Changeset 11596 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex
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NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex (modified) (26 diffs)
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NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex
r11584 r11596 2 2 3 3 \begin{document} 4 % ================================================================5 % Chapter I/O & Diagnostics6 % ================================================================7 4 \chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)} 8 5 \label{chap:DIA} … … 23 20 \end{figure} 24 21 25 \newpage26 27 % ================================================================28 % Old Model Output29 % ================================================================30 22 \section{Model output} 31 23 \label{sec:DIA_io_old} … … 53 45 %\gmcomment{ % start of gmcomment 54 46 55 % ================================================================56 % Diagnostics57 % ================================================================58 47 \section{Standard model output (IOM)} 59 48 \label{sec:DIA_iom} … … 64 53 65 54 \begin{enumerate} 66 \item 67 The complete and flexible control of the output files through external XML files adapted by 55 \item The complete and flexible control of the output files through external XML files adapted by 68 56 the user from standard templates. 69 \item 70 To achieve high performance and scalable output through the optional distribution of 57 \item To achieve high performance and scalable output through the optional distribution of 71 58 all diagnostic output related tasks to dedicated processes. 72 59 \end{enumerate} … … 76 63 77 64 \begin{itemize} 78 \item 79 The choice of output frequencies that can be different for each file (including real months and years). 80 \item 81 The choice of file contents; includes complete flexibility over which data are written in which files 65 \item The choice of output frequencies that can be different for each file (including real months and years). 66 \item The choice of file contents; includes complete flexibility over which data are written in which files 82 67 (the same data can be written in different files). 83 \item 84 The possibility to split output files at a chosen frequency. 85 \item 86 The possibility to extract a vertical or an horizontal subdomain. 87 \item 88 The choice of the temporal operation to perform, \eg: average, accumulate, instantaneous, min, max and once. 89 \item 90 Control over metadata via a large XML "database" of possible output fields. 68 \item The possibility to split output files at a chosen frequency. 69 \item The possibility to extract a vertical or an horizontal subdomain. 70 \item The choice of the temporal operation to perform, \eg: average, accumulate, instantaneous, min, max and once. 71 \item Control over metadata via a large XML "database" of possible output fields. 91 72 \end{itemize} 92 73 … … 150 131 If an additional variable must be written to a restart file, the following steps are needed: 151 132 \begin{description} 152 \item [step 1:] add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and133 \item [step 1:] add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and 153 134 define correct grid for the variable (\forcode{grid_N_3D} - 3D variable, \forcode{grid_N} - 2D variable, \forcode{grid_vector} - 154 135 1D variable, \forcode{grid_scalar} - scalar), 155 \item [step 2:] add variable to the list of fields written by restart. This can be done either in subroutine136 \item [step 2:] add variable to the list of fields written by restart. This can be done either in subroutine 156 137 \rou{iom\_set\_rstw\_core} (\mdl{iom}) or by calling \rou{iom\_set\_rstw\_active} (\mdl{iom}) with the name of a variable 157 138 as an argument. This convention follows approach for writing restart using iom, where variables are … … 159 140 \end{description} 160 141 161 162 142 An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451. 163 164 143 165 144 \subsection{XIOS: XML Inputs-Outputs Server} … … 276 255 277 256 \begin{enumerate} 278 \item [1.]257 \item [1.] 279 258 in \NEMO\ code, add a \forcode{CALL iom_put( 'identifier', array )} where you want to output a 2D or 3D array. 280 \item [2.]259 \item [2.] 281 260 If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in 282 261 the upper part of your module. 283 \item [3.]262 \item [3.] 284 263 in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code 285 264 (see subsequent sections for a details of the XML syntax and rules). … … 310 289 \xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations 311 290 (iom\_set\_field\_attr in \mdl{iom}) 312 \item [4.]291 \item [4.] 313 292 add your field in one of the output files defined in iodef.xml 314 293 (again see subsequent sections for syntax and rules) … … 737 716 738 717 \begin{enumerate} 739 \item 740 Simple computation: directly define the computation when refering to the variable in the file definition. 718 \item Simple computation: directly define the computation when refering to the variable in the file definition. 741 719 742 720 \begin{xmllines} … … 746 724 \end{xmllines} 747 725 748 \item 749 Simple computation: define a new variable and use it in the file definition. 726 \item Simple computation: define a new variable and use it in the file definition. 750 727 751 728 in field\_definition: … … 764 741 sst2 won't be evaluated. 765 742 766 \item 767 Change of variable precision: 743 \item Change of variable precision: 768 744 769 745 \begin{xmllines} … … 778 754 Forcing double precision outputs with prec="8" (for example in the field\_definition) will avoid this problem. 779 755 780 \item 781 add user defined attributes: 756 \item add user defined attributes: 782 757 783 758 \begin{xmllines} … … 794 769 \end{xmllines} 795 770 796 \item 797 use of the ``@'' function: example 1, weighted temporal average 771 \item use of the ``@'' function: example 1, weighted temporal average 798 772 799 773 - define a new variable in field\_definition … … 823 797 Note that in this case, freq\_op must be equal to the file output\_freq. 824 798 825 \item 826 use of the ``@'' function: example 2, monthly SSH standard deviation 799 \item use of the ``@'' function: example 2, monthly SSH standard deviation 827 800 828 801 - define a new variable in field\_definition … … 854 827 Note that in this case, freq\_op must be equal to the file output\_freq. 855 828 856 \item 857 use of the ``@'' function: example 3, monthly average of SST diurnal cycle 829 \item use of the ``@'' function: example 3, monthly average of SST diurnal cycle 858 830 859 831 - define 2 new variables in field\_definition … … 1326 1298 This must be set to true if these metadata are to be included in the output files. 1327 1299 1328 1329 % ================================================================1330 % NetCDF4 support1331 % ================================================================1332 1300 \section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})]{NetCDF4 support (\protect\key{netcdf4})} 1333 1301 \label{sec:DIA_nc4} … … 1446 1414 the invidual processing regions and different chunking choices may be desired. 1447 1415 1448 % -------------------------------------------------------------------------------------------------------------1449 % Tracer/Dynamics Trends1450 % -------------------------------------------------------------------------------------------------------------1451 1416 \section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd}{trd})} 1452 1417 \label{sec:DIA_trd} … … 1470 1435 1471 1436 \begin{description} 1472 \item [{\np{ln_glo_trd}{ln\_glo\_trd}}]:1437 \item [{\np{ln_glo_trd}{ln\_glo\_trd}}]: 1473 1438 at each \np{nn_trd}{nn\_trd} time-step a check of the basin averaged properties of 1474 1439 the momentum and tracer equations is performed. 1475 1440 This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$, 1476 1441 and potential energy time evolution equations properties; 1477 \item [{\np{ln_dyn_trd}{ln\_dyn\_trd}}]:1442 \item [{\np{ln_dyn_trd}{ln\_dyn\_trd}}]: 1478 1443 each 3D trend of the evolution of the two momentum components is output; 1479 \item [{\np{ln_dyn_mxl}{ln\_dyn\_mxl}}]:1444 \item [{\np{ln_dyn_mxl}{ln\_dyn\_mxl}}]: 1480 1445 each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output; 1481 \item [{\np{ln_vor_trd}{ln\_vor\_trd}}]:1446 \item [{\np{ln_vor_trd}{ln\_vor\_trd}}]: 1482 1447 a vertical summation of the moment tendencies is performed, 1483 1448 then the curl is computed to obtain the barotropic vorticity tendencies which are output; 1484 \item [{\np{ln_KE_trd}{ln\_KE\_trd}}] :1449 \item [{\np{ln_KE_trd}{ln\_KE\_trd}}] : 1485 1450 each 3D trend of the Kinetic Energy equation is output; 1486 \item [{\np{ln_tra_trd}{ln\_tra\_trd}}]:1451 \item [{\np{ln_tra_trd}{ln\_tra\_trd}}]: 1487 1452 each 3D trend of the evolution of temperature and salinity is output; 1488 \item [{\np{ln_tra_mxl}{ln\_tra\_mxl}}]:1453 \item [{\np{ln_tra_mxl}{ln\_tra\_mxl}}]: 1489 1454 each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output; 1490 1455 \end{description} … … 1497 1462 and none of the options have been tested with variable volume (\ie\ \np[=.true.]{ln_linssh}{ln\_linssh}). 1498 1463 1499 % -------------------------------------------------------------------------------------------------------------1500 % On-line Floats trajectories1501 % -------------------------------------------------------------------------------------------------------------1502 1464 \section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})]{FLO: On-Line Floats trajectories (\protect\key{floats})} 1503 1465 \label{sec:DIA_FLO} … … 1602 1564 \end{xmllines} 1603 1565 1604 1605 % -------------------------------------------------------------------------------------------------------------1606 % Harmonic analysis of tidal constituents1607 % -------------------------------------------------------------------------------------------------------------1608 1566 \section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})]{Harmonic analysis of tidal constituents (\protect\key{diaharm})} 1609 1567 \label{sec:DIA_diag_harm} … … 1654 1612 We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave. 1655 1613 1656 % -------------------------------------------------------------------------------------------------------------1657 % Sections transports1658 % -------------------------------------------------------------------------------------------------------------1659 1614 \section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})} 1660 1615 \label{sec:DIA_diag_dct} … … 1800 1755 \end{table} 1801 1756 1802 % ================================================================1803 % Steric effect in sea surface height1804 % ================================================================1805 1757 \section{Diagnosing the steric effect in sea surface height} 1806 1758 \label{sec:DIA_steric} 1807 1808 1759 1809 1760 Changes in steric sea level are caused when changes in the density of the water column imply an expansion or … … 1980 1931 Both steric and thermosteric sea level are computed in \mdl{diaar5}. 1981 1932 1982 % -------------------------------------------------------------------------------------------------------------1983 % Other Diagnostics1984 % -------------------------------------------------------------------------------------------------------------1985 1933 \section{Other diagnostics} 1986 1934 \label{sec:DIA_diag_others} … … 2001 1949 - the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) 2002 1950 2003 2004 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>2005 1951 \begin{figure}[!t] 2006 1952 \centering … … 2019 1965 \label{fig:DIA_mask_subasins} 2020 1966 \end{figure} 2021 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>2022 1967 2023 1968 % -----------------------------------------------------------
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