[10414] | 1 | \documentclass[../main/NEMO_manual]{subfiles} |
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| 2 | |
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[6997] | 3 | \begin{document} |
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[2298] | 4 | % ================================================================ |
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| 5 | % Chapter observation operator (OBS) |
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| 6 | % ================================================================ |
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[9393] | 7 | \chapter{Observation and Model Comparison (OBS)} |
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[9407] | 8 | \label{chap:OBS} |
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[2298] | 9 | |
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[4245] | 10 | Authors: D. Lea, M. Martin, K. Mogensen, A. Vidard, A. Weaver, A. Ryan, ... % do we keep that ? |
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[2298] | 11 | |
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| 12 | \minitoc |
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| 13 | |
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| 14 | \newpage |
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| 15 | |
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[10354] | 16 | The observation and model comparison code (OBS) reads in observation files |
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| 17 | (profile temperature and salinity, sea surface temperature, sea level anomaly, sea ice concentration, and velocity) and calculates an interpolated model equivalent value at the observation location and nearest model timestep. |
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| 18 | The resulting data are saved in a ``feedback'' file (or files). |
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| 19 | The code was originally developed for use with the NEMOVAR data assimilation code, |
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| 20 | but can be used for validation or verification of the model or with any other data assimilation system. |
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[2298] | 21 | |
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[10354] | 22 | The OBS code is called from \mdl{nemogcm} for model initialisation and to calculate the model equivalent values for observations on the 0th timestep. |
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| 23 | The code is then called again after each timestep from \mdl{step}. |
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| 24 | The code is only activated if the namelist logical \np{ln\_diaobs} is set to true. |
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[3294] | 25 | |
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[10354] | 26 | For all data types a 2D horizontal interpolator or averager is needed to |
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| 27 | interpolate/average the model fields to the observation location. |
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| 28 | For {\em in situ} profiles, a 1D vertical interpolator is needed in addition to |
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| 29 | provide model fields at the observation depths. |
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| 30 | This now works in a generalised vertical coordinate system. |
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[6140] | 31 | |
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[10442] | 32 | Some profile observation types (\eg tropical moored buoys) are made available as daily averaged quantities. |
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[10354] | 33 | The observation operator code can be set-up to calculate the equivalent daily average model temperature fields using |
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| 34 | the \np{nn\_profdavtypes} namelist array. |
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| 35 | Some SST observations are equivalent to a night-time average value and |
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| 36 | the observation operator code can calculate equivalent night-time average model SST fields by |
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| 37 | setting the namelist value \np{ln\_sstnight} to true. |
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| 38 | Otherwise the model value from the nearest timestep to the observation time is used. |
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[2298] | 39 | |
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[10354] | 40 | The code is controlled by the namelist \textit{namobs}. |
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| 41 | See the following sections for more details on setting up the namelist. |
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[2298] | 42 | |
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[9407] | 43 | \autoref{sec:OBS_example} introduces a test example of the observation operator code including |
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[10354] | 44 | where to obtain data and how to setup the namelist. |
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| 45 | \autoref{sec:OBS_details} introduces some more technical details of the different observation types used and |
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| 46 | also shows a more complete namelist. |
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| 47 | \autoref{sec:OBS_theory} introduces some of the theoretical aspects of the observation operator including |
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| 48 | interpolation methods and running on multiple processors. |
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[9407] | 49 | \autoref{sec:OBS_ooo} describes the offline observation operator code. |
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[10354] | 50 | \autoref{sec:OBS_obsutils} introduces some utilities to help working with the files produced by the OBS code. |
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[2298] | 51 | |
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| 52 | % ================================================================ |
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| 53 | % Example |
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| 54 | % ================================================================ |
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| 55 | \section{Running the observation operator code example} |
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[9407] | 56 | \label{sec:OBS_example} |
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[2298] | 57 | |
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| 58 | This section describes an example of running the observation operator code using |
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[10354] | 59 | profile data which can be freely downloaded. |
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| 60 | It shows how to adapt an existing run and build of NEMO to run the observation operator. |
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[2298] | 61 | |
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[2474] | 62 | \begin{enumerate} |
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[6140] | 63 | \item Compile NEMO. |
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[2298] | 64 | |
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[10354] | 65 | \item Download some EN4 data from \href{http://www.metoffice.gov.uk/hadobs}{www.metoffice.gov.uk/hadobs}. |
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| 66 | Choose observations which are valid for the period of your test run because |
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| 67 | the observation operator compares the model and observations for a matching date and time. |
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[2298] | 68 | |
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[6140] | 69 | \item Compile the OBSTOOLS code using: |
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[9388] | 70 | \begin{cmds} |
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[6140] | 71 | ./maketools -n OBSTOOLS -m [ARCH]. |
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[9388] | 72 | \end{cmds} |
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[6140] | 73 | |
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| 74 | \item Convert the EN4 data into feedback format: |
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[9388] | 75 | \begin{cmds} |
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[6140] | 76 | enact2fb.exe profiles_01.nc EN.4.1.1.f.profiles.g10.YYYYMM.nc |
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[9388] | 77 | \end{cmds} |
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[6140] | 78 | |
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[10354] | 79 | \item Include the following in the NEMO namelist to run the observation operator on this data: |
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[2474] | 80 | \end{enumerate} |
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[2298] | 81 | |
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[10354] | 82 | Options are defined through the \ngn{namobs} namelist variables. |
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| 83 | The options \np{ln\_t3d} and \np{ln\_s3d} switch on the temperature and salinity profile observation operator code. |
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| 84 | The filename or array of filenames are specified using the \np{cn\_profbfiles} variable. |
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| 85 | The model grid points for a particular observation latitude and longitude are found using |
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| 86 | the grid searching part of the code. |
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| 87 | This can be expensive, particularly for large numbers of observations, |
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| 88 | setting \np{ln\_grid\_search\_lookup} allows the use of a lookup table which |
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| 89 | is saved into an ``xypos`` file (or files). |
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| 90 | This will need to be generated the first time if it does not exist in the run directory. |
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[2474] | 91 | However, once produced it will significantly speed up future grid searches. |
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[10354] | 92 | Setting \np{ln\_grid\_global} means that the code distributes the observations evenly between processors. |
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| 93 | Alternatively each processor will work with observations located within the model subdomain |
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| 94 | (see section~\autoref{subsec:OBS_parallel}). |
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[2298] | 95 | |
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[10354] | 96 | A number of utilities are now provided to plot the feedback files, convert and recombine the files. |
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| 97 | These are explained in more detail in section~\autoref{sec:OBS_obsutils}. |
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| 98 | Utilites to convert other input data formats into the feedback format are also described in |
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| 99 | section~\autoref{sec:OBS_obsutils}. |
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[2298] | 100 | |
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[9350] | 101 | \section{Technical details (feedback type observation file headers)} |
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[9407] | 102 | \label{sec:OBS_details} |
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[2298] | 103 | |
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[10354] | 104 | Here we show a more complete example namelist \ngn{namobs} and also show the NetCDF headers of |
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| 105 | the observation files that may be used with the observation operator. |
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[2298] | 106 | |
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| 107 | %------------------------------------------namobs-------------------------------------------------------- |
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[10146] | 108 | |
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| 109 | \nlst{namobs} |
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[2298] | 110 | %------------------------------------------------------------------------------------------------------------- |
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| 111 | |
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[10354] | 112 | The observation operator code uses the "feedback" observation file format for all data types. |
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| 113 | All the observation files must be in NetCDF format. |
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| 114 | Some example headers (produced using \mbox{\textit{ncdump~-h}}) for profile data, sea level anomaly and |
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| 115 | sea surface temperature are in the following subsections. |
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[2298] | 116 | |
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[9350] | 117 | \subsection{Profile feedback} |
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[2298] | 118 | |
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[9388] | 119 | \begin{clines} |
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[2298] | 120 | netcdf profiles_01 { |
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| 121 | dimensions: |
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[2474] | 122 | N_OBS = 603 ; |
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| 123 | N_LEVELS = 150 ; |
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| 124 | N_VARS = 2 ; |
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| 125 | N_QCF = 2 ; |
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| 126 | N_ENTRIES = 1 ; |
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| 127 | N_EXTRA = 1 ; |
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| 128 | STRINGNAM = 8 ; |
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| 129 | STRINGGRID = 1 ; |
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| 130 | STRINGWMO = 8 ; |
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| 131 | STRINGTYP = 4 ; |
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| 132 | STRINGJULD = 14 ; |
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[2298] | 133 | variables: |
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[2474] | 134 | char VARIABLES(N_VARS, STRINGNAM) ; |
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| 135 | VARIABLES:long_name = "List of variables in feedback files" ; |
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| 136 | char ENTRIES(N_ENTRIES, STRINGNAM) ; |
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| 137 | ENTRIES:long_name = "List of additional entries for each variable in feedback files" ; |
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| 138 | char EXTRA(N_EXTRA, STRINGNAM) ; |
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| 139 | EXTRA:long_name = "List of extra variables" ; |
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| 140 | char STATION_IDENTIFIER(N_OBS, STRINGWMO) ; |
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| 141 | STATION_IDENTIFIER:long_name = "Station identifier" ; |
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| 142 | char STATION_TYPE(N_OBS, STRINGTYP) ; |
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| 143 | STATION_TYPE:long_name = "Code instrument type" ; |
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| 144 | double LONGITUDE(N_OBS) ; |
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| 145 | LONGITUDE:long_name = "Longitude" ; |
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| 146 | LONGITUDE:units = "degrees_east" ; |
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| 147 | LONGITUDE:_Fillvalue = 99999.f ; |
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| 148 | double LATITUDE(N_OBS) ; |
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| 149 | LATITUDE:long_name = "Latitude" ; |
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| 150 | LATITUDE:units = "degrees_north" ; |
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| 151 | LATITUDE:_Fillvalue = 99999.f ; |
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| 152 | double DEPTH(N_OBS, N_LEVELS) ; |
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| 153 | DEPTH:long_name = "Depth" ; |
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| 154 | DEPTH:units = "metre" ; |
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| 155 | DEPTH:_Fillvalue = 99999.f ; |
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| 156 | int DEPTH_QC(N_OBS, N_LEVELS) ; |
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| 157 | DEPTH_QC:long_name = "Quality on depth" ; |
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| 158 | DEPTH_QC:Conventions = "q where q =[0,9]" ; |
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| 159 | DEPTH_QC:_Fillvalue = 0 ; |
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| 160 | int DEPTH_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ; |
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| 161 | DEPTH_QC_FLAGS:long_name = "Quality flags on depth" ; |
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| 162 | DEPTH_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 163 | double JULD(N_OBS) ; |
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| 164 | JULD:long_name = "Julian day" ; |
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| 165 | JULD:units = "days since JULD_REFERENCE" ; |
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| 166 | JULD:Conventions = "relative julian days with decimal part (as parts of day)" ; |
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| 167 | JULD:_Fillvalue = 99999.f ; |
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| 168 | char JULD_REFERENCE(STRINGJULD) ; |
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| 169 | JULD_REFERENCE:long_name = "Date of reference for julian days" ; |
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| 170 | JULD_REFERENCE:Conventions = "YYYYMMDDHHMMSS" ; |
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| 171 | int OBSERVATION_QC(N_OBS) ; |
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| 172 | OBSERVATION_QC:long_name = "Quality on observation" ; |
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| 173 | OBSERVATION_QC:Conventions = "q where q =[0,9]" ; |
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| 174 | OBSERVATION_QC:_Fillvalue = 0 ; |
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| 175 | int OBSERVATION_QC_FLAGS(N_OBS, N_QCF) ; |
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| 176 | OBSERVATION_QC_FLAGS:long_name = "Quality flags on observation" ; |
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| 177 | OBSERVATION_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 178 | OBSERVATION_QC_FLAGS:_Fillvalue = 0 ; |
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| 179 | int POSITION_QC(N_OBS) ; |
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| 180 | POSITION_QC:long_name = "Quality on position (latitude and longitude)" ; |
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| 181 | POSITION_QC:Conventions = "q where q =[0,9]" ; |
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| 182 | POSITION_QC:_Fillvalue = 0 ; |
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| 183 | int POSITION_QC_FLAGS(N_OBS, N_QCF) ; |
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| 184 | POSITION_QC_FLAGS:long_name = "Quality flags on position" ; |
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| 185 | POSITION_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 186 | POSITION_QC_FLAGS:_Fillvalue = 0 ; |
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| 187 | int JULD_QC(N_OBS) ; |
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| 188 | JULD_QC:long_name = "Quality on date and time" ; |
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| 189 | JULD_QC:Conventions = "q where q =[0,9]" ; |
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| 190 | JULD_QC:_Fillvalue = 0 ; |
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| 191 | int JULD_QC_FLAGS(N_OBS, N_QCF) ; |
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| 192 | JULD_QC_FLAGS:long_name = "Quality flags on date and time" ; |
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| 193 | JULD_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 194 | JULD_QC_FLAGS:_Fillvalue = 0 ; |
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| 195 | int ORIGINAL_FILE_INDEX(N_OBS) ; |
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| 196 | ORIGINAL_FILE_INDEX:long_name = "Index in original data file" ; |
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| 197 | ORIGINAL_FILE_INDEX:_Fillvalue = -99999 ; |
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| 198 | float POTM_OBS(N_OBS, N_LEVELS) ; |
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| 199 | POTM_OBS:long_name = "Potential temperature" ; |
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| 200 | POTM_OBS:units = "Degrees Celsius" ; |
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| 201 | POTM_OBS:_Fillvalue = 99999.f ; |
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| 202 | float POTM_Hx(N_OBS, N_LEVELS) ; |
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| 203 | POTM_Hx:long_name = "Model interpolated potential temperature" ; |
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| 204 | POTM_Hx:units = "Degrees Celsius" ; |
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| 205 | POTM_Hx:_Fillvalue = 99999.f ; |
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| 206 | int POTM_QC(N_OBS) ; |
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| 207 | POTM_QC:long_name = "Quality on potential temperature" ; |
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| 208 | POTM_QC:Conventions = "q where q =[0,9]" ; |
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| 209 | POTM_QC:_Fillvalue = 0 ; |
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| 210 | int POTM_QC_FLAGS(N_OBS, N_QCF) ; |
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| 211 | POTM_QC_FLAGS:long_name = "Quality flags on potential temperature" ; |
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| 212 | POTM_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 213 | POTM_QC_FLAGS:_Fillvalue = 0 ; |
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| 214 | int POTM_LEVEL_QC(N_OBS, N_LEVELS) ; |
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| 215 | POTM_LEVEL_QC:long_name = "Quality for each level on potential temperature" ; |
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| 216 | POTM_LEVEL_QC:Conventions = "q where q =[0,9]" ; |
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| 217 | POTM_LEVEL_QC:_Fillvalue = 0 ; |
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| 218 | int POTM_LEVEL_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ; |
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| 219 | POTM_LEVEL_QC_FLAGS:long_name = "Quality flags for each level on potential temperature" ; |
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| 220 | POTM_LEVEL_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 221 | POTM_LEVEL_QC_FLAGS:_Fillvalue = 0 ; |
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| 222 | int POTM_IOBSI(N_OBS) ; |
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| 223 | POTM_IOBSI:long_name = "ORCA grid search I coordinate" ; |
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| 224 | int POTM_IOBSJ(N_OBS) ; |
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| 225 | POTM_IOBSJ:long_name = "ORCA grid search J coordinate" ; |
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| 226 | int POTM_IOBSK(N_OBS, N_LEVELS) ; |
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| 227 | POTM_IOBSK:long_name = "ORCA grid search K coordinate" ; |
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| 228 | char POTM_GRID(STRINGGRID) ; |
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| 229 | POTM_GRID:long_name = "ORCA grid search grid (T,U,V)" ; |
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| 230 | float PSAL_OBS(N_OBS, N_LEVELS) ; |
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| 231 | PSAL_OBS:long_name = "Practical salinity" ; |
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| 232 | PSAL_OBS:units = "PSU" ; |
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| 233 | PSAL_OBS:_Fillvalue = 99999.f ; |
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| 234 | float PSAL_Hx(N_OBS, N_LEVELS) ; |
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| 235 | PSAL_Hx:long_name = "Model interpolated practical salinity" ; |
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| 236 | PSAL_Hx:units = "PSU" ; |
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| 237 | PSAL_Hx:_Fillvalue = 99999.f ; |
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| 238 | int PSAL_QC(N_OBS) ; |
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| 239 | PSAL_QC:long_name = "Quality on practical salinity" ; |
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| 240 | PSAL_QC:Conventions = "q where q =[0,9]" ; |
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| 241 | PSAL_QC:_Fillvalue = 0 ; |
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| 242 | int PSAL_QC_FLAGS(N_OBS, N_QCF) ; |
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| 243 | PSAL_QC_FLAGS:long_name = "Quality flags on practical salinity" ; |
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| 244 | PSAL_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 245 | PSAL_QC_FLAGS:_Fillvalue = 0 ; |
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| 246 | int PSAL_LEVEL_QC(N_OBS, N_LEVELS) ; |
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| 247 | PSAL_LEVEL_QC:long_name = "Quality for each level on practical salinity" ; |
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| 248 | PSAL_LEVEL_QC:Conventions = "q where q =[0,9]" ; |
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| 249 | PSAL_LEVEL_QC:_Fillvalue = 0 ; |
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| 250 | int PSAL_LEVEL_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ; |
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| 251 | PSAL_LEVEL_QC_FLAGS:long_name = "Quality flags for each level on practical salinity" ; |
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| 252 | PSAL_LEVEL_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 253 | PSAL_LEVEL_QC_FLAGS:_Fillvalue = 0 ; |
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| 254 | int PSAL_IOBSI(N_OBS) ; |
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| 255 | PSAL_IOBSI:long_name = "ORCA grid search I coordinate" ; |
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| 256 | int PSAL_IOBSJ(N_OBS) ; |
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| 257 | PSAL_IOBSJ:long_name = "ORCA grid search J coordinate" ; |
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| 258 | int PSAL_IOBSK(N_OBS, N_LEVELS) ; |
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| 259 | PSAL_IOBSK:long_name = "ORCA grid search K coordinate" ; |
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| 260 | char PSAL_GRID(STRINGGRID) ; |
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| 261 | PSAL_GRID:long_name = "ORCA grid search grid (T,U,V)" ; |
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| 262 | float TEMP(N_OBS, N_LEVELS) ; |
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| 263 | TEMP:long_name = "Insitu temperature" ; |
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| 264 | TEMP:units = "Degrees Celsius" ; |
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| 265 | TEMP:_Fillvalue = 99999.f ; |
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[2298] | 266 | |
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| 267 | // global attributes: |
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[2474] | 268 | :title = "NEMO observation operator output" ; |
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| 269 | :Convention = "NEMO unified observation operator output" ; |
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[2298] | 270 | } |
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[9388] | 271 | \end{clines} |
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[2298] | 272 | |
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[9350] | 273 | \subsection{Sea level anomaly feedback} |
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[2298] | 274 | |
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[9388] | 275 | \begin{clines} |
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[2298] | 276 | netcdf sla_01 { |
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| 277 | dimensions: |
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[2474] | 278 | N_OBS = 41301 ; |
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| 279 | N_LEVELS = 1 ; |
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| 280 | N_VARS = 1 ; |
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| 281 | N_QCF = 2 ; |
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| 282 | N_ENTRIES = 1 ; |
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| 283 | N_EXTRA = 1 ; |
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| 284 | STRINGNAM = 8 ; |
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| 285 | STRINGGRID = 1 ; |
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| 286 | STRINGWMO = 8 ; |
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| 287 | STRINGTYP = 4 ; |
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| 288 | STRINGJULD = 14 ; |
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[2298] | 289 | variables: |
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[2474] | 290 | char VARIABLES(N_VARS, STRINGNAM) ; |
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| 291 | VARIABLES:long_name = "List of variables in feedback files" ; |
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| 292 | char ENTRIES(N_ENTRIES, STRINGNAM) ; |
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| 293 | ENTRIES:long_name = "List of additional entries for each variable in feedback files" ; |
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| 294 | char EXTRA(N_EXTRA, STRINGNAM) ; |
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| 295 | EXTRA:long_name = "List of extra variables" ; |
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| 296 | char STATION_IDENTIFIER(N_OBS, STRINGWMO) ; |
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| 297 | STATION_IDENTIFIER:long_name = "Station identifier" ; |
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| 298 | char STATION_TYPE(N_OBS, STRINGTYP) ; |
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| 299 | STATION_TYPE:long_name = "Code instrument type" ; |
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| 300 | double LONGITUDE(N_OBS) ; |
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| 301 | LONGITUDE:long_name = "Longitude" ; |
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| 302 | LONGITUDE:units = "degrees_east" ; |
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| 303 | LONGITUDE:_Fillvalue = 99999.f ; |
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| 304 | double LATITUDE(N_OBS) ; |
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| 305 | LATITUDE:long_name = "Latitude" ; |
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| 306 | LATITUDE:units = "degrees_north" ; |
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| 307 | LATITUDE:_Fillvalue = 99999.f ; |
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| 308 | double DEPTH(N_OBS, N_LEVELS) ; |
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| 309 | DEPTH:long_name = "Depth" ; |
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| 310 | DEPTH:units = "metre" ; |
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| 311 | DEPTH:_Fillvalue = 99999.f ; |
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| 312 | int DEPTH_QC(N_OBS, N_LEVELS) ; |
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| 313 | DEPTH_QC:long_name = "Quality on depth" ; |
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| 314 | DEPTH_QC:Conventions = "q where q =[0,9]" ; |
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| 315 | DEPTH_QC:_Fillvalue = 0 ; |
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| 316 | int DEPTH_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ; |
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| 317 | DEPTH_QC_FLAGS:long_name = "Quality flags on depth" ; |
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| 318 | DEPTH_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 319 | double JULD(N_OBS) ; |
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| 320 | JULD:long_name = "Julian day" ; |
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| 321 | JULD:units = "days since JULD_REFERENCE" ; |
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| 322 | JULD:Conventions = "relative julian days with decimal part (as parts of day)" ; |
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| 323 | JULD:_Fillvalue = 99999.f ; |
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| 324 | char JULD_REFERENCE(STRINGJULD) ; |
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| 325 | JULD_REFERENCE:long_name = "Date of reference for julian days" ; |
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| 326 | JULD_REFERENCE:Conventions = "YYYYMMDDHHMMSS" ; |
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| 327 | int OBSERVATION_QC(N_OBS) ; |
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| 328 | OBSERVATION_QC:long_name = "Quality on observation" ; |
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| 329 | OBSERVATION_QC:Conventions = "q where q =[0,9]" ; |
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| 330 | OBSERVATION_QC:_Fillvalue = 0 ; |
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| 331 | int OBSERVATION_QC_FLAGS(N_OBS, N_QCF) ; |
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| 332 | OBSERVATION_QC_FLAGS:long_name = "Quality flags on observation" ; |
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| 333 | OBSERVATION_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 334 | OBSERVATION_QC_FLAGS:_Fillvalue = 0 ; |
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| 335 | int POSITION_QC(N_OBS) ; |
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| 336 | POSITION_QC:long_name = "Quality on position (latitude and longitude)" ; |
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| 337 | POSITION_QC:Conventions = "q where q =[0,9]" ; |
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| 338 | POSITION_QC:_Fillvalue = 0 ; |
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| 339 | int POSITION_QC_FLAGS(N_OBS, N_QCF) ; |
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| 340 | POSITION_QC_FLAGS:long_name = "Quality flags on position" ; |
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| 341 | POSITION_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 342 | POSITION_QC_FLAGS:_Fillvalue = 0 ; |
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| 343 | int JULD_QC(N_OBS) ; |
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| 344 | JULD_QC:long_name = "Quality on date and time" ; |
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| 345 | JULD_QC:Conventions = "q where q =[0,9]" ; |
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| 346 | JULD_QC:_Fillvalue = 0 ; |
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| 347 | int JULD_QC_FLAGS(N_OBS, N_QCF) ; |
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| 348 | JULD_QC_FLAGS:long_name = "Quality flags on date and time" ; |
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| 349 | JULD_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 350 | JULD_QC_FLAGS:_Fillvalue = 0 ; |
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| 351 | int ORIGINAL_FILE_INDEX(N_OBS) ; |
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| 352 | ORIGINAL_FILE_INDEX:long_name = "Index in original data file" ; |
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| 353 | ORIGINAL_FILE_INDEX:_Fillvalue = -99999 ; |
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| 354 | float SLA_OBS(N_OBS, N_LEVELS) ; |
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| 355 | SLA_OBS:long_name = "Sea level anomaly" ; |
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| 356 | SLA_OBS:units = "metre" ; |
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| 357 | SLA_OBS:_Fillvalue = 99999.f ; |
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| 358 | float SLA_Hx(N_OBS, N_LEVELS) ; |
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| 359 | SLA_Hx:long_name = "Model interpolated sea level anomaly" ; |
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| 360 | SLA_Hx:units = "metre" ; |
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| 361 | SLA_Hx:_Fillvalue = 99999.f ; |
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| 362 | int SLA_QC(N_OBS) ; |
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| 363 | SLA_QC:long_name = "Quality on sea level anomaly" ; |
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| 364 | SLA_QC:Conventions = "q where q =[0,9]" ; |
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| 365 | SLA_QC:_Fillvalue = 0 ; |
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| 366 | int SLA_QC_FLAGS(N_OBS, N_QCF) ; |
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| 367 | SLA_QC_FLAGS:long_name = "Quality flags on sea level anomaly" ; |
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| 368 | SLA_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 369 | SLA_QC_FLAGS:_Fillvalue = 0 ; |
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| 370 | int SLA_LEVEL_QC(N_OBS, N_LEVELS) ; |
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| 371 | SLA_LEVEL_QC:long_name = "Quality for each level on sea level anomaly" ; |
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| 372 | SLA_LEVEL_QC:Conventions = "q where q =[0,9]" ; |
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| 373 | SLA_LEVEL_QC:_Fillvalue = 0 ; |
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| 374 | int SLA_LEVEL_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ; |
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| 375 | SLA_LEVEL_QC_FLAGS:long_name = "Quality flags for each level on sea level anomaly" ; |
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| 376 | SLA_LEVEL_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
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| 377 | SLA_LEVEL_QC_FLAGS:_Fillvalue = 0 ; |
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| 378 | int SLA_IOBSI(N_OBS) ; |
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| 379 | SLA_IOBSI:long_name = "ORCA grid search I coordinate" ; |
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| 380 | int SLA_IOBSJ(N_OBS) ; |
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| 381 | SLA_IOBSJ:long_name = "ORCA grid search J coordinate" ; |
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| 382 | int SLA_IOBSK(N_OBS, N_LEVELS) ; |
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| 383 | SLA_IOBSK:long_name = "ORCA grid search K coordinate" ; |
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| 384 | char SLA_GRID(STRINGGRID) ; |
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| 385 | SLA_GRID:long_name = "ORCA grid search grid (T,U,V)" ; |
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| 386 | float MDT(N_OBS, N_LEVELS) ; |
---|
| 387 | MDT:long_name = "Mean Dynamic Topography" ; |
---|
| 388 | MDT:units = "metre" ; |
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| 389 | MDT:_Fillvalue = 99999.f ; |
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[2298] | 390 | |
---|
| 391 | // global attributes: |
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[2474] | 392 | :title = "NEMO observation operator output" ; |
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| 393 | :Convention = "NEMO unified observation operator output" ; |
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[2298] | 394 | } |
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[9388] | 395 | \end{clines} |
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[2298] | 396 | |
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[10354] | 397 | The mean dynamic topography (MDT) must be provided in a separate file defined on |
---|
| 398 | the model grid called \ifile{slaReferenceLevel}. |
---|
| 399 | The MDT is required in order to produce the model equivalent sea level anomaly from the model sea surface height. |
---|
| 400 | Below is an example header for this file (on the ORCA025 grid). |
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[2474] | 401 | |
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[9388] | 402 | \begin{clines} |
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[2474] | 403 | dimensions: |
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| 404 | x = 1442 ; |
---|
| 405 | y = 1021 ; |
---|
| 406 | variables: |
---|
| 407 | float nav_lon(y, x) ; |
---|
| 408 | nav_lon:units = "degrees_east" ; |
---|
| 409 | float nav_lat(y, x) ; |
---|
| 410 | nav_lat:units = "degrees_north" ; |
---|
| 411 | float sossheig(y, x) ; |
---|
| 412 | sossheig:_FillValue = -1.e+30f ; |
---|
| 413 | sossheig:coordinates = "nav_lon nav_lat" ; |
---|
| 414 | sossheig:long_name = "Mean Dynamic Topography" ; |
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| 415 | sossheig:units = "metres" ; |
---|
| 416 | sossheig:grid = "orca025T" ; |
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[9388] | 417 | \end{clines} |
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[2474] | 418 | |
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[9350] | 419 | \subsection{Sea surface temperature feedback} |
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[2298] | 420 | |
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[9388] | 421 | \begin{clines} |
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[2298] | 422 | netcdf sst_01 { |
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| 423 | dimensions: |
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[2474] | 424 | N_OBS = 33099 ; |
---|
| 425 | N_LEVELS = 1 ; |
---|
| 426 | N_VARS = 1 ; |
---|
| 427 | N_QCF = 2 ; |
---|
| 428 | N_ENTRIES = 1 ; |
---|
| 429 | STRINGNAM = 8 ; |
---|
| 430 | STRINGGRID = 1 ; |
---|
| 431 | STRINGWMO = 8 ; |
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| 432 | STRINGTYP = 4 ; |
---|
| 433 | STRINGJULD = 14 ; |
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[2298] | 434 | variables: |
---|
[2474] | 435 | char VARIABLES(N_VARS, STRINGNAM) ; |
---|
| 436 | VARIABLES:long_name = "List of variables in feedback files" ; |
---|
| 437 | char ENTRIES(N_ENTRIES, STRINGNAM) ; |
---|
| 438 | ENTRIES:long_name = "List of additional entries for each variable in feedback files" ; |
---|
| 439 | char STATION_IDENTIFIER(N_OBS, STRINGWMO) ; |
---|
| 440 | STATION_IDENTIFIER:long_name = "Station identifier" ; |
---|
| 441 | char STATION_TYPE(N_OBS, STRINGTYP) ; |
---|
| 442 | STATION_TYPE:long_name = "Code instrument type" ; |
---|
| 443 | double LONGITUDE(N_OBS) ; |
---|
| 444 | LONGITUDE:long_name = "Longitude" ; |
---|
| 445 | LONGITUDE:units = "degrees_east" ; |
---|
| 446 | LONGITUDE:_Fillvalue = 99999.f ; |
---|
| 447 | double LATITUDE(N_OBS) ; |
---|
| 448 | LATITUDE:long_name = "Latitude" ; |
---|
| 449 | LATITUDE:units = "degrees_north" ; |
---|
| 450 | LATITUDE:_Fillvalue = 99999.f ; |
---|
| 451 | double DEPTH(N_OBS, N_LEVELS) ; |
---|
| 452 | DEPTH:long_name = "Depth" ; |
---|
| 453 | DEPTH:units = "metre" ; |
---|
| 454 | DEPTH:_Fillvalue = 99999.f ; |
---|
| 455 | int DEPTH_QC(N_OBS, N_LEVELS) ; |
---|
| 456 | DEPTH_QC:long_name = "Quality on depth" ; |
---|
| 457 | DEPTH_QC:Conventions = "q where q =[0,9]" ; |
---|
| 458 | DEPTH_QC:_Fillvalue = 0 ; |
---|
| 459 | int DEPTH_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ; |
---|
| 460 | DEPTH_QC_FLAGS:long_name = "Quality flags on depth" ; |
---|
| 461 | DEPTH_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
---|
| 462 | double JULD(N_OBS) ; |
---|
| 463 | JULD:long_name = "Julian day" ; |
---|
| 464 | JULD:units = "days since JULD_REFERENCE" ; |
---|
| 465 | JULD:Conventions = "relative julian days with decimal part (as parts of day)" ; |
---|
| 466 | JULD:_Fillvalue = 99999.f ; |
---|
| 467 | char JULD_REFERENCE(STRINGJULD) ; |
---|
| 468 | JULD_REFERENCE:long_name = "Date of reference for julian days" ; |
---|
| 469 | JULD_REFERENCE:Conventions = "YYYYMMDDHHMMSS" ; |
---|
| 470 | int OBSERVATION_QC(N_OBS) ; |
---|
| 471 | OBSERVATION_QC:long_name = "Quality on observation" ; |
---|
| 472 | OBSERVATION_QC:Conventions = "q where q =[0,9]" ; |
---|
| 473 | OBSERVATION_QC:_Fillvalue = 0 ; |
---|
| 474 | int OBSERVATION_QC_FLAGS(N_OBS, N_QCF) ; |
---|
| 475 | OBSERVATION_QC_FLAGS:long_name = "Quality flags on observation" ; |
---|
| 476 | OBSERVATION_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
---|
| 477 | OBSERVATION_QC_FLAGS:_Fillvalue = 0 ; |
---|
| 478 | int POSITION_QC(N_OBS) ; |
---|
| 479 | POSITION_QC:long_name = "Quality on position (latitude and longitude)" ; |
---|
| 480 | POSITION_QC:Conventions = "q where q =[0,9]" ; |
---|
| 481 | POSITION_QC:_Fillvalue = 0 ; |
---|
| 482 | int POSITION_QC_FLAGS(N_OBS, N_QCF) ; |
---|
| 483 | POSITION_QC_FLAGS:long_name = "Quality flags on position" ; |
---|
| 484 | POSITION_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
---|
| 485 | POSITION_QC_FLAGS:_Fillvalue = 0 ; |
---|
| 486 | int JULD_QC(N_OBS) ; |
---|
| 487 | JULD_QC:long_name = "Quality on date and time" ; |
---|
| 488 | JULD_QC:Conventions = "q where q =[0,9]" ; |
---|
| 489 | JULD_QC:_Fillvalue = 0 ; |
---|
| 490 | int JULD_QC_FLAGS(N_OBS, N_QCF) ; |
---|
| 491 | JULD_QC_FLAGS:long_name = "Quality flags on date and time" ; |
---|
| 492 | JULD_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
---|
| 493 | JULD_QC_FLAGS:_Fillvalue = 0 ; |
---|
| 494 | int ORIGINAL_FILE_INDEX(N_OBS) ; |
---|
| 495 | ORIGINAL_FILE_INDEX:long_name = "Index in original data file" ; |
---|
| 496 | ORIGINAL_FILE_INDEX:_Fillvalue = -99999 ; |
---|
| 497 | float SST_OBS(N_OBS, N_LEVELS) ; |
---|
| 498 | SST_OBS:long_name = "Sea surface temperature" ; |
---|
| 499 | SST_OBS:units = "Degree centigrade" ; |
---|
| 500 | SST_OBS:_Fillvalue = 99999.f ; |
---|
| 501 | float SST_Hx(N_OBS, N_LEVELS) ; |
---|
| 502 | SST_Hx:long_name = "Model interpolated sea surface temperature" ; |
---|
| 503 | SST_Hx:units = "Degree centigrade" ; |
---|
| 504 | SST_Hx:_Fillvalue = 99999.f ; |
---|
| 505 | int SST_QC(N_OBS) ; |
---|
| 506 | SST_QC:long_name = "Quality on sea surface temperature" ; |
---|
| 507 | SST_QC:Conventions = "q where q =[0,9]" ; |
---|
| 508 | SST_QC:_Fillvalue = 0 ; |
---|
| 509 | int SST_QC_FLAGS(N_OBS, N_QCF) ; |
---|
| 510 | SST_QC_FLAGS:long_name = "Quality flags on sea surface temperature" ; |
---|
| 511 | SST_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
---|
| 512 | SST_QC_FLAGS:_Fillvalue = 0 ; |
---|
| 513 | int SST_LEVEL_QC(N_OBS, N_LEVELS) ; |
---|
| 514 | SST_LEVEL_QC:long_name = "Quality for each level on sea surface temperature" ; |
---|
| 515 | SST_LEVEL_QC:Conventions = "q where q =[0,9]" ; |
---|
| 516 | SST_LEVEL_QC:_Fillvalue = 0 ; |
---|
| 517 | int SST_LEVEL_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ; |
---|
| 518 | SST_LEVEL_QC_FLAGS:long_name = "Quality flags for each level on sea surface temperature" ; |
---|
| 519 | SST_LEVEL_QC_FLAGS:Conventions = "NEMOVAR flag conventions" ; |
---|
| 520 | SST_LEVEL_QC_FLAGS:_Fillvalue = 0 ; |
---|
| 521 | int SST_IOBSI(N_OBS) ; |
---|
| 522 | SST_IOBSI:long_name = "ORCA grid search I coordinate" ; |
---|
| 523 | int SST_IOBSJ(N_OBS) ; |
---|
| 524 | SST_IOBSJ:long_name = "ORCA grid search J coordinate" ; |
---|
| 525 | int SST_IOBSK(N_OBS, N_LEVELS) ; |
---|
| 526 | SST_IOBSK:long_name = "ORCA grid search K coordinate" ; |
---|
| 527 | char SST_GRID(STRINGGRID) ; |
---|
| 528 | SST_GRID:long_name = "ORCA grid search grid (T,U,V)" ; |
---|
[2298] | 529 | |
---|
| 530 | // global attributes: |
---|
[2474] | 531 | :title = "NEMO observation operator output" ; |
---|
| 532 | :Convention = "NEMO unified observation operator output" ; |
---|
[2298] | 533 | } |
---|
[9388] | 534 | \end{clines} |
---|
[2298] | 535 | |
---|
| 536 | \section{Theoretical details} |
---|
[9407] | 537 | \label{sec:OBS_theory} |
---|
[2298] | 538 | |
---|
[9052] | 539 | \subsection{Horizontal interpolation and averaging methods} |
---|
[2298] | 540 | |
---|
[10354] | 541 | For most observation types, the horizontal extent of the observation is small compared to the model grid size and so |
---|
| 542 | the model equivalent of the observation is calculated by interpolating from |
---|
| 543 | the four surrounding grid points to the observation location. |
---|
[10442] | 544 | Some satellite observations (\eg microwave satellite SST data, or satellite SSS data) have a footprint which |
---|
[10354] | 545 | is similar in size or larger than the model grid size (particularly when the grid size is small). |
---|
| 546 | In those cases the model counterpart should be calculated by averaging the model grid points over |
---|
| 547 | the same size as the footprint. |
---|
| 548 | NEMO therefore has the capability to specify either an interpolation or an averaging |
---|
| 549 | (for surface observation types only). |
---|
[9052] | 550 | |
---|
[10354] | 551 | The main namelist option associated with the interpolation/averaging is \np{nn\_2dint}. |
---|
| 552 | This default option can be set to values from 0 to 6. |
---|
[9052] | 553 | Values between 0 to 4 are associated with interpolation while values 5 or 6 are associated with averaging. |
---|
| 554 | \begin{itemize} |
---|
[9393] | 555 | \item \np{nn\_2dint}\forcode{ = 0}: Distance-weighted interpolation |
---|
| 556 | \item \np{nn\_2dint}\forcode{ = 1}: Distance-weighted interpolation (small angle) |
---|
| 557 | \item \np{nn\_2dint}\forcode{ = 2}: Bilinear interpolation (geographical grid) |
---|
| 558 | \item \np{nn\_2dint}\forcode{ = 3}: Bilinear remapping interpolation (general grid) |
---|
| 559 | \item \np{nn\_2dint}\forcode{ = 4}: Polynomial interpolation |
---|
[10354] | 560 | \item \np{nn\_2dint}\forcode{ = 5}: Radial footprint averaging with diameter specified in the namelist as |
---|
| 561 | \np{rn\_???\_avglamscl} in degrees or metres (set using \np{ln\_???\_fp\_indegs}) |
---|
| 562 | \item \np{nn\_2dint}\forcode{ = 6}: Rectangular footprint averaging with E/W and N/S size specified in |
---|
| 563 | the namelist as \np{rn\_???\_avglamscl} and \np{rn\_???\_avgphiscl} in degrees or metres |
---|
| 564 | (set using \np{ln\_???\_fp\_indegs}) |
---|
[9052] | 565 | \end{itemize} |
---|
[10354] | 566 | The ??? in the last two options indicate these options should be specified for each observation type for |
---|
| 567 | which the averaging is to be performed (see namelist example above). |
---|
| 568 | The \np{nn\_2dint} default option can be overridden for surface observation types using |
---|
| 569 | namelist values \np{nn\_2dint\_???} where ??? is one of sla,sst,sss,sic. |
---|
[9052] | 570 | |
---|
| 571 | Below is some more detail on the various options for interpolation and averaging available in NEMO. |
---|
| 572 | |
---|
| 573 | \subsubsection{Horizontal interpolation} |
---|
[10414] | 574 | |
---|
[10354] | 575 | Consider an observation point ${\rm P}$ with with longitude and latitude $({\lambda_{}}_{\rm P}, \phi_{\rm P})$ and |
---|
| 576 | the four nearest neighbouring model grid points ${\rm A}$, ${\rm B}$, ${\rm C}$ and ${\rm D}$ with |
---|
| 577 | longitude and latitude ($\lambda_{\rm A}$, $\phi_{\rm A}$),($\lambda_{\rm B}$, $\phi_{\rm B}$) etc. |
---|
| 578 | All horizontal interpolation methods implemented in NEMO estimate the value of a model variable $x$ at point $P$ as |
---|
| 579 | a weighted linear combination of the values of the model variables at the grid points ${\rm A}$, ${\rm B}$ etc.: |
---|
[10414] | 580 | \begin{align*} |
---|
| 581 | {x_{}}_{\rm P} & \hspace{-2mm} = \hspace{-2mm} & |
---|
| 582 | \frac{1}{w} \left( {w_{}}_{\rm A} {x_{}}_{\rm A} + |
---|
| 583 | {w_{}}_{\rm B} {x_{}}_{\rm B} + |
---|
| 584 | {w_{}}_{\rm C} {x_{}}_{\rm C} + |
---|
| 585 | {w_{}}_{\rm D} {x_{}}_{\rm D} \right) |
---|
| 586 | \end{align*} |
---|
[10354] | 587 | where ${w_{}}_{\rm A}$, ${w_{}}_{\rm B}$ etc. are the respective weights for the model field at |
---|
| 588 | points ${\rm A}$, ${\rm B}$ etc., and $w = {w_{}}_{\rm A} + {w_{}}_{\rm B} + {w_{}}_{\rm C} + {w_{}}_{\rm D}$. |
---|
[2298] | 589 | |
---|
| 590 | Four different possibilities are available for computing the weights. |
---|
| 591 | |
---|
| 592 | \begin{enumerate} |
---|
| 593 | |
---|
[10354] | 594 | \item[1.] {\bf Great-Circle distance-weighted interpolation.} |
---|
| 595 | The weights are computed as a function of the great-circle distance $s(P, \cdot)$ between $P$ and |
---|
| 596 | the model grid points $A$, $B$ etc. |
---|
| 597 | For example, the weight given to the field ${x_{}}_{\rm A}$ is specified as the product of the distances |
---|
| 598 | from ${\rm P}$ to the other points: |
---|
[10414] | 599 | \begin{align*} |
---|
| 600 | {w_{}}_{\rm A} = s({\rm P}, {\rm B}) \, s({\rm P}, {\rm C}) \, s({\rm P}, {\rm D}) |
---|
| 601 | \end{align*} |
---|
[2298] | 602 | where |
---|
[10414] | 603 | \begin{align*} |
---|
| 604 | s\left ({\rm P}, {\rm M} \right ) |
---|
[2298] | 605 | & \hspace{-2mm} = \hspace{-2mm} & |
---|
| 606 | \cos^{-1} \! \left\{ |
---|
| 607 | \sin {\phi_{}}_{\rm P} \sin {\phi_{}}_{\rm M} |
---|
| 608 | + \cos {\phi_{}}_{\rm P} \cos {\phi_{}}_{\rm M} |
---|
| 609 | \cos ({\lambda_{}}_{\rm M} - {\lambda_{}}_{\rm P}) |
---|
| 610 | \right\} |
---|
[10414] | 611 | \end{align*} |
---|
[2298] | 612 | and $M$ corresponds to $B$, $C$ or $D$. |
---|
[10354] | 613 | A more stable form of the great-circle distance formula for small distances ($x$ near 1) |
---|
[11123] | 614 | involves the arcsine function (\eg see p.~101 of \citet{daley.barker_bk01}: |
---|
[10414] | 615 | \begin{align*} |
---|
| 616 | s\left( {\rm P}, {\rm M} \right) & \hspace{-2mm} = \hspace{-2mm} & \sin^{-1} \! \left\{ \sqrt{ 1 - x^2 } \right\} |
---|
| 617 | \end{align*} |
---|
[2298] | 618 | where |
---|
[10414] | 619 | \begin{align*} |
---|
| 620 | x & \hspace{-2mm} = \hspace{-2mm} & |
---|
| 621 | {a_{}}_{\rm M} {a_{}}_{\rm P} + {b_{}}_{\rm M} {b_{}}_{\rm P} + {c_{}}_{\rm M} {c_{}}_{\rm P} |
---|
| 622 | \end{align*} |
---|
[2298] | 623 | and |
---|
[10414] | 624 | \begin{align*} |
---|
| 625 | {a_{}}_{\rm M} & \hspace{-2mm} = \hspace{-2mm} & \sin {\phi_{}}_{\rm M}, \\ |
---|
| 626 | {a_{}}_{\rm P} & \hspace{-2mm} = \hspace{-2mm} & \sin {\phi_{}}_{\rm P}, \\ |
---|
| 627 | {b_{}}_{\rm M} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\rm M} \cos {\phi_{}}_{\rm M}, \\ |
---|
| 628 | {b_{}}_{\rm P} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\rm P} \cos {\phi_{}}_{\rm P}, \\ |
---|
| 629 | {c_{}}_{\rm M} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\rm M} \sin {\phi_{}}_{\rm M}, \\ |
---|
[2298] | 630 | {c_{}}_{\rm P} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\rm P} \sin {\phi_{}}_{\rm P}. |
---|
[10414] | 631 | \end{align*} |
---|
[2298] | 632 | |
---|
[10354] | 633 | \item[2.] {\bf Great-Circle distance-weighted interpolation with small angle approximation.} |
---|
| 634 | Similar to the previous interpolation but with the distance $s$ computed as |
---|
[10414] | 635 | \begin{align*} |
---|
| 636 | s\left( {\rm P}, {\rm M} \right) |
---|
| 637 | & \hspace{-2mm} = \hspace{-2mm} & |
---|
| 638 | \sqrt{ \left( {\phi_{}}_{\rm M} - {\phi_{}}_{\rm P} \right)^{2} |
---|
| 639 | + \left( {\lambda_{}}_{\rm M} - {\lambda_{}}_{\rm P} \right)^{2} |
---|
| 640 | \cos^{2} {\phi_{}}_{\rm M} } |
---|
| 641 | \end{align*} |
---|
[2298] | 642 | where $M$ corresponds to $A$, $B$, $C$ or $D$. |
---|
| 643 | |
---|
[10354] | 644 | \item[3.] {\bf Bilinear interpolation for a regular spaced grid.} |
---|
| 645 | The interpolation is split into two 1D interpolations in the longitude and latitude directions, respectively. |
---|
[2298] | 646 | |
---|
[10354] | 647 | \item[4.] {\bf Bilinear remapping interpolation for a general grid.} |
---|
| 648 | An iterative scheme that involves first mapping a quadrilateral cell into |
---|
| 649 | a cell with coordinates (0,0), (1,0), (0,1) and (1,1). |
---|
[11123] | 650 | This method is based on the \href{https://github.com/SCRIP-Project/SCRIP}{SCRIP interpolation package}. |
---|
[2298] | 651 | |
---|
| 652 | \end{enumerate} |
---|
| 653 | |
---|
[9052] | 654 | \subsubsection{Horizontal averaging} |
---|
| 655 | |
---|
| 656 | For each surface observation type: |
---|
| 657 | \begin{itemize} |
---|
[10354] | 658 | \item The standard grid-searching code is used to find the nearest model grid point to the observation location |
---|
| 659 | (see next subsection). |
---|
| 660 | \item The maximum number of grid points is calculated in the local grid domain for which |
---|
| 661 | the averaging is likely need to cover. |
---|
| 662 | \item The lats/longs of the grid points surrounding the nearest model grid box are extracted using |
---|
| 663 | existing mpi routines. |
---|
| 664 | \item The weights for each grid point associated with each observation are calculated, |
---|
| 665 | either for radial or rectangular footprints. |
---|
| 666 | For grid points completely within the footprint, the weight is one; |
---|
| 667 | for grid points completely outside the footprint, the weight is zero. |
---|
| 668 | For grid points which are partly within the footprint the ratio between the area of the footprint within |
---|
| 669 | the grid box and the total area of the grid box is used as the weight. |
---|
| 670 | \item The weighted average of the model grid points associated with each observation is calculated, |
---|
| 671 | and this is then given as the model counterpart of the observation. |
---|
[9052] | 672 | \end{itemize} |
---|
| 673 | |
---|
[10354] | 674 | Examples of the weights calculated for an observation with rectangular and radial footprints are shown in |
---|
| 675 | Figs.~\autoref{fig:obsavgrec} and~\autoref{fig:obsavgrad}. |
---|
[9052] | 676 | |
---|
| 677 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[10414] | 678 | \begin{figure} |
---|
| 679 | \begin{center} |
---|
| 680 | \includegraphics[width=0.90\textwidth]{Fig_OBS_avg_rec} |
---|
| 681 | \caption{ |
---|
| 682 | \protect\label{fig:obsavgrec} |
---|
| 683 | Weights associated with each model grid box (blue lines and numbers) |
---|
[10442] | 684 | for an observation at -170.5\deg{E}, 56.0\deg{N} with a rectangular footprint of 1\deg x 1\deg. |
---|
[10414] | 685 | } |
---|
| 686 | \end{center} |
---|
| 687 | \end{figure} |
---|
[9052] | 688 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
| 689 | |
---|
| 690 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[10414] | 691 | \begin{figure} |
---|
| 692 | \begin{center} |
---|
| 693 | \includegraphics[width=0.90\textwidth]{Fig_OBS_avg_rad} |
---|
| 694 | \caption{ |
---|
| 695 | \protect\label{fig:obsavgrad} |
---|
| 696 | Weights associated with each model grid box (blue lines and numbers) |
---|
[10442] | 697 | for an observation at -170.5\deg{E}, 56.0\deg{N} with a radial footprint with diameter 1\deg. |
---|
[10414] | 698 | } |
---|
| 699 | \end{center} |
---|
| 700 | \end{figure} |
---|
[9052] | 701 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
| 702 | |
---|
| 703 | |
---|
[2298] | 704 | \subsection{Grid search} |
---|
| 705 | |
---|
[10354] | 706 | For many grids used by the NEMO model, such as the ORCA family, the horizontal grid coordinates $i$ and $j$ are not simple functions of latitude and longitude. |
---|
| 707 | Therefore, it is not always straightforward to determine the grid points surrounding any given observational position. |
---|
| 708 | Before the interpolation can be performed, a search algorithm is then required to determine the corner points of |
---|
[2298] | 709 | the quadrilateral cell in which the observation is located. |
---|
[10354] | 710 | This is the most difficult and time consuming part of the 2D interpolation procedure. |
---|
| 711 | A robust test for determining if an observation falls within a given quadrilateral cell is as follows. |
---|
| 712 | Let ${\rm P}({\lambda_{}}_{\rm P} ,{\phi_{}}_{\rm P} )$ denote the observation point, |
---|
| 713 | and let ${\rm A}({\lambda_{}}_{\rm A} ,{\phi_{}}_{\rm A} )$, ${\rm B}({\lambda_{}}_{\rm B} ,{\phi_{}}_{\rm B} )$, |
---|
| 714 | ${\rm C}({\lambda_{}}_{\rm C} ,{\phi_{}}_{\rm C} )$ and ${\rm D}({\lambda_{}}_{\rm D} ,{\phi_{}}_{\rm D} )$ |
---|
| 715 | denote the bottom left, bottom right, top left and top right corner points of the cell, respectively. |
---|
| 716 | To determine if P is inside the cell, we verify that the cross-products |
---|
[10414] | 717 | \begin{align*} |
---|
| 718 | \begin{array}{lllll} |
---|
| 719 | {{\bf r}_{}}_{\rm PA} \times {{\bf r}_{}}_{\rm PC} |
---|
| 720 | & = & [({\lambda_{}}_{\rm A}\; -\; {\lambda_{}}_{\rm P} ) |
---|
| 721 | ({\phi_{}}_{\rm C} \; -\; {\phi_{}}_{\rm P} ) |
---|
| 722 | - ({\lambda_{}}_{\rm C}\; -\; {\lambda_{}}_{\rm P} ) |
---|
| 723 | ({\phi_{}}_{\rm A} \; -\; {\phi_{}}_{\rm P} )] \; \widehat{\bf k} \\ |
---|
| 724 | {{\bf r}_{}}_{\rm PB} \times {{\bf r}_{}}_{\rm PA} |
---|
| 725 | & = & [({\lambda_{}}_{\rm B}\; -\; {\lambda_{}}_{\rm P} ) |
---|
| 726 | ({\phi_{}}_{\rm A} \; -\; {\phi_{}}_{\rm P} ) |
---|
| 727 | - ({\lambda_{}}_{\rm A}\; -\; {\lambda_{}}_{\rm P} ) |
---|
| 728 | ({\phi_{}}_{\rm B} \; -\; {\phi_{}}_{\rm P} )] \; \widehat{\bf k} \\ |
---|
| 729 | {{\bf r}_{}}_{\rm PC} \times {{\bf r}_{}}_{\rm PD} |
---|
| 730 | & = & [({\lambda_{}}_{\rm C}\; -\; {\lambda_{}}_{\rm P} ) |
---|
| 731 | ({\phi_{}}_{\rm D} \; -\; {\phi_{}}_{\rm P} ) |
---|
| 732 | - ({\lambda_{}}_{\rm D}\; -\; {\lambda_{}}_{\rm P} ) |
---|
| 733 | ({\phi_{}}_{\rm C} \; -\; {\phi_{}}_{\rm P} )] \; \widehat{\bf k} \\ |
---|
| 734 | {{\bf r}_{}}_{\rm PD} \times {{\bf r}_{}}_{\rm PB} |
---|
| 735 | & = & [({\lambda_{}}_{\rm D}\; -\; {\lambda_{}}_{\rm P} ) |
---|
| 736 | ({\phi_{}}_{\rm B} \; -\; {\phi_{}}_{\rm P} ) |
---|
| 737 | - ({\lambda_{}}_{\rm B}\; -\; {\lambda_{}}_{\rm P} ) |
---|
| 738 | ({\phi_{}}_{\rm D} \; - \; {\phi_{}}_{\rm P} )] \; \widehat{\bf k} \\ |
---|
| 739 | \end{array} |
---|
| 740 | % \label{eq:cross} |
---|
| 741 | \end{align*} |
---|
[10354] | 742 | point in the opposite direction to the unit normal $\widehat{\bf k}$ |
---|
[10442] | 743 | (\ie that the coefficients of $\widehat{\bf k}$ are negative), |
---|
[10354] | 744 | where ${{\bf r}_{}}_{\rm PA}$, ${{\bf r}_{}}_{\rm PB}$, etc. correspond to |
---|
| 745 | the vectors between points P and A, P and B, etc.. |
---|
[11123] | 746 | The method used is similar to the method used in the \href{https://github.com/SCRIP-Project/SCRIP}{SCRIP interpolation package}. |
---|
[2298] | 747 | |
---|
[10354] | 748 | In order to speed up the grid search, there is the possibility to construct a lookup table for a user specified resolution. |
---|
| 749 | This lookup table contains the lower and upper bounds on the $i$ and $j$ indices to |
---|
| 750 | be searched for on a regular grid. |
---|
| 751 | For each observation position, the closest point on the regular grid of this position is computed and |
---|
| 752 | the $i$ and $j$ ranges of this point searched to determine the precise four points surrounding the observation. |
---|
[2298] | 753 | |
---|
| 754 | \subsection{Parallel aspects of horizontal interpolation} |
---|
[9407] | 755 | \label{subsec:OBS_parallel} |
---|
[2298] | 756 | |
---|
[10354] | 757 | For horizontal interpolation, there is the basic problem that |
---|
| 758 | the observations are unevenly distributed on the globe. |
---|
| 759 | In numerical models, it is common to divide the model grid into subgrids (or domains) where |
---|
| 760 | each subgrid is executed on a single processing element with explicit message passing for |
---|
| 761 | exchange of information along the domain boundaries when running on a massively parallel processor (MPP) system. |
---|
| 762 | This approach is used by \NEMO. |
---|
[2298] | 763 | |
---|
[10354] | 764 | For observations there is no natural distribution since the observations are not equally distributed on the globe. |
---|
| 765 | Two options have been made available: |
---|
| 766 | 1) geographical distribution; |
---|
[2298] | 767 | and 2) round-robin. |
---|
| 768 | |
---|
| 769 | \subsubsection{Geographical distribution of observations among processors} |
---|
| 770 | |
---|
[2376] | 771 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[10414] | 772 | \begin{figure} |
---|
| 773 | \begin{center} |
---|
| 774 | \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_local} |
---|
| 775 | \caption{ |
---|
| 776 | \protect\label{fig:obslocal} |
---|
| 777 | Example of the distribution of observations with the geographical distribution of observational data. |
---|
| 778 | } |
---|
| 779 | \end{center} |
---|
| 780 | \end{figure} |
---|
[2376] | 781 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[2298] | 782 | |
---|
[10354] | 783 | This is the simplest option in which the observations are distributed according to |
---|
| 784 | the domain of the grid-point parallelization. |
---|
| 785 | \autoref{fig:obslocal} shows an example of the distribution of the {\em in situ} data on processors with |
---|
| 786 | a different colour for each observation on a given processor for a 4 $\times$ 2 decomposition with ORCA2. |
---|
[2298] | 787 | The grid-point domain decomposition is clearly visible on the plot. |
---|
| 788 | |
---|
[10354] | 789 | The advantage of this approach is that all information needed for horizontal interpolation is available without |
---|
| 790 | any MPP communication. |
---|
| 791 | Of course, this is under the assumption that we are only using a $2 \times 2$ grid-point stencil for |
---|
[10442] | 792 | the interpolation (\eg bilinear interpolation). |
---|
[10354] | 793 | For higher order interpolation schemes this is no longer valid. |
---|
| 794 | A disadvantage with the above scheme is that the number of observations on each processor can be very different. |
---|
| 795 | If the cost of the actual interpolation is expensive relative to the communication of data needed for interpolation, |
---|
| 796 | this could lead to load imbalance. |
---|
[2298] | 797 | |
---|
| 798 | \subsubsection{Round-robin distribution of observations among processors} |
---|
| 799 | |
---|
[2376] | 800 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[10414] | 801 | \begin{figure} |
---|
| 802 | \begin{center} |
---|
| 803 | \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_global} |
---|
| 804 | \caption{ |
---|
| 805 | \protect\label{fig:obsglobal} |
---|
| 806 | Example of the distribution of observations with the round-robin distribution of observational data. |
---|
| 807 | } |
---|
| 808 | \end{center} |
---|
| 809 | \end{figure} |
---|
[2376] | 810 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[2298] | 811 | |
---|
[10354] | 812 | An alternative approach is to distribute the observations equally among processors and |
---|
| 813 | use message passing in order to retrieve the stencil for interpolation. |
---|
| 814 | The simplest distribution of the observations is to distribute them using a round-robin scheme. |
---|
| 815 | \autoref{fig:obsglobal} shows the distribution of the {\em in situ} data on processors for |
---|
| 816 | the round-robin distribution of observations with a different colour for each observation on a given processor for |
---|
| 817 | a 4 $\times$ 2 decomposition with ORCA2 for the same input data as in \autoref{fig:obslocal}. |
---|
[2298] | 818 | The observations are now clearly randomly distributed on the globe. |
---|
[10354] | 819 | In order to be able to perform horizontal interpolation in this case, |
---|
| 820 | a subroutine has been developed that retrieves any grid points in the global space. |
---|
[2298] | 821 | |
---|
| 822 | \subsection{Vertical interpolation operator} |
---|
| 823 | |
---|
[10354] | 824 | Vertical interpolation is achieved using either a cubic spline or linear interpolation. |
---|
| 825 | For the cubic spline, the top and bottom boundary conditions for the second derivative of |
---|
| 826 | the interpolating polynomial in the spline are set to zero. |
---|
[2298] | 827 | At the bottom boundary, this is done using the land-ocean mask. |
---|
[3294] | 828 | |
---|
| 829 | \newpage |
---|
| 830 | |
---|
[4245] | 831 | % ================================================================ |
---|
| 832 | % Offline observation operator documentation |
---|
| 833 | % ================================================================ |
---|
| 834 | |
---|
| 835 | %\usepackage{framed} |
---|
| 836 | |
---|
| 837 | \section{Offline observation operator} |
---|
[9407] | 838 | \label{sec:OBS_ooo} |
---|
[4245] | 839 | |
---|
| 840 | \subsection{Concept} |
---|
| 841 | |
---|
[10354] | 842 | The obs oper maps model variables to observation space. |
---|
| 843 | It is possible to apply this mapping without running the model. |
---|
| 844 | The software which performs this functionality is known as the \textbf{offline obs oper}. |
---|
| 845 | The obs oper is divided into three stages. |
---|
| 846 | An initialisation phase, an interpolation phase and an output phase. |
---|
| 847 | The implementation of which is outlined in the previous sections. |
---|
| 848 | During the interpolation phase the offline obs oper populates the model arrays by |
---|
| 849 | reading saved model fields from disk. |
---|
[4245] | 850 | |
---|
[10354] | 851 | There are two ways of exploiting this offline capacity. |
---|
| 852 | The first is to mimic the behaviour of the online system by supplying model fields at |
---|
| 853 | regular intervals between the start and the end of the run. |
---|
| 854 | This approach results in a single model counterpart per observation. |
---|
| 855 | This kind of usage produces feedback files the same file format as the online obs oper. |
---|
| 856 | The second is to take advantage of the offline setting in which |
---|
| 857 | multiple model counterparts can be calculated per observation. |
---|
| 858 | In this case it is possible to consider all forecasts verifying at the same time. |
---|
| 859 | By forecast, I mean any method which produces an estimate of physical reality which is not an observed value. |
---|
| 860 | In the case of class 4 files this means forecasts, analyses, persisted analyses and |
---|
| 861 | climatological values verifying at the same time. |
---|
| 862 | Although the class 4 file format doesn't account for multiple ensemble members or |
---|
| 863 | multiple experiments per observation, it is possible to include these components in the same or multiple files. |
---|
[4245] | 864 | |
---|
| 865 | %-------------------------------------------------------------------------------------------------------- |
---|
| 866 | % offline_oper.exe |
---|
| 867 | %-------------------------------------------------------------------------------------------------------- |
---|
| 868 | |
---|
| 869 | \subsection{Using the offline observation operator} |
---|
| 870 | |
---|
| 871 | \subsubsection{Building} |
---|
| 872 | |
---|
[10354] | 873 | In addition to \emph{OPA\_SRC} the offline obs oper requires the inclusion of the \emph{OOO\_SRC} directory. |
---|
| 874 | \emph{OOO\_SRC} contains a replacement \mdl{nemo} and \mdl{nemogcm} which |
---|
| 875 | overwrites the resultant \textbf{nemo.exe}. |
---|
| 876 | This is the approach taken by \emph{SAS\_SRC} and \emph{OFF\_SRC}. |
---|
[4245] | 877 | |
---|
| 878 | %-------------------------------------------------------------------------------------------------------- |
---|
| 879 | % Running |
---|
| 880 | %-------------------------------------------------------------------------------------------------------- |
---|
| 881 | \subsubsection{Running} |
---|
| 882 | |
---|
| 883 | The simplest way to use the executable is to edit and append the \textbf{ooo.nml} namelist to |
---|
| 884 | a full NEMO namelist and then to run the executable as if it were nemo.exe. |
---|
| 885 | |
---|
| 886 | \subsubsection{Quick script} |
---|
| 887 | |
---|
[10354] | 888 | A useful Python utility to control the namelist options can be found in \textbf{OBSTOOLS/OOO}. |
---|
| 889 | The functions which locate model fields and observation files can be manually specified. |
---|
| 890 | The package can be installed by appropriate use of the included setup.py script. |
---|
[4245] | 891 | |
---|
| 892 | Documentation can be auto-generated by Sphinx by running \emph{make html} in the \textbf{doc} directory. |
---|
| 893 | |
---|
| 894 | %-------------------------------------------------------------------------------------------------------- |
---|
| 895 | % Configuration section |
---|
| 896 | %-------------------------------------------------------------------------------------------------------- |
---|
| 897 | \subsection{Configuring the offline observation operator} |
---|
[10354] | 898 | The observation files and settings understood by \textbf{namobs} have been outlined in the online obs oper section. |
---|
| 899 | In addition there are two further namelists wich control the operation of the offline obs oper. |
---|
| 900 | \textbf{namooo} which controls the input model fields and \textbf{namcl4} which |
---|
| 901 | controls the production of class 4 files. |
---|
[4245] | 902 | |
---|
| 903 | \subsubsection{Single field} |
---|
| 904 | |
---|
| 905 | In offline mode model arrays are populated at appropriate time steps via input files. |
---|
| 906 | At present, \textbf{tsn} and \textbf{sshn} are populated by the default read routines. |
---|
[10354] | 907 | These routines will be expanded upon in future versions to allow the specification of any model variable. |
---|
| 908 | As such, input files must be global versions of the model domain with |
---|
[4245] | 909 | \textbf{votemper}, \textbf{vosaline} and optionally \textbf{sshn} present. |
---|
| 910 | |
---|
[10354] | 911 | For each field read there must be an entry in the \textbf{namooo} namelist specifying |
---|
| 912 | the name of the file to read and the index along the \emph{time\_counter}. |
---|
| 913 | For example, to read the second time counter from a single file the namelist would be. |
---|
[4245] | 914 | |
---|
[9388] | 915 | \begin{forlines} |
---|
[4245] | 916 | !---------------------------------------------------------------------- |
---|
| 917 | ! namooo Offline obs_oper namelist |
---|
| 918 | !---------------------------------------------------------------------- |
---|
| 919 | ! ooo_files specifies the files containing the model counterpart |
---|
| 920 | ! nn_ooo_idx specifies the time_counter index within the model file |
---|
| 921 | &namooo |
---|
| 922 | ooo_files = "foo.nc" |
---|
| 923 | nn_ooo_idx = 2 |
---|
| 924 | / |
---|
[9388] | 925 | \end{forlines} |
---|
[4245] | 926 | |
---|
| 927 | \subsubsection{Multiple fields per run} |
---|
| 928 | |
---|
[10354] | 929 | Model field iteration is controlled via \textbf{nn\_ooo\_freq} which |
---|
| 930 | specifies the number of model steps at which the next field gets read. |
---|
| 931 | For example, if 12 hourly fields are to be interpolated in a setup where 288 steps equals 24 hours. |
---|
[4245] | 932 | |
---|
[9388] | 933 | \begin{forlines} |
---|
[4245] | 934 | !---------------------------------------------------------------------- |
---|
| 935 | ! namooo Offline obs_oper namelist |
---|
| 936 | !---------------------------------------------------------------------- |
---|
| 937 | ! ooo_files specifies the files containing the model counterpart |
---|
| 938 | ! nn_ooo_idx specifies the time_counter index within the model file |
---|
| 939 | ! nn_ooo_freq specifies number of time steps between read operations |
---|
| 940 | &namooo |
---|
| 941 | ooo_files = "foo.nc" "foo.nc" |
---|
| 942 | nn_ooo_idx = 1 2 |
---|
| 943 | nn_ooo_freq = 144 |
---|
| 944 | / |
---|
[9388] | 945 | \end{forlines} |
---|
[4245] | 946 | |
---|
[10354] | 947 | The above namelist will result in feedback files whose first 12 hours contain the first field of foo.nc and |
---|
| 948 | the second 12 hours contain the second field. |
---|
[4245] | 949 | |
---|
| 950 | %\begin{framed} |
---|
| 951 | \textbf{Note} Missing files can be denoted as "nofile". |
---|
| 952 | %\end{framed} |
---|
| 953 | |
---|
[10354] | 954 | It is easy to see how a collection of fields taken fron a number of files at different indices can be combined at |
---|
| 955 | a particular frequency in time to generate a pseudo model evolution. |
---|
| 956 | As long as all that is needed is a single model counterpart at a regular interval then |
---|
| 957 | namooo is all that needs to be edited. |
---|
| 958 | However, a far more interesting approach can be taken in which multiple forecasts, analyses, persisted analyses and |
---|
| 959 | climatologies are considered against the same set of observations. |
---|
| 960 | For this a slightly more complicated approach is needed. |
---|
| 961 | It is referred to as \emph{Class 4} since it is the fourth metric defined by the GODAE intercomparison project. |
---|
[4245] | 962 | |
---|
| 963 | %-------------------------------------------------------------------------------------------------------- |
---|
| 964 | % Class 4 file section |
---|
| 965 | %-------------------------------------------------------------------------------------------------------- |
---|
| 966 | \subsubsection{Multiple model counterparts per observation a.k.a Class 4} |
---|
| 967 | |
---|
[10354] | 968 | A generalisation of feedback files to allow multiple model components per observation. |
---|
| 969 | For a single observation, as well as previous forecasts verifying at the same time |
---|
| 970 | there are also analyses, persisted analyses and climatologies. |
---|
[4245] | 971 | |
---|
| 972 | |
---|
[10354] | 973 | The above namelist performs two basic functions. |
---|
| 974 | It organises the fields given in \textbf{namooo} into groups so that observations can be matched up multiple times. |
---|
| 975 | It also controls the metadata and the output variable of the class 4 file when a write routine is called. |
---|
[4245] | 976 | |
---|
| 977 | %\begin{framed} |
---|
[10354] | 978 | \textbf{Note: ln\_cl4} must be set to \forcode{.true.} in \textbf{namobs} to use class 4 outputs. |
---|
[4245] | 979 | %\end{framed} |
---|
| 980 | |
---|
| 981 | \subsubsection{Class 4 naming convention} |
---|
| 982 | |
---|
| 983 | The standard class 4 file naming convention is as follows. |
---|
| 984 | |
---|
| 985 | \noindent |
---|
| 986 | \linebreak |
---|
[9393] | 987 | \textbf{\$\{prefix\}\_\$\{yyyymmdd\}\_\$\{sys\}\_\$\{cfg\}\_\$\{vn\}\_\$\{kind\}\_\$\{nproc\}}.nc |
---|
[4245] | 988 | |
---|
| 989 | \noindent |
---|
| 990 | \linebreak |
---|
[10354] | 991 | Much of the namelist is devoted to specifying this convention. |
---|
| 992 | The following namelist settings control the elements of the output file names. |
---|
| 993 | Each should be specified as a single string of character data. |
---|
[4245] | 994 | |
---|
| 995 | \begin{description} |
---|
| 996 | \item[cl4\_prefix] |
---|
[10442] | 997 | Prefix for class 4 files \eg class4 |
---|
[4245] | 998 | \item[cl4\_date] |
---|
[10354] | 999 | YYYYMMDD validity date |
---|
[4245] | 1000 | \item[cl4\_sys] |
---|
[10442] | 1001 | The name of the class 4 model system \eg FOAM |
---|
[4245] | 1002 | \item[cl4\_cfg] |
---|
[10442] | 1003 | The name of the class 4 model configuration \eg orca025 |
---|
[4245] | 1004 | \item[cl4\_vn] |
---|
[10442] | 1005 | The name of the class 4 model version \eg 12.0 |
---|
[4245] | 1006 | \end{description} |
---|
| 1007 | |
---|
| 1008 | \noindent |
---|
[10354] | 1009 | The kind is specified by the observation type internally to the obs oper. |
---|
| 1010 | The processor number is specified internally in NEMO. |
---|
[4245] | 1011 | |
---|
| 1012 | \subsubsection{Class 4 file global attributes} |
---|
| 1013 | |
---|
[10354] | 1014 | Global attributes necessary to fulfill the class 4 file definition. |
---|
| 1015 | These are also useful pieces of information when collaborating with external partners. |
---|
[4245] | 1016 | |
---|
| 1017 | \begin{description} |
---|
| 1018 | \item[cl4\_contact] |
---|
[10354] | 1019 | Contact email for class 4 files. |
---|
[4245] | 1020 | \item[cl4\_inst] |
---|
[10354] | 1021 | The name of the producers institution. |
---|
[4245] | 1022 | \item[cl4\_cfg] |
---|
[10442] | 1023 | The name of the class 4 model configuration \eg orca025 |
---|
[4245] | 1024 | \item[cl4\_vn] |
---|
[10442] | 1025 | The name of the class 4 model version \eg 12.0 |
---|
[4245] | 1026 | \end{description} |
---|
| 1027 | |
---|
| 1028 | \noindent |
---|
[10354] | 1029 | The obs\_type, creation date and validity time are specified internally to the obs oper. |
---|
[4245] | 1030 | |
---|
| 1031 | \subsubsection{Class 4 model counterpart configuration} |
---|
| 1032 | |
---|
[10354] | 1033 | As seen previously it is possible to perform a single sweep of the obs oper and |
---|
| 1034 | specify a collection of model fields equally spaced along that sweep. |
---|
| 1035 | In the class 4 case the single sweep is replaced with multiple sweeps and |
---|
| 1036 | a certain ammount of book keeping is needed to ensure each model counterpart makes its way to |
---|
| 1037 | the correct piece of memory in the output files. |
---|
[4245] | 1038 | |
---|
| 1039 | \noindent |
---|
| 1040 | \linebreak |
---|
[10354] | 1041 | In terms of book keeping, the offline obs oper needs to know how many full sweeps need to be performed. |
---|
| 1042 | This is specified via the \textbf{cl4\_match\_len} variable and |
---|
| 1043 | is the total number of model counterparts per observation. |
---|
| 1044 | For example, a 3 forecasts plus 3 persistence fields plus an analysis field would be 7 counterparts per observation. |
---|
[4245] | 1045 | |
---|
[9388] | 1046 | \begin{forlines} |
---|
[4245] | 1047 | cl4_match_len = 7 |
---|
[9388] | 1048 | \end{forlines} |
---|
[4245] | 1049 | |
---|
[10354] | 1050 | Then to correctly allocate a class 4 file the forecast axis must be defined. |
---|
| 1051 | This is controlled via \textbf{cl4\_fcst\_len}, which in out above example would be 3. |
---|
[4245] | 1052 | |
---|
[9388] | 1053 | \begin{forlines} |
---|
[4245] | 1054 | cl4_fcst_len = 3 |
---|
[9388] | 1055 | \end{forlines} |
---|
[4245] | 1056 | |
---|
[10354] | 1057 | Then for each model field it is necessary to designate what class 4 variable and index along |
---|
| 1058 | the forecast dimension the model counterpart should be stored in the output file. |
---|
| 1059 | As well as a value for that lead time in hours, this will be useful when interpreting the data afterwards. |
---|
[4245] | 1060 | |
---|
[9388] | 1061 | \begin{forlines} |
---|
[4245] | 1062 | cl4_vars = "forecast" "forecast" "forecast" "persistence" "persistence" |
---|
| 1063 | "persistence" "best_estimate" |
---|
| 1064 | cl4_fcst_idx = 1 2 3 1 2 3 1 |
---|
| 1065 | cl4_leadtime = 12 36 60 |
---|
[9388] | 1066 | \end{forlines} |
---|
[4245] | 1067 | |
---|
[10354] | 1068 | In terms of files and indices of fields inside each file the class 4 approach makes use of |
---|
| 1069 | the \textbf{namooo} namelist. |
---|
| 1070 | If our fields are in separate files with a single field per file our example inputs will be specified. |
---|
[4245] | 1071 | |
---|
[9388] | 1072 | \begin{forlines} |
---|
[4245] | 1073 | ooo_files = "F.1.nc" "F.2.nc" "F.3.nc" "P.1.nc" "P.2.nc" "P.3.nc" "A.1.nc" |
---|
| 1074 | nn_ooo_idx = 1 1 1 1 1 1 1 |
---|
[9388] | 1075 | \end{forlines} |
---|
[4245] | 1076 | |
---|
[10354] | 1077 | When we combine all of the naming conventions, global attributes and i/o instructions the class 4 namelist becomes. |
---|
[4245] | 1078 | |
---|
[9388] | 1079 | \begin{forlines} |
---|
[4245] | 1080 | !---------------------------------------------------------------------- |
---|
| 1081 | ! namooo Offline obs_oper namelist |
---|
| 1082 | !---------------------------------------------------------------------- |
---|
| 1083 | ! ooo_files specifies the files containing the model counterpart |
---|
| 1084 | ! nn_ooo_idx specifies the time_counter index within the model file |
---|
| 1085 | ! nn_ooo_freq specifies number of time steps between read operations |
---|
| 1086 | &namooo |
---|
| 1087 | ooo_files = "F.1.nc" "F.2.nc" "F.3.nc" "P.1.nc" "P.2.nc" "P.3.nc" "A.1.nc" |
---|
| 1088 | nn_ooo_idx = 1 1 1 1 1 1 1 |
---|
| 1089 | / |
---|
| 1090 | !---------------------------------------------------------------------- |
---|
| 1091 | ! namcl4 Offline obs_oper class 4 namelist |
---|
| 1092 | !---------------------------------------------------------------------- |
---|
| 1093 | ! |
---|
| 1094 | ! Naming convention |
---|
| 1095 | ! ----------------- |
---|
| 1096 | ! cl4_prefix specifies the output file prefix |
---|
| 1097 | ! cl4_date specifies the output file validity date |
---|
| 1098 | ! cl4_sys specifies the model counterpart system |
---|
| 1099 | ! cl4_cfg specifies the model counterpart configuration |
---|
| 1100 | ! cl4_vn specifies the model counterpart version |
---|
| 1101 | ! cl4_inst specifies the model counterpart institute |
---|
| 1102 | ! cl4_contact specifies the file producers contact details |
---|
| 1103 | ! |
---|
| 1104 | ! I/O specification |
---|
| 1105 | ! ----------------- |
---|
| 1106 | ! cl4_vars specifies the names of the output file netcdf variable |
---|
| 1107 | ! cl4_fcst_idx specifies output file forecast index |
---|
| 1108 | ! cl4_fcst_len specifies forecast axis length |
---|
| 1109 | ! cl4_match_len specifies number of unique matches per observation |
---|
| 1110 | ! cl4_leadtime specifies the forecast axis lead time |
---|
| 1111 | ! |
---|
| 1112 | &namcl4 |
---|
| 1113 | cl4_match_len = 7 |
---|
| 1114 | cl4_fcst_len = 3 |
---|
| 1115 | cl4_fcst_idx = 1 2 3 1 2 3 1 |
---|
| 1116 | cl4_vars = "forecast" "forecast" "forecast" "persistence" "persistence" |
---|
| 1117 | "persistence" "best_estimate" |
---|
| 1118 | cl4_leadtime = 12 36 60 |
---|
| 1119 | cl4_prefix = "class4" |
---|
| 1120 | cl4_date = "20130101" |
---|
| 1121 | cl4_vn = "12.0" |
---|
| 1122 | cl4_sys = "FOAM" |
---|
| 1123 | cl4_cfg = "AMM7" |
---|
| 1124 | cl4_contact = "example@example.com" |
---|
| 1125 | cl4_inst = "UK Met Office" |
---|
| 1126 | / |
---|
[9388] | 1127 | \end{forlines} |
---|
[4245] | 1128 | |
---|
| 1129 | \subsubsection{Climatology interpolation} |
---|
| 1130 | |
---|
[10354] | 1131 | The climatological counterpart is generated at the start of the run by |
---|
| 1132 | restarting the model from climatology through appropriate use of \textbf{namtsd}. |
---|
| 1133 | To override the offline observation operator read routine and to take advantage of the restart settings, |
---|
| 1134 | specify the first entry in \textbf{cl4\_vars} as "climatology". |
---|
| 1135 | This will then pipe the restart from climatology into the output class 4 file. |
---|
| 1136 | As in every other class 4 matchup the input file, input index and output index must be specified. |
---|
| 1137 | These can be replaced with dummy data since they are not used but |
---|
| 1138 | they must be present to cycle through the matchups correctly. |
---|
[4245] | 1139 | |
---|
| 1140 | \subsection{Advanced usage} |
---|
| 1141 | |
---|
[10354] | 1142 | In certain cases it may be desirable to include both multiple model fields per observation window with |
---|
| 1143 | multiple match ups per observation. |
---|
| 1144 | This can be achieved by specifying \textbf{nn\_ooo\_freq} as well as the class 4 settings. |
---|
| 1145 | Care must be taken in generating the ooo\_files list such that the files are arranged into |
---|
| 1146 | consecutive blocks of single match ups. |
---|
| 1147 | For example, 2 forecast fields of 12 hourly data would result in 4 separate read operations but |
---|
| 1148 | only 2 write operations, 1 per forecast. |
---|
[4245] | 1149 | |
---|
[9388] | 1150 | \begin{forlines} |
---|
[4245] | 1151 | ooo_files = "F1.nc" "F1.nc" "F2.nc" "F2.nc" |
---|
| 1152 | ... |
---|
| 1153 | cl4_fcst_idx = 1 2 |
---|
[9388] | 1154 | \end{forlines} |
---|
[4245] | 1155 | |
---|
[10354] | 1156 | The above notation reveals the internal split between match up iterators and file iterators. |
---|
| 1157 | This technique has not been used before so experimentation is needed before results can be trusted. |
---|
[4245] | 1158 | |
---|
| 1159 | \newpage |
---|
| 1160 | |
---|
[9393] | 1161 | \section{Observation utilities} |
---|
[9407] | 1162 | \label{sec:OBS_obsutils} |
---|
[3294] | 1163 | |
---|
[10354] | 1164 | Some tools for viewing and processing of observation and feedback files are provided in |
---|
| 1165 | the NEMO repository for convenience. |
---|
[10442] | 1166 | These include OBSTOOLS which are a collection of \fortran programs which are helpful to deal with feedback files. |
---|
[10354] | 1167 | They do such tasks as observation file conversion, printing of file contents, |
---|
| 1168 | some basic statistical analysis of feedback files. |
---|
| 1169 | The other tool is an IDL program called dataplot which uses a graphical interface to |
---|
| 1170 | visualise observations and feedback files. |
---|
| 1171 | OBSTOOLS and dataplot are described in more detail below. |
---|
[3294] | 1172 | |
---|
| 1173 | \subsection{Obstools} |
---|
| 1174 | |
---|
[10442] | 1175 | A series of \fortran utilities is provided with NEMO called OBSTOOLS. |
---|
[10354] | 1176 | This are helpful in handling observation files and the feedback file output from the NEMO observation operator. |
---|
[3294] | 1177 | The utilities are as follows |
---|
| 1178 | |
---|
[4245] | 1179 | \subsubsection{c4comb} |
---|
| 1180 | |
---|
[10354] | 1181 | The program c4comb combines multiple class 4 files produced by individual processors in |
---|
| 1182 | an MPI run of NEMO offline obs\_oper into a single class 4 file. |
---|
| 1183 | The program is called in the following way: |
---|
[4245] | 1184 | |
---|
[9376] | 1185 | |
---|
[4245] | 1186 | \footnotesize |
---|
[9388] | 1187 | \begin{cmds} |
---|
[4245] | 1188 | c4comb.exe outputfile inputfile1 inputfile2 ... |
---|
[9388] | 1189 | \end{cmds} |
---|
[4245] | 1190 | |
---|
[3294] | 1191 | \subsubsection{corio2fb} |
---|
| 1192 | |
---|
[10354] | 1193 | The program corio2fb converts profile observation files from the Coriolis format to the standard feedback format. |
---|
| 1194 | The program is called in the following way: |
---|
[3294] | 1195 | |
---|
| 1196 | \footnotesize |
---|
[9388] | 1197 | \begin{cmds} |
---|
[3294] | 1198 | corio2fb.exe outputfile inputfile1 inputfile2 ... |
---|
[9388] | 1199 | \end{cmds} |
---|
[3294] | 1200 | |
---|
| 1201 | \subsubsection{enact2fb} |
---|
| 1202 | |
---|
[10354] | 1203 | The program enact2fb converts profile observation files from the ENACT format to the standard feedback format. |
---|
| 1204 | The program is called in the following way: |
---|
[3294] | 1205 | |
---|
| 1206 | \footnotesize |
---|
[9388] | 1207 | \begin{cmds} |
---|
[3294] | 1208 | enact2fb.exe outputfile inputfile1 inputfile2 ... |
---|
[9388] | 1209 | \end{cmds} |
---|
[3294] | 1210 | |
---|
| 1211 | \subsubsection{fbcomb} |
---|
| 1212 | |
---|
[10354] | 1213 | The program fbcomb combines multiple feedback files produced by individual processors in |
---|
| 1214 | an MPI run of NEMO into a single feedback file. |
---|
| 1215 | The program is called in the following way: |
---|
[3294] | 1216 | |
---|
| 1217 | \footnotesize |
---|
[9388] | 1218 | \begin{cmds} |
---|
[3294] | 1219 | fbcomb.exe outputfile inputfile1 inputfile2 ... |
---|
[9388] | 1220 | \end{cmds} |
---|
[3294] | 1221 | |
---|
| 1222 | \subsubsection{fbmatchup} |
---|
| 1223 | |
---|
[10354] | 1224 | The program fbmatchup will match observations from two feedback files. |
---|
| 1225 | The program is called in the following way: |
---|
[3294] | 1226 | |
---|
| 1227 | \footnotesize |
---|
[9388] | 1228 | \begin{cmds} |
---|
[3294] | 1229 | fbmatchup.exe outputfile inputfile1 varname1 inputfile2 varname2 ... |
---|
[9388] | 1230 | \end{cmds} |
---|
[3294] | 1231 | |
---|
| 1232 | \subsubsection{fbprint} |
---|
| 1233 | |
---|
| 1234 | The program fbprint will print the contents of a feedback file or files to standard output. |
---|
[10354] | 1235 | Selected information can be output using optional arguments. |
---|
| 1236 | The program is called in the following way: |
---|
[3294] | 1237 | |
---|
| 1238 | \footnotesize |
---|
[9388] | 1239 | \begin{cmds} |
---|
[3294] | 1240 | fbprint.exe [options] inputfile |
---|
| 1241 | |
---|
| 1242 | options: |
---|
| 1243 | -b shorter output |
---|
| 1244 | -q Select observations based on QC flags |
---|
| 1245 | -Q Select observations based on QC flags |
---|
| 1246 | -B Select observations based on QC flags |
---|
| 1247 | -u unsorted |
---|
| 1248 | -s ID select station ID |
---|
| 1249 | -t TYPE select observation type |
---|
| 1250 | -v NUM1-NUM2 select variable range to print by number |
---|
| 1251 | (default all) |
---|
| 1252 | -a NUM1-NUM2 select additional variable range to print by number |
---|
| 1253 | (default all) |
---|
| 1254 | -e NUM1-NUM2 select extra variable range to print by number |
---|
| 1255 | (default all) |
---|
| 1256 | -d output date range |
---|
| 1257 | -D print depths |
---|
| 1258 | -z use zipped files |
---|
[9388] | 1259 | \end{cmds} |
---|
[3294] | 1260 | |
---|
| 1261 | \subsubsection{fbsel} |
---|
| 1262 | |
---|
[10354] | 1263 | The program fbsel will select or subsample observations. |
---|
| 1264 | The program is called in the following way: |
---|
[3294] | 1265 | |
---|
| 1266 | \footnotesize |
---|
[9388] | 1267 | \begin{cmds} |
---|
[3294] | 1268 | fbsel.exe <input filename> <output filename> |
---|
[9388] | 1269 | \end{cmds} |
---|
[3294] | 1270 | |
---|
| 1271 | \subsubsection{fbstat} |
---|
| 1272 | |
---|
[10354] | 1273 | The program fbstat will output summary statistics in different global areas into a number of files. |
---|
| 1274 | The program is called in the following way: |
---|
[3294] | 1275 | |
---|
| 1276 | \footnotesize |
---|
[9388] | 1277 | \begin{cmds} |
---|
[3294] | 1278 | fbstat.exe [-nmlev] <filenames> |
---|
[9388] | 1279 | \end{cmds} |
---|
[3294] | 1280 | |
---|
| 1281 | \subsubsection{fbthin} |
---|
| 1282 | |
---|
[10354] | 1283 | The program fbthin will thin the data to 1 degree resolution. |
---|
| 1284 | The code could easily be modified to thin to a different resolution. |
---|
| 1285 | The program is called in the following way: |
---|
[3294] | 1286 | |
---|
| 1287 | \footnotesize |
---|
[9388] | 1288 | \begin{cmds} |
---|
[3294] | 1289 | fbthin.exe inputfile outputfile |
---|
[9388] | 1290 | \end{cmds} |
---|
[3294] | 1291 | |
---|
| 1292 | \subsubsection{sla2fb} |
---|
| 1293 | |
---|
[10354] | 1294 | The program sla2fb will convert an AVISO SLA format file to feedback format. |
---|
| 1295 | The program is called in the following way: |
---|
[3294] | 1296 | |
---|
| 1297 | \footnotesize |
---|
[9388] | 1298 | \begin{cmds} |
---|
[3294] | 1299 | sla2fb.exe [-s type] outputfile inputfile1 inputfile2 ... |
---|
| 1300 | |
---|
| 1301 | Option: |
---|
| 1302 | -s Select altimeter data_source |
---|
[9388] | 1303 | \end{cmds} |
---|
[3294] | 1304 | |
---|
| 1305 | \subsubsection{vel2fb} |
---|
| 1306 | |
---|
[10354] | 1307 | The program vel2fb will convert TAO/PIRATA/RAMA currents files to feedback format. |
---|
| 1308 | The program is called in the following way: |
---|
[3294] | 1309 | |
---|
| 1310 | \footnotesize |
---|
[9388] | 1311 | \begin{cmds} |
---|
[3294] | 1312 | vel2fb.exe outputfile inputfile1 inputfile2 ... |
---|
[9388] | 1313 | \end{cmds} |
---|
[3294] | 1314 | |
---|
[9393] | 1315 | \subsection{Building the obstools} |
---|
[3294] | 1316 | |
---|
| 1317 | To build the obstools use in the tools directory use ./maketools -n OBSTOOLS -m [ARCH]. |
---|
| 1318 | |
---|
| 1319 | \subsection{Dataplot} |
---|
| 1320 | |
---|
[10354] | 1321 | An IDL program called dataplot is included which uses a graphical interface to |
---|
| 1322 | visualise observations and feedback files. |
---|
| 1323 | It is possible to zoom in, plot individual profiles and calculate some basic statistics. |
---|
| 1324 | To plot some data run IDL and then: |
---|
[3294] | 1325 | \footnotesize |
---|
[9376] | 1326 | \begin{minted}{idl} |
---|
[3294] | 1327 | IDL> dataplot, "filename" |
---|
[9376] | 1328 | \end{minted} |
---|
[3294] | 1329 | |
---|
[10354] | 1330 | To read multiple files into dataplot, |
---|
| 1331 | for example multiple feedback files from different processors or from different days, |
---|
| 1332 | the easiest method is to use the spawn command to generate a list of files which can then be passed to dataplot. |
---|
[3294] | 1333 | \footnotesize |
---|
[9376] | 1334 | \begin{minted}{idl} |
---|
[3294] | 1335 | IDL> spawn, 'ls profb*.nc', files |
---|
| 1336 | IDL> dataplot, files |
---|
[9376] | 1337 | \end{minted} |
---|
[3294] | 1338 | |
---|
[9407] | 1339 | \autoref{fig:obsdataplotmain} shows the main window which is launched when dataplot starts. |
---|
[10354] | 1340 | This is split into three parts. |
---|
| 1341 | At the top there is a menu bar which contains a variety of drop down menus. |
---|
| 1342 | Areas - zooms into prespecified regions; |
---|
| 1343 | plot - plots the data as a timeseries or a T-S diagram if appropriate; |
---|
| 1344 | Find - allows data to be searched; |
---|
| 1345 | Config - sets various configuration options. |
---|
[3294] | 1346 | |
---|
[10354] | 1347 | The middle part is a plot of the geographical location of the observations. |
---|
| 1348 | This will plot the observation value, the model background value or observation minus background value depending on |
---|
| 1349 | the option selected in the radio button at the bottom of the window. |
---|
| 1350 | The plotting colour range can be changed by clicking on the colour bar. |
---|
| 1351 | The title of the plot gives some basic information about the date range and depth range shown, |
---|
| 1352 | the extreme values, and the mean and rms values. |
---|
| 1353 | It is possible to zoom in using a drag-box. |
---|
| 1354 | You may also zoom in or out using the mouse wheel. |
---|
[3294] | 1355 | |
---|
[10354] | 1356 | The bottom part of the window controls what is visible in the plot above. |
---|
| 1357 | There are two bars which select the level range plotted (for profile data). |
---|
| 1358 | The other bars below select the date range shown. |
---|
| 1359 | The bottom of the figure allows the option to plot the mean, root mean square, standard deviation or |
---|
| 1360 | mean square values. |
---|
| 1361 | As mentioned above you can choose to plot the observation value, the model background value or |
---|
| 1362 | observation minus background value. |
---|
| 1363 | The next group of radio buttons selects the map projection. |
---|
| 1364 | This can either be regular latitude longitude grid, or north or south polar stereographic. |
---|
| 1365 | The next group of radio buttons will plot bad observations, switch to salinity and |
---|
| 1366 | plot density for profile observations. |
---|
| 1367 | The rightmost group of buttons will print the plot window as a postscript, save it as png, or exit from dataplot. |
---|
[3294] | 1368 | |
---|
| 1369 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[10414] | 1370 | \begin{figure} |
---|
| 1371 | \begin{center} |
---|
| 1372 | % \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_main} |
---|
| 1373 | \includegraphics[width=9cm,angle=-90.]{Fig_OBS_dataplot_main} |
---|
| 1374 | \caption{ |
---|
| 1375 | \protect\label{fig:obsdataplotmain} |
---|
| 1376 | Main window of dataplot. |
---|
| 1377 | } |
---|
| 1378 | \end{center} |
---|
| 1379 | \end{figure} |
---|
[3294] | 1380 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
| 1381 | |
---|
[10354] | 1382 | If a profile point is clicked with the mouse button a plot of the observation and background values as |
---|
| 1383 | a function of depth (\autoref{fig:obsdataplotprofile}). |
---|
[3294] | 1384 | |
---|
| 1385 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[10414] | 1386 | \begin{figure} |
---|
| 1387 | \begin{center} |
---|
| 1388 | % \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_prof} |
---|
| 1389 | \includegraphics[width=7cm,angle=-90.]{Fig_OBS_dataplot_prof} |
---|
| 1390 | \caption{ |
---|
| 1391 | \protect\label{fig:obsdataplotprofile} |
---|
| 1392 | Profile plot from dataplot produced by right clicking on a point in the main window. |
---|
| 1393 | } |
---|
| 1394 | \end{center} |
---|
| 1395 | \end{figure} |
---|
[3294] | 1396 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
| 1397 | |
---|
[10414] | 1398 | \biblio |
---|
[3294] | 1399 | |
---|
[10442] | 1400 | \pindex |
---|
| 1401 | |
---|
[6997] | 1402 | \end{document} |
---|