask is builded. Outside
this area, the mask is set to 0.
Need mesh_zgr.nc
[-zoomvar varname varmin varmax] : range of varname variable used to
limit the area where the mask is builded. Outside
this area, the mask is set to 0.
[-time ] : If further time step is available
a mask for each time step is done
[-o OUT-file ] : output file name to be used in place of standard
name [ mask_sal.nc ]
REQUIRED FILES :
If option -zoombat is used, file mesh_zgr.nc is required.
If option T-file is -maskfile then mask.nc is required.
If option T-file is -mbathy then bathylevel.nc and mesh_zgr.nc
are required.
OUTPUT :
netcdf file : mask_sal.nc or OUT-file.
variables : tmask, umask, vmask, fmask
fmask can differ from standard fmask because it does not
reflect the slip/noslip lateral condition. usage : cdfmltmask -f IN-file -m MSK-file -v LST-var -p C-type ...
... [-s _Fillvalue] [-o OUT-file] [-M MSK-var] [-noup]
PURPOSE :
This program is used to apply masking (multiply by 1 or 0 ) some
selected variables from the input file, according to their position
on the C-grid. The use of polymask (polygon shape mask, created by
cdfpolymask) is possible.
Once the variables are masked, the '_FillValue' attribute of the
variables is changed to its correct new value. However, when working
with NETCDF4/HDF4 files, it fails with segmentation fault. The actual
workaround is either to transform the input file in NETCDF classical, or
to use -noup option to prevent the update of the _FillValue attribute.
ARGUMENTS :
-f IN-file : input netcdf file.
-m MSK-file : input netcdf mask file.
-v LST-var : Comma separated list of variable names to mask.
-p C-type : one of T|U|V|F|W|P indicating the C-grid position of the
variables. P indicates a polygon mask created by cdfpolymask.
OPTIONS :
[-s _FillValue] : specify values for masked areas [0 by default]
[-o OUT-file] : name of output file, instead of <IN-file>_masked
[-M MSK-var] : use MSK-var in the MSK-file, instead of the one defined
by default according to the -p option. Overrid -p option.
[-noup] : do not update the _FillValue attribute of the masked
variables. Usefull for NETCDF4/HDF5 files, to prevent program
crash (a better fix will be provided, if possible).
REQUIRED FILES :
none, all are given as arguments.
OUTPUT : (jvar)
The output file is a copy of the input file with only
the requested variable masked.
netcdf file : IN-file_masked unless specified with -o
variables : IN-var (same as input). usage : cdfpolymask -p POLY-file -ref REF-file [-r] [-o OUT_file]
PURPOSE :
Create a maskfile with polymask variable having 1 inside the
polygon, and 0 outside. Option -r revert the behaviour (0 inside,
1 outside).
ARGUMENTS :
-p POLY-file : input ASCII file describing a polyline in I J grid.
This file is structured by block, one block corresponding
to a polygon:
1rst line of the block gives a polygon name
2nd line gives the number of vertices (nvert) and a dummy 0
the block finishes with nvert pairs of (I,J) describing
the polygon vertices.
-ref REF-file : reference netcdf file for header of polymask file.
This file will be used to look for domain dimensions, and
in order to build the output file (nav_lon, nav_lat etc ...)
OPTIONS :
[-r ] : revert option. When used, 0 is inside the polygon,1 outside.
[-o OUT-file ] : spefify the name of the output mask file instead
of polymask.nc
REQUIRED FILES :
none
OUTPUT :
netcdf file : polymask.nc
variables : polymask
usage : cdfimprovechk -v IN-var -obs OBS-file -r REF-file -t TST-file ...
... [-o OUT-file] [-nc4]
PURPOSE :
Estimates the improvement/deterioration of a test run, compared with a
reference run relative to some observations.
This program computes the field zchk= ( REF - TST )/(REF - OBS).
Where 0 < zchk <= 1, the TST is better than the reference
Where 1 < zchk, the TST was corrected in the right sense but too much
Where zchk < 0, the TST was corrected was corrected in the wrong way.
Although not very much used, this program is maintained as one of the
first CDFTOOLS.
ARGUMENTS :
-v IN-var : netcdf input variable
-obs OBS-file: netcdf observation file
-r REF-file : netcdf reference file
-t TST-file : netcdf test file
OPTIONS :
[-o OUT-file] : specifiy the output file name instead of chk.nc
[-nc4] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : chk.nc
variables : same as input variable.
usage : cdfmxl -t T-file [-s S-file] [-o OUT-file] [-nc4]
PURPOSE :
Compute 7 estimates of the mixed layer depth from temperature and
salinity given in the input file, based on 7 different criteria:
1- Density criterion (0.01 kg/m3 difference between surface and MLD)
2- Density criterion (0.03 kg/m3 difference between surface and MLD)
3- Temperature criterion (0.2 C absolute difference between surface
and MLD)
4- Temperature criterion (0.2 C absolute difference between T at 10m
and MLD)
5- Temperature criterion (0.5 C absolute difference between T at 10m
and MLD)
6- Density criterion (0.03 kg/m3 difference between rho at 10m and MLD)
7- Density criterion (0.125 kg/m3 difference between rho at 10m and MLD)
ARGUMENTS :
-t T-file : input netcdf file (gridT)
OPTIONS :
[-s S-file] : input netcdf file (gridS), if vosaline not in T-file
[-o OUT-file] : specify the name of output file instead of mxl.nc
[-nc4] : use netcdf4 chunking and deflation on output
REQUIRED FILES :
mesh_zgr.nc
In case of FULL STEP configuration, bathy_level.nc is also required.
OUTPUT :
netcdf file : mxl.nc
variables : somxl010 = mld on density criterion 0.01 ref. surf.
somxl030 = mld on density criterion 0.03 ref. surf.
somxlt02 = mld on temperature criterion -0.2 ref. surf.
somxlt02z10 = mld on temperature criterion -0.2 ref. 10m
somxlt05z10 = mld on temperature criterion -0.5 ref. 10m
somxl030z10 = mld on density criterion 0.03 ref. 10m
somxl125z10 = mld on density criterion 0.125 ref. 10m
usage : cdfmxlhcsc -f T-file -C criteria -t THRESH-value [-hmin hmin] ...
... [-o OUT-file] [-nc4] [-vvl] [-mld MLD-file MLD-var]
PURPOSE :
Compute the MiXed Layer depth, the Heat Content and Salt Content.
ARGUMENTS :
-f T-file : netcdf input file for temperature and salinity (gridT).
-C criteria : Specify the type of criteria to use for MXL computation
can be one of temperature, t, T for temperature criteria.
or one of density, d, D for density criteria.
-t THRESH-value : threshold value for the criteria.
(eg: 0.2 for temp, 0.01 or 0.03 for dens)
OPTIONS :
[-hmin hmin ] : limit the vertical integral from hmin to mld. By default
,
hmin is set to 0 so that the integral is performed on the
whole mixed layer.
[-o OUT-file ] : specify output file name instead of mxlhcsc.nc
[ -nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl ] : use time-varying vertical metrics
[-mld MLD-file MLD-var]: This option replaces both '-C' and '-t'
arguments, indicating that the mixed layer depth is to be read
as the variable MLD-var in the MLD-file. With this option, the
heat and salt content can be computed from the MLD estimates
provided by 'cdfmxl'.
REQUIRED FILES :
mesh_hgr.nc mesh_zgr.nc and mask.nc
In case of full step configuration, bathy_level.nc is also required.
OUTPUT :
netcdf file : mxlhcsc.nc unless -o option is used
variables : - somxl010 (mld based on density criterion 0.01)
(2D) or somxl030 (mld on density criterion 0.03)
or somxlt02 (mld on temperature criterion -0.2)
- somxlheatc (heat content computed in the MLD)
- somxlsaltc (salt content computed in the MLD)
SEE ALSO :
cdfmxl, cdfmxlheatc and cdfmxlsaltc.
usage : cdfmxlheatc -f T-file [-mxlf MXL-file] [-full] [-vvl] ...
... [-o OUT-file] [-nc4]
PURPOSE :
Compute the heat content in the mixed layer (Joules/m2).
ARGUMENTS :
-f T-file : netcdf input file with temperature and mld (gridT).
OPTIONS :
[-mxlf MXL-file] : netcdf input file with mld if not in T-file.
[-full ] : for full step configurations, default is partial step.
[-o OUT-file ] : specify output file instead of mxlheatc.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl ] : use time-varying vertical metrics.
REQUIRED FILES :
mesh_zgr.nc and mask.nc
OUTPUT :
netcdf file : mxlheatc.nc unless option -o is used.
variables : somxlheatc (Joules/m2)
SEE ALSO :
cdfmxl, cdfmxlhcsc and cdfmxlsaltc.
usage : cdfmxlsaltc -f T-file [-mxlf MXL-file] [-full] [-vvl] ...
... [-o OUT-file] [-nc4] [-vvl]
PURPOSE :
Compute the salt content in the mixed layer.
ARGUMENTS :
-f T-file : netcdf input file with salinity and mld (gridT).
OPTIONS :
[-mxlf MXL-file]: netcdf input file with mld if not in T-file.
[-full ] : for full step configurations, default is partial step.
[-o OUT-file ] : specify output file instead of mxlsaltc.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl ] : use time-varying vertical metrics.
REQUIRED FILES :
mesh_zgr.nc and mask.nc
OUTPUT :
netcdf file : mxlsaltc.nc unless option -o is used.
variables : somxlsaltc (Kg/m2)
SEE ALSO :
cdfmxl, cdfmxlhcsc, cdfmxlheatc
usage : cdffracinv -trc TRC-file [-inv INV-name] [-o OUT-file] [-nc4]
PURPOSE :
Compute the fraction of inventory for passive tracers, which is
the ratio between inventory at a grid point and the total inventory.
ARGUMENTS :
-trc TRC-file : netcdf file with tracer inventory.
OPTIONS :
[-inv INV-name ]: netcdf variable name for inventory [ invcfc ]
[-o OUT-file ]: specify output file name instead of fracinv.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : fracinv.nc
variables : fracinv
usage : cdfpendep -trc TRC-file -i INV-file [-o OUT-file] [-nc4] ...
... [-vinv inventory_name -vtrc trc_name ]
PURPOSE :
Compute the penetration depth for passive tracers. It is the ratio
between the inventory and the surface concentration of the tracer.
ARGUMENTS :
-trc TRC-file : netcdf file with tracer concentration.
-i INV-file : netcdf file with inventory of the tracer.
OPTIONS :
[-vinv inventory_name ] : specify netcdf variable name for inventory.
Default is INVCFC
[-vtrc trc_name ] : specify netcdf variable name for tracer.
Default is CFC11
[-o OUT-file ] : specify output file name instead of pendep.nc
[ -nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : pendep.nc
variables : pendep (m)
usage : cdfcofdis -H HGR-file -M MSK-file -T gridT.nc [-jperio jperio ]...
... [-surf] [-o OUT-file[ [-nc4]
PURPOSE :
Compute the distance to the coast and create a file with the Tcoast
variable, indicating the distance to the coast. This computation is
done for every model level, unless -surf option is used.
This file is used in NEMO tradmp routine for fading out restoring
in vicinity of the coast line.
ARGUMENTS :
-H HGR-file : name of the mesh_hgr file
-M MSK-file : name of the mask file
-T T-file : netcdf file at T point ( used for looking at jpk)
OPTIONS :
[-jperio jperio ] : define the NEMO jperio variable for north fold
condition. Default is 4.
[-surf ] : only compute distance at the surface.
[-o OUT-file ] : specify name of the output file instead of dist.coast
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : dist.coast unless -o option is used.
variables : Tcoast (m)
usage : cdfmaskdmp -t T-file [-s S-file] [-refdep REF-depth] ...
... [-dens smin width] [-dep hmin width] [-lat latmax width] ...
... [-o OUT-file] [-nc4]
PURPOSE :
Compute a damping mask with smooth transition according to density,
depth and latitude criteria. For each kind of criterion, a minimum
value and a width of transition is used. Both minimum and width can
be adjusted with corresponding options. Reasonable default values are
provided.
This tool was designed for building a mask in the deep Southern Ocean,
for dense waters. This explains that we consider the limit as a minimum
depth and density, but a maximum latitude. It needs some adjustments for
other situations.
ARGUMENTS :
-t T-file : temperature/salinity file used to compute the potential
density relative to the reference depth.
OPTIONS :
[-s S-file] : salinity file in case it differs from the temperature file
.
[-refdep REF-depth] : reference depth for potential density.
[-dens smin width] : set minimum density and width for density tapering
[-dep hmin width] : set minimum depth and width for depth tapering
[-lat latmax width]: set max latitude and width for latitude tapering
[-o OUT-file] : specify output file name instead of mask_dmp.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
Actual default values are :
-refdep 2000.
-dens 37.160 0.025
-dep 1000. 100.
-lat -20. 2.
REQUIRED FILES :
mask.nc
OUTPUT :
netcdf file : mask_dmp.nc unless -o option is used.
variables : wdmp usage : cdfmppini -i jpni -j jpnj [-m/-b/-z] [-jperio jperio]
PURPOSE :
Performs the mpp initialisation with NEMO routine mpp_init2 and gives
some statistics about the domains. Save the layout on a text file.
ARGUMENTS :
-i jpni : number of domains in the i direction.
-j jpnj : number of domains in the j direction.
OPTIONS :
[-m/-b/-z] : use one of these option to choose the land/sea mask.
m : take mask from mask.nc (tmask) [ default ]
b : take mask from bathy_meter.nc (Bathymetry)
z : take mask from mesh_zgr.nc (mbathy)
Default is m
[-jperio jperio ] : specify jperio.
default value is 6
REQUIRED FILES :
one of mask.nc, bathy_meter.nc or mesh_zgr.nc according to option
OUTPUT :
- Standard output
- ASCII file mppini.txt usage : cdfuv -c CONFIG-CASE -l LST-tags [-opt] [-o OUT-file] [-nc4]
PURPOSE :
Compute the time average values for U.V product, at T point.
Mean U, mean V and mean U'.V' at T point are also computed.
ARGUMENTS :
-c CONFIG-CASE is the config name of a given experiment (eg ORCA025-G70)
The program will look for gridU and gridV files for this config
grid_U and grid_V are also accepted).
-l LST-tags : a list of time tags that will be used for time averaging.
e.g. : y2000m01d05 y2000m01d10 ...
OPTIONS :
[-opt :] use optimized algorithm, minimizing truncation errors in the
evaluation of mean U, meanV and mean (U'.V').
[-o OUT-file] : specify output filename instead of uv.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : uv.nc
variables : vouv : Mean U.V at T point
vozocrtx_t : Mean U at T point
vomecrty_t : Mean V at T point
vouv_prime : Mean U'.V' at T point
usage : cdfuvwt -c CONFCASE -l LST-tags [-w imin imax jmin jmax] ...
... [-o OUT-file] [-nc4]
PURPOSE :
Compute the time-mean fields for velocity components (u,v,w) and
temperature (t), as well as second order moments ( u2, v2, t2, uv, ut,
vt, wt).
These fields are required in other cdftools which computes either
barotropic (cdfnrj_bti) or baroclinic (cdfnrj_bci) instabilities, and a
global energy balance (cdfnrj_components)
ARGUMENTS :
-c CONFCASE : the root name for the data files. Grid files are assumed
to be gridT, gridU, gridV, gridW. (grid_T, grid_U, grid_V and
grid_W are also supported).
-l LST-tags : set the list of time tags corresponding to the time serie
whose mean is being computed.
OPTIONS :
[-w imin imax jmin jmax ] : model window limiting the area where the
time-means will be computed.
[-o OUT-file] : specify output file name instead of moyuvwt.nc
[-nc4] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : moyuvwt.nc
variables : There are 11 variables produced by this program.
tbar, t2bar : mean t (Kelvin) and mean t^2 (K^2) [T-point]
ubar, u2bar : mean u (m/s) and mean u^2 (m2/s2) [U-point]
vbar, v2bar : mean v (m/s) and mean v^2 (m2/s2) [V-point]
wbar : mean w (m/s) [W-point]
uvbar : mean product u . v (m2/s2) [T-point]
utbar, vtbar, wtbar : mean product [uvw].t (m/s.K) [T-point]
SEE ALSO :
cdfnrj_bti, cdfnrj_bci, cdfnrj_components and cdfnrj_transfert.
usage : cdfvT -c CONFIG-CASE -l LST-tags [-o OUT-file ] [-nc4 ] [-vvl]
PURPOSE :
Compute the time average values for second order moments V.T, V.S, U.T
and U.S used in heat and salt transport computation.
ARGUMENTS :
-c CONFIG-CASE is the config name of a given experiment (eg ORCA025-G70)
The program will look for gridT, gridU and gridV files for this
config ( grid_T, grid_U and grid_V are also accepted).
Additionaly, if gridS or grid_S file is found, it will be taken
in place of gridT for the salinity variable.
-l LST-tags : a blank-separated list of time tags that will be used for
time averaging, e.g.: y2000m01d05 y2000m01d10 ...
OPTIONS :
[-o OUT-file] : specify output file name instead of vt.nc
[-nc4 ] use netcdf4 output with chunking and deflation 1
[-vvl ] use time varying vertical metrics.
REQUIRED FILES :
none
OUTPUT :
netcdf file : vt.nc unless -o option used.
variables : vozout time-mean ( U.T ) at U point.
vozous time-mean ( U.S ) at U point.
vomevt time-mean ( V.T ) at V point.
vomevs time-mean ( V.S ) at V point.
usage : cdfvsig -c CONFIG-CASE -l LST-tags [-o OUT-root] [-nc4] [-no-w] ...
... [-no-sig] [-no-uv] [-T ] [-depref LST-depht]
PURPOSE :
Compute the time average values for second order moments U.sig, V.sig
and W.sig. By default sig is sigma-0, the potential density refered to
the surface. The user can provide a list of reference depths, to force
the computation of the respective second order moments, e.g U.sig-2 ...
In order to ease the post processing, time-mean densities interpolated
at velocity points, as well as mean velocity components are also saved.
Various options allows the modulation of the output.
ARGUMENTS :
-c CONFIG-CASE is the config name of a given experiment (eg ORCA025-G70)
The program will look for gridT, gridU, gridV and gridW files for
this config ( grid_T, grid_U, grid_V and grid_W are also accepted).
-l LST-tags : a blank-separated list of time tags that will be used for
time averaging, e.g. y2000m01d05 y2000m01d10.
OPTIONS :
[-o OUT-root]: specify the file name root used for the output.
Output file names will be <ROOT>usig.nc, <ROOT>vsig and <ROOT>wsig.
Default <ROOT> is empty. Consider then to add an '_' in the root
name.
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-no-w] : do not compute the mean vertical products.
[-no-sig] : do not output the mean density on U V points.
[-no-uv ] : do not output the mean velocity components.
[-T ] : computes U and V at T points, so that U.sig, V.sig will be at
at T point.
[-depref LST-depht] : give a comma-separated list of reference depths
for potential density computation. eg : '-depref 0,2000,3000'
If not specified the unique reference depth is 0m (surface).
REQUIRED FILES :
mask.nc
OUTPUT :
netcdf file : usig.nc, vsig.nc and wsig.nc
variables : vousig, vovsig, vowsig : mean product v x sigma-0
at velocity point.
vosigu, vosigv, vosigw : mean sigma-0 at velocity point.
vozocrtx, vomecrty, vovecrtz : mean velocity components.
usage : cdflinreg -l LST-files [-o OUT-file] [-nc4]
PURPOSE :
Compute the linear regression coefficients for a bunch of input files.
ARGUMENTS :
-l LST-files: A blank-separated list of netcdf model file of same kind.
OPTIONS :
[-o OUT-file ] : specify name of the output file instead of linreg.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : linreg.nc unless option -o is used.
variables : for each input variables, there are 3 computed field
- slope coefficient
- barycenter
- Pearson Coefficient usage : cdfpdf -f IN-file -v IN-var [-zoom imin imax jmin jmax] ..
[-lev level] [-range vmin vmax nbin ] [-o OUT-ncfile] [-a OUT-ascfile]
PURPOSE :
Build the pdf of a given variable, on a given area, according
to bin specifications passed as argument of the program. If no
particular specification is passed to the program, build 100
bins between minimum and maximum value of the variable.
ARGUMENTS :
-f IN-file : input file
-v IN-var : variable name
OPTIONS :
[-zoom imin imax jmin jmax] : define a sub-area, in model
coordinates
[-lev level ] : choose a level for pdf computation
If not specified, takes level 1.
[-range vmin vmax nbin ] : define the limit for binning
and number of bins.
[-o OUT-file] : specify name for netcdf output file
[-a ASC-file] : specify name for ascii output file
REQUIRED FILES :
OUTPUT :
(1) ascii file with bin number, value and mean field in bin
(2) netcdf file for 2d array where x dimension corresponds to bins
y dimension corresponds to time, thus the field value being
an array count(bin,time). The output file follows the nemo
standards, even, if nav_lon, nav_lat are no more longitude or
latitude.
netdf variable is <IN-var>_pdf
SEE ALSO : usage : cdfrmsssh -t T-file -t2 T2-file [-o OUT-file] [-nc4]
PURPOSE :
Compute the standard deviation of the SSH from its mean value
its mean square value.
Note that what is computed in this program is stictly the
standard deviation. It is very often called RMS, which is
an abuse. It is the same only in the case of zero mean value.
However, for historical reason, the name of this tool, remains
unchanged: cdfrmsssh
ARGUMENTS :
-t T-file : netcdf file with mean values for SSH
-t2 T2-file : netcdf file with mean squared values for SSH
OPTIONS :
[-o OUT-file] : specify the name of the output file instead
of default name rms.nc
[-nc4] : use netcdf4 with chunking and deflation
REQUIRED FILES :
none
OUTPUT :
netcdf file : rms.nc unless option -o is used.
variables : sossheig_rms, same unit than the input.
SEA ALSO :
cdfstd, cdfstdevw, cdfstdevts. usage : cdfstatcoord -c COOR-file -m MSK-file [-v MSK-var ]
PURPOSE :
Compute and displays statistics about grid metrics vs latitude.
Bins e1 and e2 by latitude bins, and compute the mean of each bin.
ARGUMENTS :
-c COOR-file : coordinates file with e1 e2 metrics
-m MSK-file : mask file
OPTIONS :
[-v MSK-var] : mask variable name. Default is tmask
REQUIRED FILES :
none apart those requested on command line.
OUTPUT :
Standard output usage : cdfstats -f IN-file -r REF-file -ncy ncy [-v1 VAR-name1] ...
... [-v2 VAR-name2] [-m MSH-MSK-file ] [-o OUT-file] [-nc4]
PURPOSE :
This tool computes some statistics (rms, correlation, signal/noise
ratio and signal ratio [ratio of std deviation]) between two files.
In this tool, the files are supposed to hold monthly averages values,
for many years. Specifying ncy=12, allows to remove the seasonal
cycle of the data.
This program was initially written for SSH statistics between model
output and AVISO files (default variable names are sossheig
for this reason ). It can now be used with any variables.
ARGUMENTS :
-f IN-file : Model data file.
-r REF-file : Reference data file (usually observation file)
-ncy ncy : ncy can only be 1 or 12. If set to 12, annual cycle is
removed from the data.
OPTIONS :
[-v1 VAR-name1] : Variable name in the model file. Default is sossheig.
[-v2 VAR-name2] : Variable name in the reference file. If not specified
assumes that it is the same than in the model file.
[-m MSH-MSK-file] : specify a mesh_mask file holding the tmaskutil
and the horizontal metrics. If this option is not used,
mask are taken in mask.nc and horizontal metric
is taken in mesh_hgr.nc
[-o OUT-file] : specify the output file name instead of stats.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mask.nc and mesh_hgr.nc
or mesh_mask file specified in -m option
OUTPUT :
netcdf file : stats.nc
variables are :
rms : RMS between the input files
correl : CORREL between the input files
rrat : Signal to noise ratio
srat : Signal ratio (stdev ratio)
usage : cdfstd -l LST-files [-save] [-spval0] [-mskmiss] [-opt] ...
... [-o STD-fileout] [-m MEAN-fileout] [-nc4]
PURPOSE :
Compute the standard deviation of the variables belonging to a set of
files given as arguments. This computation is direct and does not
required a pre-processing with any of the cdfmoy tools.
ARGUMENTS :
-l LST-files : A blank-separated List on netcdf files of the same type,
forming a time-series
OPTIONS :
[-save ] : Save the mean value of the field, in addition to the
std deviation.
[-spval0 ] : set missing_value attribute to 0 for all output
variables and take care of the input missing_value.
This option is usefull if missing_values differ from files
to files.
[-mskmiss ] : with this option, the output std and mean are set to
missing value at any gridpoint where the variable contains a
missing value for at least one timestep. You should combine
with -spval0 if missing values are not 0 in all the input files.
[-opt ]: use an optimal algorithm to compute std deviation and use an
unbiased standard deviation estimates.
[-o STD-fileout]: specify std dev output file name instead of cdfstd.nc
[-m MEAN-fileout]: specify mean output file name instead of cdfmoy.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
- netcdf file : cdfstd.nc
variables : IN-var_std, same units than input variables.
- netcdf file : cdfmoy.nc in case of -save option.
variables : IN-var, same units than input variables.
SEE ALSO :
cdfmoy, cdfrmsssh, cdfstdevw usage : cdfstdevts -t T-file -t2 T2-file [-o OUT-file] [-nc4]
PURPOSE :
Compute the standard deviation of the temperature and salinity from
their mean and mean squared values. The mean squared values for T
and S are not automatically computed with cdfmoy (need some namelist
modification). Consider using the more generic program 'cdfstd' if
you do not already have the mean T2 and mean S2.
ARGUMENTS :
-t T-file : netcdf file with mean values for T, S
-t T2-file : netcdf file with mean squared values for T,S
OPTIONS :
[-o OUT-file] : specify output file name instead of stdevts.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : stdevts.nc
variables : votemper_stdev, same unit than the input.
vosaline_stdev, same unit than the input.
SEA ALSO :
cdfstd, cdfrmsssh, cdfstdevw, cdfstats.
usage : cdfstdevw -w W-file -w2 W2-file [-v IN-var] [-o OUT-file] [-nc4]
PURPOSE :
Compute the standard deviation of the vertical velocity from its mean
value and its mean square value. If a variable name is given ,then
the standard deviation of this variable instead of the vertical
velocity.
ARGUMENTS :
-w W-file : netcdf file with mean values for w or <IN-var>
-w2 W2-file : netcdf file with mean squared values for w or <IN-var>
OPTIONS:
[-v IN-var] : give name of variable if not vovecrtz
[-o OUT-file] : specify the name of the output file instead of rmsw.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : rmsw.nc (if IN-var specified, output file is rms_var.nc)
variables : vovecrtz_rms, (or IN-var_rms) same unit than the input.
SEE ALSO :
cdfstd, cdfrmsssh, cdfstdevts, cdfstats.
usage : cdfmoy -l LST-files [-spval0] [-cub] [-zeromean] [-max] [-mskmiss] ...
... [-var VAR-name] [-vvl] [-o OUT-rootname] [-nc4]
PURPOSE :
Compute the 'time average' of a list of files given as arguments.
The program assumes that all files in the list are of same type (shape,
variables, etc...). Any file in the list may have many time frames,
they will be taken into account in the average.
For some variables, the program also computes the time average of the
squared variables, which is used in other cdftools (cdfeke, cdfrmsssh,
cdfstdevw, cdfstddevts...). The actual variables selected for squared
average are :
- vozocrtx
- vomecrty
- vovecrtz
- sossheig
This selection can be adapted with the nam_cdf_namelist process.
(See cdfnamelist -i for details).
If you want to compute the average of already averaged files, consider
using cdfmoy_weighted instead, in order to take into account a
particular weight for each file in the list.
ARGUMENTS :
-l LST-files : A list of similar model output files, whose time average
will be computed.
OPTIONS :
[-spval0 ] : set missing_value attribute to 0 for all variables and
take care of the input missing_value. This option is usefull
if missing_values differ from files to files.
[-cub ] : use this option if you want to compute third order moments
for the eligible variables, which are at present :
- sossheig
- votemper
This selection can be adapted with the nam_cdf_namelist process.
(See cdfnamelist -i for details).
[-zeromean ] : with this option, the spatial mean value for each time
frame is substracted from the original field before averaging,
square averaging and eventually cubic averaging.
[-max ] : with this option, a file with the minimum and maximum values
of the variables (through the list of files) is created.
[-mskmiss ] : with this option, the output average is set to missing
value at any gridpoint where the variable contains a missing
value for at least one timestep. You should combine with option
-spval0 if missing values are not 0 in all the input files.
[-var VAR-name] : Only process VAR-name, instead of all variables.
[-vvl ] : take into account the time varying vertical scale factor.
[-o OUT-rootname] : Define output root-name instead of cdfmoy
[-nc4 ]: Use netcdf4 output with chunking and deflation level 1..
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
If -zeromean option is used, need mesh_hgr.nc and mask.nc
OUTPUT :
netcdf file : cdfmoy.nc and cdfmoy2.nc
Variables name are the same than in the input files.
For squared averages '_sqd' is appended to the original variable name.
If -cub option is used, the file cdfmoy3.nc is also created with
'_cub' appended to the original variable name.
If -max option is used, the file cdfmoy_minmax.nc is also created with
'_max' and '_min' appended to the original variable name.
SEE ALSO :
cdfmoy_weighted, cdfstdev
usage : cdfmoy_freq -f IN-file -avg AVG-length [-v3d] [-v4d] [-o OUT-rootname]
... [-nc4]
PURPOSE :
This program takes a file covering 1 year of data (evenly spaced) and
sub-samples the data by performing box averages, which span is given as
argument. The original data sampling can be hours, days, monthes or
even seasons.
The program recognizes leap years, and when feb. 29 is found, it is
included in the current 'box' (averaging length is thus increased by
1 day.)
ARGUMENTS :
-f IN-file : gives the name of the yearly file containing either 365
or 366 days
-avg AVG-length : Set the time size of the averaging box. Averaging
length is specified using XIOS convention (e.g. 1d,5d, 1mo, 1y ;
4mo stands for seasonal means )
OPTIONS :
[-v3d] : use 3d variable (x,y,t) : save execution time, increase memory
[-v4d] : use 4d variable (x,y,z,t): save execution time, increase memory
[-o OUT-rootname] : specify the root of the output file name instead
of cdfmoy_. Final name will have <freq> appened
to the root.
[-nc4] : use netcdf4 with chunking and deflation for the output file
REQUIRED FILES :
none.
OUTPUT :
netcdf file : cdfmoy_output<freq>.nc
variables : same as variables in input file.
SEE ALSO :
cdfmoy, cdfmoy_weighted
usage : cdfmoy_weighted -l LST-files [-old5d ] [-month] [-leap] ...
... [-skip variable] [-vvl] [-o OUT-file] [-nc4]
PURPOSE :
Compute weighted average of files. The weight for each file is read from
the iweight variable attribute. In particular, this attribute is set to
the number of elements used when computing a time average ('cdfmoy').
A primary application is thus for computing annual mean from monthly
means.
ARGUMENTS :
-l LST-files : The list of files to be averaged, which are supposed to
be of the same type and to contain the same variables.
OPTIONS :
[-old5d ] : This option is used to mimic/replace the cdfmoy_annual which
is no longer available. With this option, 12 monthly files must be
given, and it is assumed that the monthly means were computed from
5d output of a simulation using a noleap calendar (weights are
fixed, predetermined).
[-month ] : This option is used to build annual mean from true month
output (1mo) in XIOS output for instance.
[-leap ] : This option has only effect together with the -month option.
When used set 29 days in february.
[-skip variable ] : name of variable to skip, in the input file.
[-vvl ] : Use time-varying vertical metrics for weighted averages.
[-o OUT-file] : Specify the name for output file instead of
cdfmoy_weighted.nc
[-nc4 ] : Use netcdf4 chunking and deflation in output file.
REQUIRED FILES :
none
OUTPUT :
netcdf file : cdfmoy_weighted.nc
variables : same as in the input files
SEE ALSO :
cdfmoy, cdfmoyt, cdfmoy_freq
usage : cdfmoyt -l LST-files [-spval0] [-vvl] [-o OUT-rootname] [-nc4]
PURPOSE :
Compute the 'file average' of the files listed on the command line.
The 'file average' will have the same number of time frame than any
individual file in the list, the average being done frame by frame.
The main use of this program is the calculation of a climatological
average, for instance. It can also be used for the calculation of an
ensemble mean, although cdfenstat is more appropriate.
The program assumes that all files in the list are of same type (shape,
variables, and number of time frames).
For some variables, the program also computes the 'file average' of the
squared variables, which is used in other cdftools (cdfeke, cdfrmsssh,
cdfstdevw, cdfstddevts...). The actual variables selected for squared
average are :
- vozocrtx
- vomecrty
- vovecrtz
- sossheig
This selection can be adapted with the nam_cdf_namelist process.
(See cdfnamelist -i for details).
ARGUMENTS :
-l LST-files: List of files whose average will be computed.
OPTIONS :
[-spval0 ] : set missing_value attribute to 0 for all variables and
take care of the input missing_value. This option is usefull
if missing_values differ from files to files.
[-vvl] : Use time-varying vertical metrics.
[-o OUT-rootname] : Define output root-name instead of cdfmoyt
[-nc4 ]: Use netcdf4 output with chunking and deflation level 1..
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
none
OUTPUT :
netcdf file : cdfmoyt.nc and cdfmoyt2.nc
Variables name are the same than in the input files.
For squared averages '_sqd' is appended to the original variable name. usage : cdf_xtrac_brokenline -t T-file -u U-file -v V-file [-i ICE-file] ...
... [-b BAT-file] [-mxl MXL-file] [-f section_filei,sec_file2,..] ...
... [-l LST-sections] [-ssh] [-mld] [-vt] [-vecrot] [-vvl W-file] ...
... [-o ROOT_name] [-ice] [-verbose]
PURPOSE :
This tool extracts model variables from model files for a geographical
broken line, similar to an oceanographic campaign where an oceanic
section is formed by one or more legs.
The broken line is specified by the position of ending points of each
leg, given in an ASCII file. OVIDE section is taken as default, when no
section file is provided.
This tool provides a netcdf file similar to a model file, but with a
degenerated 'y' dimension (1). In order to be able to use standard
CDFTOOLS, relevant metric variables are saved into the output file, such
as pseudo e1v and e3v and vmask. Therefore the output file can be
considered as a mesh_hgr, mesh_zgr and mask file for any 'meridional'
computation. In the relevant CDFTOOLS, the option '-self' tells the
program that input data file can be considered as mesh_mask file as well.
This tools works with temperatures, salinities and normal velocities.
The broken line is approximated in the model, by a succession of segments
joining F-points. The velocity is taken as either U or V depending on the
orientation of the segment, temperatures and salinities are interpolated
on the velocity points. When progressing along the broken line, normal
velocity is positive when heading to the right of the progression.
The barotropic transport across the broken line is computed, using the
same sign convention. On a closed broken line, the barotropic transport
should be very small.
ARGUMENTS :
-t T-file : model gridT file
-u U-file : model gridU file
-v V-file : model gridV file
OPTIONS :
[-l LST-sections ] : provides a blank-separated list of files for section
definitions. Section_file is an ascii file as follows :
* line #1 : name of the section (e.g. ovide).
Will be used for naming the output file.
* line #2 : number of points defining the broken line.
* line #3-end : a pair of Longitude latitude values defining
the points. If not supplied, use hard-coded information
for OVIDE section. A comment can be added at the end of
of the lines, using a # as separator
[-f section_file1,section_file2,...] : provide a comma-separated list of
files for section definition. This option will be deprecated in
favor of '-l' option, which passes the same file names, but
easier to parse when using a big number of files.
[-b BAT-file] : Specify a bathymetric file in case the ocean bathymetry
is not in mesh_zgr.nc (variable hdepw).
[-mxl MXL-file] : Give the name of the file containing the MLD if it is
not in T-file.
[-verbose] : increase verbosity
[-ssh] : also save ssh along the broken line.
[-mld] : also save mld along the broken line.
[-i ICE-file] : also save ice properties (concentration, thickness)
extracted from ICE-file along the broken line.
[-vt] : also save products vt and vs along the broken line.
[-vvl W-file] : use time-varying vertical metrics. Specify a W-file in
order to read time-varying e3w needed in the computation of
depu3d.
[-o ROOT-name]: specified the prefix to be used for the output file name.
Note that it may be a good idea to include a separator character
such as '_' at the end of the ROOT_name.
[-vecrot] : also save normal and tangent velocities along the broken line
(for plots purpose only).
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc in the current directory
OUTPUT :
netcdf file : <section_name>.nc (default). If -o option is used, the
name will be <ROOT-name><section_name>.nc
variables : temperature, salinity, normal velocity, pseudo V metrics,
mask, barotropic transport, bathymetry of velocity points.
Additional variables can be set when using options.
ASCII file : <section_name>_section.dat usefull for cdftransport, gives
the position in I,J of the geographical input points.
SEE ALSO :
cdftransport, cdfmoc, cdfmocsig. This tool replaces cdfovide.
usage : cdfisopsi -ref REF-level -sig TGT-sigma -f T-file [-o OUT-file]...
... [-nc4] [-vvl]
PURPOSE :
Compute a 'geostrophic streamfunction', projected on an isopycn.
In this program, temperature and salinities on the selected isopync
are saved, as well as the depth of the isopycnal surface.
Then the specific volume anomaly at each model level (1/rho0 -1/rho)
is integrated from top to isopycnal surface. The resulting 3D field
is finally projected (and normalized) on the isopycnal surface.
ARGUMENTS :
-ref REF-level: reference level for pot. density.
-sig TGT-sigma: target density level to project on.
-f T-file : input file for temperature and salinity.
OPTIONS :
[-o OUT-file ]: specify output filename instead of isopsi.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
[-vvl ] : use time varying vertical metrics.
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
netcdf file : isopsi.nc unless -o option is used.
7 variables :
votemper_interp : Temperature interpolated on isopycnal layer
vosaline_interp : Salinity interpolated on isopycnal layer
depth_interp : Depth of the isopycnal layer
soisopsi : Total streamfunction on the isopycnal layer
soisopsi1 : Contribution of the SSH
soisopsi2 : Contribution of specific volume anomaly vertical
integration
soisopsi3 : Contribution of pressure term on the isopycnal
layer
SEE ALSO :
cdfhdy
usage : cdfmaxmoc -f OVT-file -b BASIN-name -w latmin latmax depmin depmax ...
... [-o OUT-file]
PURPOSE :
Compute the maximum and minimum of the overturning, from OVT-file,
for the specified oceanic basin, and in the geographical window
defined with '-w' option as a range of latitudes and depths.
ARGUMENTS :
-f OVT-file : overturning file from cdfmoc, with or w/o sub basins.
-b BASIN-name : name of oceanic subbasin as defined in new_maskglo.nc
usually it can be one of atl, glo, inp, ind or pac. glo means
no subbasins.
-w latmin latmax depmin depmax : specify the geographical window in
maximum and minimum of the overturning will be computed:
latmin latmax : limits in latitudes (deg N).
depmin depmax : limits in depths (meters).
OPTIONS :
[-o OUT-file] : specify the output file name instead of maxmoc.nc
REQUIRED FILES :
none
OUTPUT :
netcdf file : maxmoc.nc
6 variables :
maxmoc, minmoc ( sv ) : max and min of overturning
latmaxmoc latminmoc ( deg) : latitudes of max and min.
depmaxmoc depminmoc ( m) : depth of max amd min .
SEE ALSO :
cdfmoc
usage : cdfmhst -vt VT-file | (-v V-file -t T-file [-s S-file]) [-MST] ...
... [-b BASIN-mask] [-full] [-Zdim] [-o OUT-file] [-vvl]
PURPOSE :
Compute the meridional heat/salt transport as a function of latitude.
If the basin mask-file new_maskglo.nc is provided, the meridional
heat/salt transport for each sub-basin is also computed.
This program is designed to read the time-average products V.T into
the corresponding VT-file (produced by cdfvT). If VT-files are not
available, or if working with model snapshot, V-file and T-file can
be specified as an alternative.
In the evaluation of the 'meridional' component, a 'zonal' integration
is performed. Note that in CDFTOOLS, as far as 'zonal' integrals
are concerned, they in-fact correspond to 'along-model I' integrals.
ARGUMENTS :
-vt VT-file : netcdf file containing the mean value of the products
U.S, U.T, V.S and V.T (obtained with cdfvT).
or
-v V-file : specify V-file
-t T-file : specify T-file
If not using '-vt' option, both V-file and T-file MUST be specified.
OPTIONS :
[-s S-file] : specify S-file (salinity) if the salinity field is not in
T-file.
[-MST ] : Indicates the the meridional Salt transport will also be
computed. If not specified, only the MHT is output.
[-full ] : to be set for full step case.
[-Zdim ] : to be set to output vertical structure of Heat/salt transport
[-b BASIN-mask ] : use BASIN-mask instead of default new_maskglo.nc
[-o OUT-file ] : change name of the output file. Default:mhst.nc
[-vvl ] : use time-varying vertical metrics.
REQUIRED FILES :
mesh_hgr.nc, mesh_zgr.nc and mask.nc
If new_maskglo.nc is also available, sub-basin meridional transports
are also computed.
OUTPUT :
ASCII files : zonal_heat_trp.dat : Meridional Heat Transport
zonal_salt_trp.dat : Meridional Salt Transport
netcdf file : mhst.nc unless -o option is used.
variables : ( [... ] : -MST option )
zomht_glo : Meridional Heat Transport (global)
[ zomst_glo : Meridional Salt Transport (global) ]
If new_maskglo.nc is available, per basin meridional transport
are also available:
zomht_atl : Meridional Heat Transport
[ zomst_atl : Meridional Salt Transport ]
zomht_inp : Meridional Heat Transport
[ zomst_inp : Meridional Salt Transport ]
zomht_ind : Meridional Heat Transport
[ zomst_ind : Meridional Salt Transport ]
zomht_pac : Meridional Heat Transport
[ zomst_pac : Meridional Salt Transport ]
zomht_inp0 : Meridional Heat Transport
[ zomst_inp0 : Meridional Salt Transport ]
usage : cdfmht_gsop -v V-file -t T-file [-o OUT-file]
PURPOSE :
Compute the meridional heat transport(MHT) for the Atlantic basin.
Compute 3 components of the MHT :
- Barotropic component
- Vertical shear geostrophic component
- Vertical shear ageostrophic component (Ekman + residual)
REMARKS :
This program has been ported to CDFTOOLS4, without major changes.
It should work as before but is not optimized for memory (lot of
3D arrays declared).
ARGUMENTS :
-v V-file : name of the meridional velocity file.
-t T-file : name of the temperatture file.
OPTIONS :
[-o OUT-file] : output file name instead of gsopmht.nc
REQUIRED FILES :
mesh_hgr.nc, mesh_zgr.nc and new_maskglo.nc
OUTPUT :
netcdf file : gsopmht.nc
variables : zomhtatl : MHT Atlantic Ocean
zobtmhta : Barotropic component
zoshmhta : Vertical shear geostrophic component
zoagmhta : vertical shear ageostrophic component
SEE ALSO :
cdfmhst (compute MHT without decomposition), cdfmoc
usage : cdfmoc -v V-file [-decomp] [-rapid] [-t T-file] [-s S-file] ...
... [-u U-file] [-full] [-vvl ] [-o OUT-file]
PURPOSE :
The primary purpose of this tool is to compute the MOC for oceanic
sub-basins as described in new_maskglo.nc. If this sub-basins
file is not found, then only computes the global MOC.
The option '-decomp' was developped in order to decompose the MOC
into its 3 components : Geostrophic, Barotropic and Ageostrophic.
With the option '-rapid', the model MOC at the latitude of the RAPID
section (26.5 N) is evaluated in the same manner as it is done with
observations of the RAPID MOCHA array, (see details below).
REFERENCES :
- MOC decomposition:
Lee & Marotzke (1998), Baehr, Hirschi, Beismann & Marotzke (2004),
Cabanes, Lee, & Fu (2007), Koehl & Stammer (2007).
- RAPID MOCHA array evaluation:
See : http://www.rapid.ac.uk
ARGUMENTS :
-v V-file : file with meridional velocity component (mandatory).
OPTIONS :
[-decomp ] : decompose MOC in 3 components: Geostrophic, Barotropic and
Ageostrophic. For this option temperatures and salinity are
needed (for density calculation), hence T-file/S-file.
[-rapid ] : Compute the AMOC at 26.5 N in the same manner than the
RAPID MOCHA array, separating the Gulfstream transport and the
contribution of different water masses :
- 0-800m : Thermocline recirculation
- 800-1100m : AIW recirculation
- 1100-3000m : upper-NADW recirculation
- 3000-5000m : lower-NADW recirculation
- 5000-bottom : AABW recirculation
[-t T-file] : file with temperature and salinity. Required for
'-decomp' and '-rapid' options.
[-s S-file]: Specify a salinity only file if the salinity is not
available in T-file. Required for '-decomp' and
'-rapid' options.
[-u U-file]: Specify the U-file (zonal wind-stress), required only for
'-rapid' option, for the evaluation of Ekman transport.
[-full ] : use full step instead of default partial step
[-vvl ] : Use time-varying vertical metrics
[-o OUT-file] : specify output file instead of moc.nc
REQUIRED FILES :
Files mesh_hgr.nc mesh_hgr.nc and mask.nc
File new_maskglo.nc. If this latter file is not available
only the MOC for the global domain is computed
OPENMP SUPPORT : yes
OUTPUT :
netcdf file : moc.nc
variables zomsfglo : Global ocean
variables zomsfatl : Atlantic Ocean
variables zomsfinp : Indo Pacific
variables zomsfind : Indian Ocean alone
variables zomsfpac : Pacific Ocean alone
variables zomsfinp0 : Indo Pacific Net
If decomposition is required , ( option -decomp ) add 3 additional
variables per basin with suffixes _sh, _bt, _ag.
If option -rapid is used the output file (rapid_moc.nc) is degenerated
into 6 scalar values : tr_gs, tr_THERM, tr_AIW, tr_UNADW, tr_LNADW,
tr_BW and a vertical profile of the AMOC at 26.5N, as computed
traditionally.
Additional variables are also computed following CLIVAR-GODAE
reanalysis intercomparison project recommendations.
usage : cdfmocsig -v V-file -t T-file -r REF-depth | -ntr [-eiv] [-full] ...
... [-sigmin sigmin] [-sigstp sigstp] [-nbins nbins] [-isodep] ...
... [-o OUT-file] [-vvl] [-verbose]
PURPOSE :
Compute the MOC in density-latitude coordinates. The global value is
always computed. Values for oceanic sub-basins are calculated if the
new_maskglo.nc file is provided.
The reference depth for potential density is given with '-D' option.
Density ranges and number of bins to use are pre-defined only for three
reference depth (0, 1000 and 2000 m). For other reference depth, the
density binning must be specified using the relevant options for setting
the minimum density, the density step and the number of bins to use.
ARGUMENTS :
-v V-file : Netcdf gridV file.
-t T-file : Netcdf gridT file.
-r ref-depth : reference depth for density.
For depth values of 0 1000 or 2000 m, pre-defined limits for
minimum density, number of density bins and width of density
bins are provided. For other reference depth, you must use the
options '-sigmin', '-sigstp' and '-nbins' (see below).
or
-ntr : uses neutral density (no default bin defined so far), no '-r'
OPTIONS :
[-eiv ] : takes into account VEIV Meridional eddy induced velocity.
-> To be used only if Gent and McWilliams parameterization
has been used.
[-full ] : Works with full step instead of standard partial steps.
[-sigmin ] : Specify minimum of density for bining.
[-sigstp ] : Specify density step for bining.
[-nbins ] : Specify the number of density bins you want.
[-isodep ] : Compute the zonal mean of isopycnal depths used for
mocsig.
[-o OUT-file ] : Specify output file name instead of mocsig.nc
[-vvl ] : Use time-varying vertical metrics.
[-verbose ] : Verbose option for more info during execution.
REQUIRED FILES :
Files mesh_zgr.nc, mesh_hgr.nc, mask.nc
File new_maskglo.nc is optional [sub basins masks]
OPENMP SUPPORT : yes
OUTPUT :
netcdf file : mocsig.nc
variables zomsfglo : Global ocean
variables zomsfatl : Atlantic Ocean
variables zomsfinp : Indo Pacific
variables zomsfind : Indian Ocean alone
variables zomsfpac : Pacific Ocean alone
If file new_maskglo.nc is not present, mask.nc file is used and
only zomsfglo is produced.
If option -isodep is used, each MOC variable is complemented by a iso
variable, giving the zonal mean of ispycnal depth (e.g.zoisoglo).
SEE ALSO :
cdfmoc
usage : cdfpsi -u U-file -v V-file [-V] [-full] [-mask] [-mean] [-nc4] ...
... [-ssh T-file] [-open] [-ref iref jref] [-o OUT-file] [-vvl] ...
... [-lev]
PURPOSE :
Compute the barotropic stream function (a proxy) as the integral of
the transport. It is a proxy, as far as the flow in not strictly non-
divergent.
ARGUMENTS :
-u U-file : netcdf file of zonal velocity.
-v V-file : netcdf file of meridional velocity.
OPTIONS :
[-V ] : use V field instead of U field for integration.
[-full ] : indicates a full step case. Default is partial steps.
[-mask ] : mask output fields. Note that the land value is significant.
It correspond to the potential on this continent.
[-mean ] : save the average of the computations done with U and V.
[-ssh T-file ] : compute the transport in the 'ssh' layer, using
surface velocities. Take the ssh from T-file specified in this
option. This is an experimental option, not certified ...
[-open ] : for open domain configuration. See also -ref to set
reference point.
[-ref iref jref ] : Set the reference point in i,j coordinates. BSF at
reference point is arbitrarly set to zero.
[-o OUT-file ] : specify output file name instead of default psi.nc
[-nc4 ] : use netcdf4 output files with chunking and deflation
[-vvl ] : use time-varying vertical metrics
[-lev] : This option is still experimental. It has been added to cdfpsi
in order to mimic former 'cdfpsi_level', now removed.
With this option, integral of transports is saved at every level,
giving a 'pseudo' stream-function. It works only for global
configurations, so far.
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc.
mask.nc is required only if -mask option used.
OUTPUT :
netcdf file : psi.nc
variables : sobarstf (m3/s )
If option -ssh is used, 2 additional variables are added to the file :
sobarstfssh (m3/s ) : contribution of SSH
sobarstftotal (m3/s ) : total BSF
usage : cdfsigtrp -t T-file -u U-file -v V-file [-brk BRK-file] ...
... -smin sigma_min -smax sigma_max -nbins nbins [-print] ...
... [-xtra] [-full ] [-vvl W-file] [-refdep ref_depth] ...
... [-neutral ] [-section file ] [-temp] [-help]
PURPOSE :
Compute density class transports, according to the density class
definition (minimum, maximum and number of bins) given in arguments.
Sections information are read from the file dens_section.dat
which is a text file built with pairs of lines giving: (1) section name
and (2) section location.
First line with section name may also have 2 additional strings holding
a prefix for variable output, and a long name to be used as attribute in
the output file.
Second line gives the location of the section with specification of four
integer values (imin imax jmin jmax), relative to the model grid.
Only zonal or meridional sections are allowed.
This program also offer the possibilty to read 'broken-line' files,
holding already extracted data along a pseudo zonal section. In this
particular case, ('-brk' switch), no additional information about the
section is required, nor metric files, as it is already available in the
input file.
This program can also be used to compute transport by temperatures
classes, provided the temperatures decrease monotonically downward.
In this case, use -temp option and of course specify sigma_min,
sigma_max as temperatures.
ARGUMENTS :
Input data file can be specified either using the 3 following switches:
-t T-file : netcdf file with temperature and salinity
-u U-file : netcdf file with zonal velocity component
-v V-file : netcdf file with meridional velocity component
Or, using the '-brk' switch.
-brk BRK-file : specify a 'broken-line' file produced by the tool
cdf_xtrac_brokenline, which is considered already as a pseudo
zonal section, holding all the relevant metrics for the section.
-smin sigma_min : minimum density for binning
-smax sigma_max : maximum density for binning
-nbins nbins : number of bins. This will fix the bin 'width'
OPTIONS :
[-full] : for full step configuration
[-vvl W-file]: use time varying vertical metrics. Need a W-file for e3w.
[-xtra] : produce extra netcdf output file which shows the details
of the sections (normal velocity, density, temperature,
salinity, transports, isopycnal depths.
[-print]: write the binned transports on standard output, for each
sections.
[-refdep ref_depth ]: give a reference depths for the computation of
potential density. Sigma_min, sigma_max must be adapted
accordingly.
[-neutral]: use neutral density instead of potential density
[-section file] : give the name of section file.
Default is dens_section.dat
[-temp] : use temperature instead of density for binning
[-help] : give commented example for the section file.
REQUIRED FILES :
mesh_hgr.nc, mesh_zgr.nc and dens_section.dat
If option '-brk' is used, there is no need for these files, the
metrics being already embarked into this section file.
OUTPUT :
Netcdf file : There is 1 netcdf file per section. File name is build
from section name : Section_name_trpsig.nc
variables : sigma_class (upper limit of the bin)
sigtrp : transport (Sv per bin)
ascii file : trpsig.txt
Standard output : the results are written on standard output only if
the -print option is used.
SEE ALSO :
cdfrhoproj, cdftransport, cdfsigintegr
usage : cdfsigtrp_broken -f BRK-file -bin sigma_min sigma_max nbins ...
... [-print ] [-full ] [ -refdep ref_depth] ...
... [-neutral ] [-section file ] [-temp ]
PURPOSE :
Compute density class transports, according to the density class
definition ( minimum, maximum and number of bins) given in arguments.
Section position are given in dens_section.dat, an ASCII file
with pairs of lines giving section name and section location as
imin imax jmin jmax. Only zonal or meridional section are allowed.
The name of this file can be specified with the -section option, if
it differs from the standard name. Optionaly, a netcdf root variable
name and a netcdf root long-name can be provided on the line giving
the section name.
In this particular tool, the section used is the result of
cdf_xtrac_brokenline. In this way, it is possible to calculate the
transport of density class in oblicous sections (non dependance on
zonal or meridional).
This program can also be used to compute transport by class of
temperatures, provided the temperatures decrease monotonically
downward. In this case, use -temp option and of course specify
sigma_min, sigma_max as temperatures.
ARGUMENTS :
-f BRK-file : netcdf_broken_line file with temperature, salinity
and the normal velocity through the section + some
usefull metrics.
-bin sigma_min sigma_max nbins : 3 values follow -bin switch :
sigma_min : minimum density for binning
sigma_max : maximum density for binning
nbins : number of bins. This will fix the bin 'width'
OPTIONS :
[-full ] : for full step configuration
[-ncdf ] : produce extra netcdf output file which shows the details
of the sections (normal velocity, density, temperature,
salinity, transports, isopycnal depths.
[-print ]: write the binned transports on standard output, for each
sections.
[-refdep ref_depth ]: give a reference depths for the computation of
potential density. Sigma_min, sigma_max must be adapted
accordingly.
[-neutral ]: use neutral density instead of potential density
[-section file] : give the name of section file.
Default is dens_section.dat
[-temp ] : use temperature instead of density for binning
REQUIRED FILES :
mesh_zgr.nc and dens_section.dat
OUTPUT :
Netcdf file : There is 1 netcdf file per section. File name is build
from section name : Section_name_trpsig.nc
variables : sigma_class (upper limit of the bin)
sigtrp : transport (Sv per bin)
ascii file : trpsig.txt
Standard output : the results are written on standard output only if
the -print option is used.
SEE ALSO :
cdfrhoproj, cdftransport, cdfsigintegr, cdfsigtrp, cdf_xtrac_brokenline
usage : cdftransig_xy3d -c CONFIG-CASE -l LST-tags [-code code ] ...
... [-depref depref ] [ -nbins nbins ] ...
... [-sigmin smin s-scal] [-sigzoom sminr s-scalr ] ...
... [-full ] [-v ] [-vvl ] [-o OUT-file] [-nc4]
PURPOSE :
Compute the time average volume transport at each grid cell in density
space, for the list of tags given as arguments. Results must be
condidered as intermediate for further integration.
ARGUMENTS :
-c CONFCASE : a DRAKKAR CONFIG-CASE name
-l LST-tags : a blank-separated list of time tags to be processed.
OPTIONS :
[-code code ] : code corresponds to pre-defined parameters settings
in term of reference depths, density limits for binning, number
of bins, deeper layer refinement.
AVAILABLE code are :
_______________________________________________________________
code | depth_ref nbins smin s-scal szoommin szoom-scal
---------------------------------------------------------------
0 | 0 101 23.0 0.05
1000 | 1000 93 24.2 0.10 32.3 0.05
1000-acc | 1000 88 24.5 0.10
2000 | 2000 174 29.0 0.05
none | parameters must be set individually
---------------------------------------------------------------
DEFAULT code is : 1000
For other setting use the options to specify the settings
individually.
[-depref depref ] : give the depth reference for potential density
[-nbins nbins ] : give the number of density bins.
[-sigmin smin s-scal ] : give the minimum of density for binning and
the bin width. ( take care of the reference depth).
[-sigzoom sminr s-scalr ] : allow density refinement from sminr, with
s-scalr bin width.
[-full ] : indicate a full step configuration.
[-v ] : verbose mode : extra print are performed during execution.
[-vvl ] : use time-varying vertical metrics.
[-o OUT-file ] : specify output file name instead of uvxysig.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc
OUTPUT :
netcdf file : uvxysig.nc unless -o option is used.
variables : vouxysig and vovxysig in m3/s.
SEE ALSO :
cdfrhoproj, cdfsigtrp
usage : cdftransport -u U-file -v V-file [-t T-file] [-vt VT-file] ...
... [-test u v ] [-noheat ] [-pm ] [-obc] [-TS] ...
... [-full] [-time jt] [-vvl] [-self] ...
... [-zlimit dep_list] [-sfx suffix]
PURPOSE :
Compute the transports (volume, heat and salt) accross a section.
The name of the section and the imin, imax, jmin, jmax for the section
is read from the standard input. To finish the program use the key name
'EOF' for the section name. It may be usefull to use the syntax :
'cdftransport [..options.. ] < section_file.txt'. Section corresponds
to a line between 2 F-points A(imin, jmin) and B(imax,jmax). The order
of the points does matter: when travelling from A to B, transports to
the right are positive, transports to the left are negative.
OBC U,V files can be used if -obc option is specified.
Extracted broken lines files can also be used with option -self.
ARGUMENTS :
-u U-file : netcdf file with the zonal velocity component.
-v V-file : netcdf file with the meridional velocity component.
OPTIONS :
[-vt VT-file]: netcdf file with mean values of vt, vs, ut, us for heat
and salt transport. This option is mandatory unless
-noheat option is used.
[-t T-file]: Temperature and Salinity file used with -TS option.
[-test u v]: use constant the u and v velocity components for sign
test purpose.
[-noheat ] : use when heat and salt transport are not requested.
[-pm ] : separate positive and negative contribution to
the volume transport. This option implicitly set -noheat,
and must be used before the file names.
[-obc ] : indicates that input files are obc files (vertical slices)
Take care that for this case, mesh files must be adapted.
This option implicitly set -noheat, and must be used before
the file names.
[-TS ] : Indicate that UT VT US VS will be recomputed from T U V
files. In this case use -t T-file option.
[-full ] : use for full step configurations.
[-time jt ]: compute transports for time index jt. Default is 1.
[-vvl ] : use time varying vertical metrics e3 read in the data file
[-zlimit dep_list] : Specify a list of depth (meters) defining the
limits of classes for which transports will be computed.
If not used, the transports are computed for the whole water
column. Example : -zlimit 500 1000 creates 3 classes :
0-500
500-1000
1000-bottom
[-self ] : This option indicates that input files corresponds to a
broken line, hence data files hold the metrics. In this
case, the input file is considered as a V-file, and must
specified with -v option.
[-sfx suffix] : use suffix instead of transport in the netcdf
output file.
REQUIRED FILES :
Files mesh_hgr.nc, mesh_zgr.nc must be in the current directory.
unless -self option is used.
OUTPUT :
- Standard output
- ASCII file reflecting the standard output: section_<SUFFIX>.dat
- ASCII files for volume, heat and salt transport: v<SUFFIX>.txt,
h<SUFFIX>.txt and s<SUFFIX>.txt.
- Netcdf files for each section. <SECTION>_<SUFFIX>.nc.
Default <SUFFIX> is transport and can be changed with -sfx option.
SEE ALSO :
cdfsigtrp cdf_xtrac_brokenline
usage : cdfvFWov -v V-secfile -s S-secfile -zgr ZGR-secfile -hgr HGR-secfile
... -msk MSK-secfile [-o OUT-file] [-vvl]
PURPOSE :
Compute the fresh water transport and its overturning component through
a section specified by the input files (data and metrics).
All input files corresponds to a zonal extraction holding 2 rows of
data. In fact the 2 rows are needed for the salinity to be interpolated
on the V-points.
ARGUMENTS :
All arguments are 'section files', which are assumed to be files with
2 zonal lines of data ( j and j+1 ):
-v V_secfile : meridional velocity section file.
-s S_secfile : salinity section file.
-zgr ZGR_secfile : mesh_zgr section file
-hgr HGR_secfile : mesh_hgr section file
-msk MSK_secfile : mask section file
OPTIONS :
[-o OUT-file] : specify output file name instead of vFWov.nc
[-vvl] : use time-varying vertical metrics.
REQUIRED FILES :
none
OUTPUT :
netcdf file : vFWov.nc unless option -o is used.
variables : netvFW, totvFW, ovFW
Output file only has time relevant dimension. Other dims are set to 1.
Degenerated dimensions can be removed with :
ncwga -a x,y,depthw vFWov.nc -o out.nc
usage : cdfvhst -f VT-file [-full] [-vvl] [-o OUT-file] [-nc4]
PURPOSE :
Compute the vertically integrated heat and salt transports
at each grid cell. In other words, it is the vertical integral
of the VT-file.
ARGUMENTS :
-f VT-file : file which contains UT, VT, US, VS quantities
(produced by cdfvT.f90)
OPTIONS :
[-full ] : use full step computation (default is partial steps).
[-vvl ] : use time-varying vertical metrics.
[-o OUT-file ] : specify output file name, instead of trp.nc
[-nc4 ] : use netcdf4 chunking and deflation.
REQUIRED FILES :
Files mesh_hgr.nc, mesh_zgr.nc
OUTPUT :
Netcdf file : trp.nc unless -o option is used.
Variables : somevt, somevs, sozout and sozous usage : cdfvtrp -u U-file -v V-file [-full] [-bathy] [-vvl] ...
... [-o OUT-file] [-nc4]
PURPOSE :
Compute the vertically integrated transports at each grid cell.
ARGUMENTS :
-u U-file : netcdf gridU file
-v V-file : netcdf gridV file
OPTIONS :
[-full ] : To be used in case of full step configuration.
Default is partial steps.
[-bathy ] : When used, cdfvtrp also compute the along slope and cross
slope transport components.
Bathymetry is read from mesh_zgr.nc file.
[-vvl ] : Use time-varying vertical metrics
[-o OUT-file ] : specify output file name instead of trp.nc
[-nc4 ] : Use netcdf4 output with chunking and deflation level 1.
This option is effective only if cdftools are compiled with
a netcdf library supporting chunking and deflation.
REQUIRED FILES :
mesh_hgr.nc and mesh_zgr.nc
mask.nc is required only with -bathy option.
OUTPUT :
netcdf file : trp.nc
variables :
sozoutrp : zonal transport.
somevtrp : meridional transport.
If option -bathy is used :
soastrp : along slope transport
socstrp : cross slope transport
Project headed by Jean-Marc Molines, (IGE, Grenoble - France)
Contributors (alphabetic order ) : C.Q. Akuetevi, M. Balmaseda, E. Behrens, F. Castruccio, M. Chekki, P. Colombo, J. Deshayes, N. Djath, N. Ducousso, C. Dufour, R. Dussin, N. Ferry, F. Hernandez, M. Juza, A. Lecointre, S. Leroux, C. Lique, x G. Mainsant, P. Mathiot, A. Melet, X. Meunier, G. Moreau, N. Merino, W. Rath, J. Regidor, M. Scheinert, A.M. Treguier
Copyright (C) 1998-2016 IGE-MEOM (Jean-Marc.Molines@univ-grenoble-alpes.fr )
This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".
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