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branches/2011/dev_NEMO_MERGE_2011/DOC/TexFiles/Chapters/Chap_OBS.tex
r2483 r3116 13 13 $\ $\newline % force a new line 14 14 15 The observation and model comparison code (OBS) reads in observation files 16 (profile temperature and salinity, sea surface temperature, sea level anomaly,17 sea ice concentration, and velocity) and calculates an interpolated model equivalent 18 value at the observation location and nearest model timestep. The OBS code is 19 called from \np{opa.F90} in order to initialise the model and to calculate the 20 model equivalent values for observations on the 0th timestep. The code is then 21 called again after each timestep from \np{step.F90}. The code was originally 22 developed for use with NEMOVAR. 23 24 For all data types a 2D horizontal interpolator is needed 25 to interpolate the model fields to the observation location.26 For {\em in situ} profiles, a 1D vertical interpolator is needed in addition to 27 provide model fields at the observation depths. Currently this only works in 28 z-level model configurations, but is being developed to work with a 29 generalised vertical coordinate system. 30 Temperature data from moored buoys (TAO, TRITON, PIRATA) in the 31 ENACT/ENSEMBLES data-base are available as daily averaged quantities. For this 32 type of observation the 33 observation operator will compare such observations to the model temperature15 The observation and model comparison code (OBS) reads in observation files (profile 16 temperature and salinity, sea surface temperature, sea level anomaly, sea ice concentration, 17 and velocity) and calculates an interpolated model equivalent value at the observation 18 location and nearest model timestep. The resulting data are saved in a ``feedback'' file (or 19 files). The code was originally developed for use with the NEMOVAR data assimilation code, but 20 can be used for validation or verification of model or any other data assimilation system. 21 22 The OBS code is called from \np{opa.F90} for model initialisation and to calculate the model 23 equivalent values for observations on the 0th timestep. The code is then called again after 24 each timestep from \np{step.F90}. To build with the OBS code active \key{diaobs} must be 25 set. 26 27 For all data types a 2D horizontal interpolator is needed to interpolate the model fields to 28 the observation location. For {\em in situ} profiles, a 1D vertical interpolator is needed in 29 addition to provide model fields at the observation depths. Currently this only works in 30 z-level model configurations, but is being developed to work with a generalised vertical 31 coordinate system. Temperature data from moored buoys (TAO, TRITON, PIRATA) in the 32 ENACT/ENSEMBLES data-base are available as daily averaged quantities. For this type of 33 observation the observation operator will compare such observations to the model temperature 34 34 fields averaged over one day. The relevant observation type may be specified in the namelist 35 using \np{endailyavtypes}. Otherwise the model value from the nearest 36 timestep to the observation time is used. 37 38 The resulting data are saved in a ``feedback'' file (or files) which can be used 39 for model validation and verification and also to provide information for data 40 assimilation. This code is controlled by the namelist \textit{nam\_obs}. To 41 build with the OBS code active \key{diaobs} must be set. 42 43 Section~\ref{OBS_example} introduces a test example of the observation operator 44 code including where to obtain data and how to setup the namelist. 45 Section~\ref{OBS_details} introduces some more technical details of the 46 different observation types used and also shows a more complete namelist. 47 Finally section~\ref{OBS_theory} introduces some of the theoretical aspects of 48 the observation operator including interpolation methods and running on multiple 49 processors. 35 using \np{endailyavtypes}. Otherwise the model value from the nearest timestep to the 36 observation time is used. 37 38 The code is controlled by the namelist \textit{nam\_obs}. See the following sections for more 39 details on setting up the namelist. 40 41 Section~\ref{OBS_example} introduces a test example of the observation operator code including 42 where to obtain data and how to setup the namelist. Section~\ref{OBS_details} introduces some 43 more technical details of the different observation types used and also shows a more complete 44 namelist. Section~\ref{OBS_theory} introduces some of the theoretical aspects of the 45 observation operator including interpolation methods and running on multiple processors. 46 Section~\ref{OBS_obsutils} introduces some utilities to help working with the files produced 47 by the OBS code. 50 48 51 49 % ================================================================ … … 69 67 \item Add the following to the NEMO namelist to run the observation 70 68 operator on this data. Set the \np{enactfiles} namelist parameter to the 71 observation file name (or link in to \np{profiles\_01\.nc}):69 observation file name: 72 70 \end{enumerate} 73 71 … … 76 74 %------------------------------------------------------------------------------------------------------------- 77 75 78 The option \np{ln\_t3d} and \np{ln\_s3d} switch on the temperature and salinity76 The options \np{ln\_t3d} and \np{ln\_s3d} switch on the temperature and salinity 79 77 profile observation operator code. The \np{ln\_ena} switch turns on the reading 80 78 of ENACT/ENSEMBLES type profile data. The filename or array of filenames are … … 88 86 Setting \np{ln\_grid\_global} means that the code distributes the observations 89 87 evenly between processors. Alternatively each processor will work with 90 observations located within the model subdomain .91 92 The NEMOVAR system contains utilitiesto plot the feedback files, convert and93 recombine the files. These are available on request from the NEMOVAR team.88 observations located within the model subdomain (see section~\ref{OBS_parallel}). 89 90 A number of utilities are now provided to plot the feedback files, convert and 91 recombine the files. These are explained in more detail in section~\ref{OBS_obsutils}. 94 92 95 93 \section{Technical details} … … 713 711 714 712 \subsection{Parallel aspects of horizontal interpolation} 713 \label{OBS_parallel} 715 714 716 715 For horizontal interpolation, there is the basic problem that the … … 779 778 \subsection{Vertical interpolation operator} 780 779 781 The vertical interpolation is achieved using either a cubic spline or780 Vertical interpolation is achieved using either a cubic spline or 782 781 linear interpolation. For the cubic spline, the top and 783 782 bottom boundary conditions for the second derivative of the 784 783 interpolating polynomial in the spline are set to zero. 785 784 At the bottom boundary, this is done using the land-ocean mask. 785 786 \newpage 787 788 \section{Observation Utilities} 789 \label{OBS_obsutils} 790 791 Some tools for viewing and processing of observation and feedback files are provided in the 792 NEMO repository for convenience. These include OBSTOOLS which are a collection of Fortran 793 programs which are helpful to deal with feedback files. They do such tasks as observation file 794 conversion, printing of file contents, some basic statistical analysis of feedback files. The 795 other tool is an IDL program called dataplot which uses a graphical interface to visualise 796 observations and feedback files. OBSTOOLS and dataplot are described in more detail below. 797 798 \subsection{Obstools} 799 800 A series of Fortran utilities is provided with NEMO called OBSTOOLS. This are helpful in 801 handling observation files and the feedback file output from the NEMO observation operator. 802 The utilities are as follows 803 804 \subsubsection{corio2fb} 805 806 The program corio2fb converts profile observation files from the Coriolis format to the 807 standard feedback format. The program is called in the following way: 808 809 \begin{alltt} 810 \footnotesize 811 \begin{verbatim} 812 corio2fb.exe outputfile inputfile1 inputfile2 ... 813 \end{verbatim} 814 \end{alltt} 815 816 \subsubsection{enact2fb} 817 818 The program enact2fb converts profile observation files from the ENACT format to the standard 819 feedback format. The program is called in the following way: 820 821 \begin{alltt} 822 \footnotesize 823 \begin{verbatim} 824 enact2fb.exe outputfile inputfile1 inputfile2 ... 825 \end{verbatim} 826 \end{alltt} 827 828 \subsubsection{fbcomb} 829 830 The program fbcomb combines multiple feedback files produced by individual processors in an 831 MPI run of NEMO into a single feedback file. The program is called in the following way: 832 833 \begin{alltt} 834 \footnotesize 835 \begin{verbatim} 836 fbcomb.exe outputfile inputfile1 inputfile2 ... 837 \end{verbatim} 838 \end{alltt} 839 840 \subsubsection{fbmatchup} 841 842 The program fbmatchup will match observations from two feedback files. The program is called 843 in the following way: 844 845 \begin{alltt} 846 \footnotesize 847 \begin{verbatim} 848 fbmatchup.exe outputfile inputfile1 varname1 inputfile2 varname2 ... 849 \end{verbatim} 850 \end{alltt} 851 852 853 \subsubsection{fbprint} 854 855 The program fbprint will print the contents of a feedback file or files to standard output. 856 Selected information can be output using optional arguments. The program is called in the 857 following way: 858 859 \begin{alltt} 860 \footnotesize 861 \begin{verbatim} 862 fbprint.exe [options] inputfile 863 864 options: 865 -b shorter output 866 -q Select observations based on QC flags 867 -Q Select observations based on QC flags 868 -B Select observations based on QC flags 869 -u unsorted 870 -s ID select station ID 871 -t TYPE select observation type 872 -v NUM1-NUM2 select variable range to print by number 873 (default all) 874 -a NUM1-NUM2 select additional variable range to print by number 875 (default all) 876 -e NUM1-NUM2 select extra variable range to print by number 877 (default all) 878 -d output date range 879 -D print depths 880 -z use zipped files 881 \end{verbatim} 882 \end{alltt} 883 884 \subsubsection{fbsel} 885 886 The program fbsel will select or subsample observations. The program is called in the 887 following way: 888 889 \begin{alltt} 890 \footnotesize 891 \begin{verbatim} 892 fbsel.exe <input filename> <output filename> 893 \end{verbatim} 894 \end{alltt} 895 896 \subsubsection{fbstat} 897 898 The program fbstat will output summary statistics in different global areas into a number of 899 files. The program is called in the following way: 900 901 \begin{alltt} 902 \footnotesize 903 \begin{verbatim} 904 fbstat.exe [-nmlev] <filenames> 905 \end{verbatim} 906 \end{alltt} 907 908 \subsubsection{fbthin} 909 910 The program fbthin will thin the data to 1 degree resolution. The code could easily be 911 modified to thin to a different resolution. The program is called in the following way: 912 913 \begin{alltt} 914 \footnotesize 915 \begin{verbatim} 916 fbthin.exe inputfile outputfile 917 \end{verbatim} 918 \end{alltt} 919 920 \subsubsection{sla2fb} 921 922 The program sla2fb will convert an AVISO SLA format file to feedback format. The program is 923 called in the following way: 924 925 \begin{alltt} 926 \footnotesize 927 \begin{verbatim} 928 sla2fb.exe [-s type] outputfile inputfile1 inputfile2 ... 929 930 Option: 931 -s Select altimeter data_source 932 \end{verbatim} 933 \end{alltt} 934 935 \subsubsection{vel2fb} 936 937 The program vel2fb will convert TAO/PIRATA/RAMA currents files to feedback format. The program 938 is called in the following way: 939 940 \begin{alltt} 941 \footnotesize 942 \begin{verbatim} 943 vel2fb.exe outputfile inputfile1 inputfile2 ... 944 \end{verbatim} 945 \end{alltt} 946 947 \subsection{building the obstools} 948 949 To build the obstools use in the tools directory use ./maketools -n OBSTOOLS -m [ARCH]. 950 951 \subsection{Dataplot} 952 953 An IDL program called dataplot is included which uses a graphical interface to visualise 954 observations and feedback files. It is possible to zoom in, plot individual profiles and 955 calculate some basic statistics. To plot some data run IDL and then: 956 \begin{alltt} 957 \footnotesize 958 \begin{verbatim} 959 IDL> dataplot, "filename" 960 \end{verbatim} 961 \end{alltt} 962 963 To read multiple files into dataplot, for example multiple feedback files from different 964 processors or from different days, the easiest method is to use the spawn command to generate 965 a list of files which can then be passed to dataplot. 966 \begin{alltt} 967 \footnotesize 968 \begin{verbatim} 969 IDL> spawn, 'ls profb*.nc', files 970 IDL> dataplot, files 971 \end{verbatim} 972 \end{alltt} 973 974 Fig~\ref{fig:obsdataplotmain} shows the main window which is launched when dataplot starts. 975 This is split into three parts. At the top there is a menu bar which contains a variety of 976 drop down menus. Areas - zooms into prespecified regions; plot - plots the data as a 977 timeseries or a T-S diagram if appropriate; Find - allows data to be searched; Config - sets 978 various configuration options. 979 980 The middle part is a plot of the geographical location of the observations. This will plot the 981 observation value, the model background value or observation minus background value depending 982 on the option selected in the radio button at the bottom of the window. The plotting colour 983 range can be changed by clicking on the colour bar. The title of the plot gives some basic 984 information about the date range and depth range shown, the extreme values, and the mean and 985 rms values. It is possible to zoom in using a drag-box. You may also zoom in or out using the 986 mouse wheel. 987 988 The bottom part of the window controls what is visible in the plot above. There are two bars 989 which select the level range plotted (for profile data). The other bars below select the date 990 range shown. The bottom of the figure allows the option to plot the mean, root mean square, 991 standard deviation or mean square values. As mentioned above you can choose to plot the 992 observation value, the model background value or observation minus background value. The next 993 group of radio buttons selects the map projection. This can either be regular latitude 994 longitude grid, or north or south polar stereographic. The next group of radio buttons will 995 plot bad observations, switch to salinity and plot density for profile observations. The 996 rightmost group of buttons will print the plot window as a postscript, save it as png, or exit 997 from dataplot. 998 999 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1000 \begin{figure} \begin{center} 1001 %\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 1002 \includegraphics[width=9cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 1003 \caption{ \label{fig:obsdataplotmain} 1004 Main window of dataplot.} 1005 \end{center} \end{figure} 1006 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1007 1008 If a profile point is clicked with the mouse button a plot of the observation and background 1009 values as a function of depth (Fig~\ref{fig:obsdataplotprofile}). 1010 1011 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1012 \begin{figure} \begin{center} 1013 %\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 1014 \includegraphics[width=7cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 1015 \caption{ \label{fig:obsdataplotprofile} 1016 Profile plot from dataplot produced by right clicking on a point in the main window.} 1017 \end{center} \end{figure} 1018 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1019 1020 1021 1022
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