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\section{Profiles: transect and float ocean sampling of MITgcm |
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\label{sectionprofiles}} |
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\begin{rawhtml} |
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<!-- CMIREDIR:profiles: --> |
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\end{rawhtml} |
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Author: Gael Forget |
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\bigskip |
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The purpose of pkg/profiles is to allow sampling of MITgcm runs according to a chosen pathway (after a ship or a drifter, along altimeter tracks, etc.), typically leading to easy model-data comparisons. Given input files that contain positions and dates, pkg/profiles will interpolate the model trajectory at the observed location. In particular, pkg/profiles can be used to do model-data comparison online and formulate a least-squares problem (ECCO application). |
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\bigskip |
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pkg/profiles is associated with three CPP keys: \\ |
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(k1) ALLOW\_PROFILES \\ |
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(k2) ALLOW\_PROFILES\_GENERICGRID \\ |
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(k3) ALLOW\_PROFILES\_CONTRIBUTION \\ |
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k1 switches the package on. By default, pkg/profiles assumes a regular lat-long grid. For other grids such as the cubed sphere, k2 and pre-processing (see below) are necessary. k3 switches the least-squares application on (pkg/ecco needed). pkg/profiles requires needs pkg/cal and netcdf libraries. |
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\bigskip |
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The namelist (data.profiles) is illustrated in table \ref{PkgProfNamelist}. This example includes two input netcdf files name (ARGOifremer\_r8.nc and XBT\_v5.nc are to be provided) and {\it cost function} multipliers (for least-squares only). The first index is a file number and the second index (in mult* only) is a variable number. By convention, the variable number is an integer ranging 1 to 6: temperature, salinity, zonal velocity, meridional velocity, sea surface height anomaly, and passive tracer. |
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\bigskip |
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The input file structure is illustrated in table \ref{PkgProfInput}. To create such files, one can use the netcdf\_ecco\_create.m matlab script, which can be checked out of \\ |
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MITgcm\_contrib/gael/profilesMatlabProcessing/ \\ |
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along with a full suite of matlab scripts associated with pkg/profiles. At run time, each file is scanned to determine which variables are included; these will be interpolated. The (final) output file structure is similar but with interpolated model values in prof\_T etc., and it contains model mask variables (e.g. prof\_Tmask). The very model output consists of one binary (or netcdf) file per processor. The final netcdf output is to be built from those using netcdf\_ecco\_recompose.m (offline). |
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\bigskip |
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When the k2 option is used (e.g. for cubed sphere runs), the input file is to be completed with interpolation grid points and coefficients computed offline using netcdf\_ecco\_GenericgridMain.m. Typically, you would first provide the standard namelist and files. After detecting that interpolation information is missing, the model will generate special grid files (profilesXCincl1PointOverlap* etc.) and then stop. You then want to run netcdf\_ecco\_GenericgridMain.m using the special grid files. {\it This operation could eventually be inlined.} |
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\bigskip |
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\begin{table}[htbp] |
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\begin{tabbing} |
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\#\\ |
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\# ******************\\ |
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\# PROFILES cost function\\ |
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\# ****************** \\ |
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\&PROFILES\_NML\\ |
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\#\\ |
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profilesfiles(1)= 'ARGOifremer\_r8',\\ |
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mult\_profiles(1,1) = 1.,\\ |
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mult\_profiles(1,2) = 1.,\\ |
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profilesfiles(2)= 'XBT\_v5',\\ |
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mult\_profiles(2,1) = 1.,\\ |
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\#\\ |
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/\\ |
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\end{tabbing} |
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\caption{pkg/profiles: data.profiles example.} |
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\label{PkgProfNamelist} |
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\end{table} |
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\begin{table}[phtb] |
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\begin{tabbing} |
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netcdf XBT\_v5 \{\\ |
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dimensions:\\ |
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\hspace{0.1cm} \= i\=PROF = 278026 ;\\ |
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\> iDEPTH = 55 ;\\ |
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\> lTXT = 30 ;\\ |
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variables:\\ |
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\> double depth(iDEPTH) ;\\ |
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\> \> depth:units = "meters" ;\\ |
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\> double prof\_YYYYMMDD(iPROF) ;\\ |
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\> \> prof\_YYYYMMDD:missing\_value = -9999. ;\\ |
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\> \> prof\_YYYYMMDD:long\_name = "year (4 digits), month (2 digits), day (2 digits)" ;\\ |
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\> double prof\_HHMMSS(iPROF) ;\\ |
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\> \> prof\_HHMMSS:missing\_value = -9999. ;\\ |
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\> \> prof\_HHMMSS:long\_name = "hour (2 digits), minute (2 digits), seconde (2 digits)" ;\\ |
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\> double prof\_lon(iPROF) ;\\ |
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\> \> prof\_lon:units = "(degree E)" ;\\ |
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\> \> prof\_lon:missing\_value = -9999. ;\\ |
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\> double prof\_lat(iPROF) ;\\ |
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\> \> prof\_lat:units = "(degree N)" ;\\ |
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\> \> prof\_lat:missing\_value = -9999. ;\\ |
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\> char prof\_descr(iPROF, lTXT) ;\\ |
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\> \> prof\_descr:long\_name = "profile description" ;\\ |
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\> double prof\_T(iPROF, iDEPTH) ;\\ |
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\> \> prof\_T:long\_name = "potential temperature" ;\\ |
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\> \> prof\_T:units = "degree Celsius" ;\\ |
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\> \> prof\_T:missing\_value = -9999. ;\\ |
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\> double prof\_Tweight(iPROF, iDEPTH) ;\\ |
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\> \> prof\_Tweight:long\_name = "weights" ;\\ |
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\> \> prof\_Tweight:units = "(degree Celsius)\^-2" ;\\ |
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\> \> prof\_Tweight:missing\_value = -9999. ;\\ |
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\}\\ |
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\end{tabbing} |
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\caption{pkg/profiles: input file structure as would be shown by "ncdump -h ARGOifremer\_r8.nc".} |
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\label{PkgProfInput} |
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\end{table} |
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