[9389] | 1 | \documentclass[../tex_main/NEMO_manual]{subfiles} |
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[6997] | 2 | \begin{document} |
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[2541] | 3 | % ================================================================ |
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[4153] | 4 | % Chapter I/O & Diagnostics |
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[2541] | 5 | % ================================================================ |
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[6140] | 6 | \chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)} |
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[9407] | 7 | \label{chap:DIA} |
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[2541] | 8 | \minitoc |
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| 9 | |
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| 10 | \newpage |
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[6140] | 11 | $\ $\newline % force a new line |
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[2541] | 12 | |
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| 13 | % ================================================================ |
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| 14 | % Old Model Output |
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| 15 | % ================================================================ |
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[9393] | 16 | \section{Old model output (default)} |
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[9407] | 17 | \label{sec:DIA_io_old} |
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[2541] | 18 | |
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[10368] | 19 | The model outputs are of three types: the restart file, the output listing, and the diagnostic output file(s). |
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| 20 | The restart file is used internally by the code when the user wants to start the model with |
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[9413] | 21 | initial conditions defined by a previous simulation. |
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[10368] | 22 | It contains all the information that is necessary in order for there to be no changes in the model results |
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| 23 | (even at the computer precision) between a run performed with several restarts and |
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[9413] | 24 | the same run performed in one step. |
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[10368] | 25 | It should be noted that this requires that the restart file contains two consecutive time steps for |
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| 26 | all the prognostic variables, and that it is saved in the same binary format as the one used by the computer that |
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| 27 | is to read it (in particular, 32 bits binary IEEE format must not be used for this file). |
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[4153] | 28 | |
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[10368] | 29 | The output listing and file(s) are predefined but should be checked and eventually adapted to the user's needs. |
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[9413] | 30 | The output listing is stored in the $ocean.output$ file. |
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| 31 | The information is printed from within the code on the logical unit $numout$. |
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| 32 | To locate these prints, use the UNIX command "\textit{grep -i numout}" in the source code directory. |
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[2541] | 33 | |
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[9413] | 34 | By default, diagnostic output files are written in NetCDF format. |
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[10368] | 35 | Since version 3.2, when defining \key{iomput}, an I/O server has been added which |
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| 36 | provides more flexibility in the choice of the fields to be written as well as how |
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| 37 | the writing work is distributed over the processors in massively parallel computing. |
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| 38 | A complete description of the use of this I/O server is presented in the next section. |
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[2541] | 39 | |
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[10368] | 40 | By default, \key{iomput} is not defined, |
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| 41 | NEMO produces NetCDF with the old IOIPSL library which has been kept for compatibility and its easy installation. |
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| 42 | However, the IOIPSL library is quite inefficient on parallel machines and, since version 3.2, |
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| 43 | many diagnostic options have been added presuming the use of \key{iomput}. |
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| 44 | The usefulness of the default IOIPSL-based option is expected to reduce with each new release. |
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| 45 | If \key{iomput} is not defined, output files and content are defined in the \mdl{diawri} module and |
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| 46 | contain mean (or instantaneous if \key{diainstant} is defined) values over a regular period of |
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[9413] | 47 | nn\_write time-steps (namelist parameter). |
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[4153] | 48 | |
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[2541] | 49 | %\gmcomment{ % start of gmcomment |
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| 50 | |
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| 51 | % ================================================================ |
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| 52 | % Diagnostics |
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| 53 | % ================================================================ |
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[9393] | 54 | \section{Standard model output (IOM)} |
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[9407] | 55 | \label{sec:DIA_iom} |
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[2541] | 56 | |
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[10368] | 57 | Since version 3.2, iomput is the NEMO output interface of choice. |
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| 58 | It has been designed to be simple to use, flexible and efficient. |
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[6289] | 59 | The two main purposes of iomput are: |
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[9413] | 60 | |
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[4153] | 61 | \begin{enumerate} |
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[10368] | 62 | \item |
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| 63 | The complete and flexible control of the output files through external XML files adapted by |
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| 64 | the user from standard templates. |
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| 65 | \item |
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| 66 | To achieve high performance and scalable output through the optional distribution of |
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| 67 | all diagnostic output related tasks to dedicated processes. |
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[4153] | 68 | \end{enumerate} |
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[9413] | 69 | |
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[6289] | 70 | The first functionality allows the user to specify, without code changes or recompilation, |
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| 71 | aspects of the diagnostic output stream, such as: |
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[9413] | 72 | |
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[4153] | 73 | \begin{itemize} |
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[10368] | 74 | \item |
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| 75 | The choice of output frequencies that can be different for each file (including real months and years). |
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| 76 | \item |
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| 77 | The choice of file contents; includes complete flexibility over which data are written in which files |
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| 78 | (the same data can be written in different files). |
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| 79 | \item |
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| 80 | The possibility to split output files at a chosen frequency. |
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| 81 | \item |
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| 82 | The possibility to extract a vertical or an horizontal subdomain. |
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| 83 | \item |
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| 84 | The choice of the temporal operation to perform, $e.g.$: average, accumulate, instantaneous, min, max and once. |
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| 85 | \item |
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| 86 | Control over metadata via a large XML "database" of possible output fields. |
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[4153] | 87 | \end{itemize} |
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[2541] | 88 | |
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[10368] | 89 | In addition, iomput allows the user to add in the code the output of any new variable (scalar, 2D or 3D) |
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| 90 | in a very easy way. |
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[9413] | 91 | All details of iomput functionalities are listed in the following subsections. |
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[10368] | 92 | Examples of the XML files that control the outputs can be found in: \path{NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml}, |
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| 93 | \path{NEMOGCM/CONFIG/SHARED/field_def.xml} and \path{NEMOGCM/CONFIG/SHARED/domain_def.xml}. \\ |
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[2541] | 94 | |
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[9413] | 95 | The second functionality targets output performance when running in parallel (\key{mpp\_mpi}). |
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[10368] | 96 | Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO processes) |
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| 97 | to collect and write the outputs. |
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| 98 | With an appropriate choice of N by the user, the bottleneck associated with the writing of |
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[9413] | 99 | the output files can be greatly reduced. |
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| 100 | |
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[10368] | 101 | In version 3.6, the iom\_put interface depends on |
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| 102 | an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/branchs/xios-1.0}{XIOS-1.0} |
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[9413] | 103 | (use of revision 618 or higher is required). |
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[10368] | 104 | This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to |
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[9413] | 105 | create a single output file and therefore to bypass the rebuilding phase. |
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[10368] | 106 | Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to |
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| 107 | an HDF5 library that has been correctly compiled ($i.e.$ with the configure option $--$enable-parallel). |
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[9413] | 108 | Note that the files created by iomput through XIOS are incompatible with NetCDF3. |
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[10368] | 109 | All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3. |
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[2541] | 110 | |
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[10368] | 111 | Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers, |
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| 112 | where N is typically much less than the number of NEMO processors, will reduce the number of output files created. |
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| 113 | This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors. |
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| 114 | Note that for smaller configurations, the rebuilding phase can be avoided, |
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| 115 | even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server. |
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[2541] | 116 | |
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[9393] | 117 | \subsection{XIOS: XML Inputs-Outputs Server} |
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[4153] | 118 | |
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| 119 | \subsubsection{Attached or detached mode?} |
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| 120 | |
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[10368] | 121 | Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS}, |
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[9413] | 122 | the io\_server developed by Yann Meurdesoif from IPSL. |
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| 123 | The behaviour of the I/O subsystem is controlled by settings in the external XML files listed above. |
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| 124 | Key settings in the iodef.xml file are the tags associated with each defined file. |
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| 125 | |
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| 126 | \xmlline|<variable id="using_server" type="bool"></variable>| |
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| 127 | |
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[10368] | 128 | The {\tt using\_server} setting determines whether or not the server will be used in \textit{attached mode} |
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| 129 | (as a library) [{\tt> false <}] or in \textit{detached mode} |
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| 130 | (as an external executable on N additional, dedicated cpus) [{\tt > true <}]. |
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[9413] | 131 | The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications. |
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[6289] | 132 | The type of each file can be either ''multiple\_file'' or ''one\_file''. |
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[4153] | 133 | |
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[10368] | 134 | In \textit{attached mode} and if the type of file is ''multiple\_file'', |
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[9413] | 135 | then each NEMO process will also act as an IO server and produce its own set of output files. |
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| 136 | Superficially, this emulates the standard behaviour in previous versions. |
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[10368] | 137 | However, the subdomain written out by each process does not correspond to |
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[9413] | 138 | the \forcode{jpi x jpj x jpk} domain actually computed by the process (although it may if \forcode{jpni=1}). |
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| 139 | Instead each process will have collected and written out a number of complete longitudinal strips. |
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[10368] | 140 | If the ''one\_file'' option is chosen then all processes will collect their longitudinal strips and |
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[9413] | 141 | write (in parallel) to a single output file. |
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[4153] | 142 | |
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[10368] | 143 | In \textit{detached mode} and if the type of file is ''multiple\_file'', |
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| 144 | then each stand-alone XIOS process will collect data for a range of complete longitudinal strips and |
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[9413] | 145 | write to its own set of output files. |
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[10368] | 146 | If the ''one\_file'' option is chosen then all XIOS processes will collect their longitudinal strips and |
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[9413] | 147 | write (in parallel) to a single output file. |
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| 148 | Note running in detached mode requires launching a Multiple Process Multiple Data (MPMD) parallel job. |
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[10368] | 149 | The following subsection provides a typical example but the syntax will vary in different MPP environments. |
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[4153] | 150 | |
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| 151 | \subsubsection{Number of cpu used by XIOS in detached mode} |
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| 152 | |
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[9413] | 153 | The number of cores used by the XIOS is specified when launching the model. |
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| 154 | The number of cores dedicated to XIOS should be from \texttildelow1/10 to \texttildelow1/50 of the number of |
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| 155 | cores dedicated to NEMO. |
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[10368] | 156 | Some manufacturers suggest using O($\sqrt{N}$) dedicated IO processors for N processors but |
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[9413] | 157 | this is a general recommendation and not specific to NEMO. |
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[10368] | 158 | It is difficult to provide precise recommendations because the optimal choice will depend on |
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[9413] | 159 | the particular hardware properties of the target system |
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[10368] | 160 | (parallel filesystem performance, available memory, memory bandwidth etc.) |
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| 161 | and the volume and frequency of data to be created. |
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[6289] | 162 | Here is an example of 2 cpus for the io\_server and 62 cpu for nemo using mpirun: |
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[9413] | 163 | \cmd|mpirun -np 62 ./nemo.exe : -np 2 ./xios_server.exe| |
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[4153] | 164 | |
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[9393] | 165 | \subsubsection{Control of XIOS: the context in iodef.xml} |
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[4153] | 166 | |
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[10368] | 167 | As well as the {\tt using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml. |
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[6289] | 168 | See the XML basics section below for more details on XML syntax and rules. |
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[4153] | 169 | |
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[9413] | 170 | \begin{table} \scriptsize |
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| 171 | \begin{tabularx}{\textwidth}{|lXl|} \hline |
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| 172 | variable name & |
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| 173 | description & |
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| 174 | example \\ \hline \hline |
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| 175 | buffer\_size & |
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| 176 | buffer size used by XIOS to send data from NEMO to XIOS. |
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| 177 | Larger is more efficient. |
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| 178 | Note that needed/used buffer sizes are summarized at the end of the job & |
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| 179 | 25000000 \\ \hline |
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| 180 | buffer\_server\_factor\_size & |
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| 181 | ratio between NEMO and XIOS buffer size. |
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| 182 | Should be 2. & |
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| 183 | 2 \\ \hline |
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| 184 | info\_level & |
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| 185 | verbosity level (0 to 100) & |
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| 186 | 0 \\ \hline |
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| 187 | using\_server & |
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| 188 | activate attached(false) or detached(true) mode & |
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| 189 | true \\ \hline |
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| 190 | using\_oasis & |
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| 191 | XIOS is used with OASIS(true) or not (false) & |
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| 192 | false \\ \hline |
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| 193 | oasis\_codes\_id & |
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| 194 | when using oasis, define the identifier of NEMO in the namcouple. |
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| 195 | Note that the identifier of XIOS is xios.x & |
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| 196 | oceanx \\ \hline |
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| 197 | \end{tabularx} |
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| 198 | \end{table} |
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[4153] | 199 | |
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| 200 | \subsection{Practical issues} |
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| 201 | |
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| 202 | \subsubsection{Installation} |
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| 203 | |
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[10368] | 204 | As mentioned, XIOS is supported separately and must be downloaded and compiled before it can be used with NEMO. |
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| 205 | See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance. |
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[9413] | 206 | NEMO will need to link to the compiled XIOS library. |
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[10368] | 207 | The \href{https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ModelInterfacing/InputsOutputs#Inputs-OutputsusingXIOS} |
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| 208 | {XIOS with NEMO} guide provides an example illustration of how this can be achieved. |
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[4153] | 209 | |
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| 210 | \subsubsection{Add your own outputs} |
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| 211 | |
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[9413] | 212 | It is very easy to add your own outputs with iomput. |
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[10368] | 213 | Many standard fields and diagnostics are already prepared ($i.e.$, steps 1 to 3 below have been done) and |
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[9413] | 214 | simply need to be activated by including the required output in a file definition in iodef.xml (step 4). |
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[6289] | 215 | To add new output variables, all 4 of the following steps must be taken. |
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[4153] | 216 | |
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[9413] | 217 | \begin{enumerate} |
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[10368] | 218 | \item[1.] |
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| 219 | in NEMO code, add a \forcode{CALL iom\_put( 'identifier', array )} where you want to output a 2D or 3D array. |
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| 220 | \item[2.] |
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| 221 | If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in |
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| 222 | the upper part of your module. |
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| 223 | \item[3.] |
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| 224 | in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code |
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| 225 | (see subsequent sections for a details of the XML syntax and rules). |
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| 226 | For example: |
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[4153] | 227 | |
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[9392] | 228 | \begin{xmllines} |
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[9413] | 229 | <field_definition> |
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| 230 | <field_group id="grid_T" grid_ref="grid_T_3D"> <!-- T grid --> |
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| 231 | ... |
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| 232 | <field id="identifier" long_name="blabla" ... /> |
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| 233 | ... |
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| 234 | </field_definition> |
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| 235 | \end{xmllines} |
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[4153] | 236 | |
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[10368] | 237 | Note your definition must be added to the field\_group whose reference grid is consistent with the size of |
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| 238 | the array passed to iomput. |
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| 239 | The grid\_ref attribute refers to definitions set in iodef.xml which, in turn, |
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| 240 | reference grids and axes either defined in the code |
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| 241 | (iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file. |
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[9413] | 242 | $e.g.$: |
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| 243 | |
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[9392] | 244 | \begin{xmllines} |
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[9413] | 245 | <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> |
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[9392] | 246 | \end{xmllines} |
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[9413] | 247 | |
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[10368] | 248 | Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step, |
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[9413] | 249 | add the field definition within the field\_group defined with the id "SBC": |
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[10368] | 250 | \xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations |
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| 251 | (iom\_set\_field\_attr in \mdl{iom}) |
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| 252 | \item[4.] |
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| 253 | add your field in one of the output files defined in iodef.xml |
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| 254 | (again see subsequent sections for syntax and rules) |
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[4153] | 255 | |
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[9392] | 256 | \begin{xmllines} |
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[9413] | 257 | <file id="file1" .../> |
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| 258 | ... |
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| 259 | <field field_ref="identifier" /> |
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| 260 | ... |
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| 261 | </file> |
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[9392] | 262 | \end{xmllines} |
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[4153] | 263 | |
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[9413] | 264 | \end{enumerate} |
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[9393] | 265 | |
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[4153] | 266 | \subsection{XML fundamentals} |
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| 267 | |
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[2541] | 268 | \subsubsection{ XML basic rules} |
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| 269 | |
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[9413] | 270 | XML tags begin with the less-than character ("$<$") and end with the greater-than character ("$>$"). |
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[10368] | 271 | You use tags to mark the start and end of elements, which are the logical units of information in an XML document. |
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| 272 | In addition to marking the beginning of an element, XML start tags also provide a place to specify attributes. |
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| 273 | An attribute specifies a single property for an element, using a name/value pair, for example: |
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[9413] | 274 | \xmlcode{<a b="x" c="y" d="z"> ... </a>}. |
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[2541] | 275 | See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details. |
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| 276 | |
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[9393] | 277 | \subsubsection{Structure of the XML file used in NEMO} |
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[2541] | 278 | |
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[10368] | 279 | The XML file used in XIOS is structured by 7 families of tags: |
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[9413] | 280 | context, axis, domain, grid, field, file and variable. |
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[6289] | 281 | Each tag family has hierarchy of three flavors (except for context): |
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[4148] | 282 | |
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[9413] | 283 | \begin{table} \scriptsize |
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| 284 | \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} \hline |
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| 285 | flavor & description & |
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| 286 | example \\ \hline \hline |
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| 287 | root & declaration of the root element that can contain element groups or elements & |
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| 288 | \xmlcode{<file_definition ... >} \\ \hline |
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| 289 | group & declaration of a group element that can contain element groups or elements & |
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| 290 | \xmlcode{<file_group ... >} \\ \hline |
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| 291 | element & declaration of an element that can contain elements & |
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| 292 | \xmlcode{<file ... >} \\ \hline |
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| 293 | \end{tabular*} |
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| 294 | \end{table} |
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| 295 | |
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| 296 | Each element may have several attributes. |
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[10368] | 297 | Some attributes are mandatory, other are optional but have a default value and other are completely optional. |
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[9413] | 298 | Id is a special attribute used to identify an element or a group of elements. |
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| 299 | It must be unique for a kind of element. |
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[6289] | 300 | It is optional, but no reference to the corresponding element can be done if it is not defined. |
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[4148] | 301 | |
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[10368] | 302 | The XML file is split into context tags that are used to isolate IO definition from |
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| 303 | different codes or different parts of a code. |
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[9413] | 304 | No interference is possible between 2 different contexts. |
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| 305 | Each context has its own calendar and an associated timestep. |
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| 306 | In \NEMO, we used the following contexts (that can be defined in any order): |
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[4148] | 307 | |
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[9413] | 308 | \begin{table} \scriptsize |
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| 309 | \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} \hline |
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| 310 | context & description & |
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| 311 | example \\ \hline \hline |
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| 312 | context xios & context containing information for XIOS & |
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| 313 | \xmlcode{<context id="xios" ... >} \\ \hline |
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| 314 | context nemo & context containing IO information for NEMO (mother grid when using AGRIF) & |
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| 315 | \xmlcode{<context id="nemo" ... >} \\ \hline |
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| 316 | context 1\_nemo & context containing IO information for NEMO child grid 1 (when using AGRIF) & |
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| 317 | \xmlcode{<context id="1_nemo" ... >} \\ \hline |
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| 318 | context n\_nemo & context containing IO information for NEMO child grid n (when using AGRIF) & |
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| 319 | \xmlcode{<context id="n_nemo" ... >} \\ \hline |
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| 320 | \end{tabular} |
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| 321 | \end{table} |
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| 322 | |
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[4153] | 323 | \noindent The xios context contains only 1 tag: |
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[2541] | 324 | |
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[9413] | 325 | \begin{table} \scriptsize |
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| 326 | \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} \hline |
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| 327 | context tag & |
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| 328 | description & |
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| 329 | example \\ \hline \hline |
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| 330 | variable\_definition & |
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| 331 | define variables needed by XIOS. |
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| 332 | This can be seen as a kind of namelist for XIOS. & |
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| 333 | \xmlcode{<variable_definition ... >} \\ \hline |
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| 334 | \end{tabular} |
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| 335 | \end{table} |
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| 336 | |
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[6289] | 337 | \noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts |
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[9413] | 338 | (that can be defined in any order): |
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[2541] | 339 | |
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[9413] | 340 | \begin{table} \scriptsize |
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| 341 | \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} \hline |
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| 342 | context tag & description & |
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| 343 | example \\ \hline \hline |
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| 344 | field\_definition & define all variables that can potentially be outputted & |
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| 345 | \xmlcode{<field_definition ... >} \\ \hline |
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| 346 | file\_definition & define the netcdf files to be created and the variables they will contain & |
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| 347 | \xmlcode{<file_definition ... >} \\ \hline |
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| 348 | axis\_definition & define vertical axis & |
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| 349 | \xmlcode{<axis_definition ... >} \\ \hline |
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| 350 | domain\_definition & define the horizontal grids & |
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| 351 | \xmlcode{<domain_definition ... >} \\ \hline |
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| 352 | grid\_definition & define the 2D and 3D grids (association of an axis and a domain) & |
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| 353 | \xmlcode{<grid_definition ... >} \\ \hline |
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| 354 | \end{tabular} |
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| 355 | \end{table} |
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| 356 | |
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[4153] | 357 | \subsubsection{Nesting XML files} |
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[4148] | 358 | |
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[9413] | 359 | The XML file can be split in different parts to improve its readability and facilitate its use. |
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| 360 | The inclusion of XML files into the main XML file can be done through the attribute src: |
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| 361 | \xmlline|<context src="./nemo_def.xml" />| |
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[4153] | 362 | |
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| 363 | \noindent In NEMO, by default, the field and domain definition is done in 2 separate files: |
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[10368] | 364 | \path{NEMOGCM/CONFIG/SHARED/field_def.xml} and \path{NEMOGCM/CONFIG/SHARED/domain_def.xml} that |
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| 365 | are included in the main iodef.xml file through the following commands: |
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[9413] | 366 | \begin{xmllines} |
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| 367 | <field_definition src="./field_def.xml" /> |
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| 368 | <domain_definition src="./domain_def.xml" /> |
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| 369 | \end{xmllines} |
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[9376] | 370 | |
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[4148] | 371 | \subsubsection{Use of inheritance} |
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| 372 | |
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[9413] | 373 | XML extensively uses the concept of inheritance. |
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[10368] | 374 | XML has a tree based structure with a parent-child oriented relation: all children inherit attributes from parent, |
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| 375 | but an attribute defined in a child replace the inherited attribute value. |
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| 376 | Note that the special attribute ''id'' is never inherited. |
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| 377 | \\ |
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| 378 | \\ |
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[4153] | 379 | example 1: Direct inheritance. |
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[9413] | 380 | |
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[9392] | 381 | \begin{xmllines} |
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[9413] | 382 | <field_definition operation="average" > |
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| 383 | <field id="sst" /> <!-- averaged sst --> |
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| 384 | <field id="sss" operation="instant"/> <!-- instantaneous sss --> |
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| 385 | </field_definition> |
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[9392] | 386 | \end{xmllines} |
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[9413] | 387 | |
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[10368] | 388 | The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average'' of |
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| 389 | the attribute ''operation'' from its parent. |
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[9413] | 390 | Note that a child can overwrite the attribute definition inherited from its parents. |
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[10368] | 391 | In the example above, the field ''sss'' will for example output instantaneous values instead of average values. |
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| 392 | \\ |
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| 393 | \\ |
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[4153] | 394 | example 2: Inheritance by reference. |
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[9413] | 395 | |
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[9392] | 396 | \begin{xmllines} |
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[9413] | 397 | <field_definition> |
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| 398 | <field id="sst" long_name="sea surface temperature" /> |
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| 399 | <field id="sss" long_name="sea surface salinity" /> |
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| 400 | </field_definition> |
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| 401 | <file_definition> |
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| 402 | <file id="myfile" output_freq="1d" /> |
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| 403 | <field field_ref="sst" /> <!-- default def --> |
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| 404 | <field field_ref="sss" long_name="my description" /> <!-- overwrite --> |
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| 405 | </file> |
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| 406 | </file_definition> |
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| 407 | \end{xmllines} |
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[2541] | 408 | |
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[4153] | 409 | Inherit (and overwrite, if needed) the attributes of a tag you are refering to. |
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[2541] | 410 | |
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[9393] | 411 | \subsubsection{Use of groups} |
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[2541] | 412 | |
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[9413] | 413 | Groups can be used for 2 purposes. |
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[10368] | 414 | Firstly, the group can be used to define common attributes to be shared by the elements of |
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[9413] | 415 | the group through inheritance. |
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| 416 | In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''. |
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[10368] | 417 | Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''. |
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[9413] | 418 | |
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[9392] | 419 | \begin{xmllines} |
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[9413] | 420 | <field_group id="grid_T" grid_ref="grid_T_2D"> |
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| 421 | <field id="toce" long_name="temperature" unit="degC" grid_ref="grid_T_3D"/> |
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| 422 | <field id="sst" long_name="sea surface temperature" unit="degC" /> |
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| 423 | <field id="sss" long_name="sea surface salinity" unit="psu" /> |
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| 424 | <field id="ssh" long_name="sea surface height" unit="m" /> |
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| 425 | ... |
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[9392] | 426 | \end{xmllines} |
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[2541] | 427 | |
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[9413] | 428 | Secondly, the group can be used to replace a list of elements. |
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| 429 | Several examples of groups of fields are proposed at the end of the file \path{CONFIG/SHARED/field_def.xml}. |
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[6289] | 430 | For example, a short list of the usual variables related to the U grid: |
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[9413] | 431 | |
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[9392] | 432 | \begin{xmllines} |
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[9413] | 433 | <field_group id="groupU" > |
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| 434 | <field field_ref="uoce" /> |
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| 435 | <field field_ref="suoce" /> |
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| 436 | <field field_ref="utau" /> |
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| 437 | </field_group> |
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[9392] | 438 | \end{xmllines} |
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[9413] | 439 | |
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[4153] | 440 | that can be directly included in a file through the following syntax: |
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[9413] | 441 | |
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[9392] | 442 | \begin{xmllines} |
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[9413] | 443 | <file id="myfile_U" output_freq="1d" /> |
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| 444 | <field_group group_ref="groupU" /> |
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| 445 | <field field_ref="uocetr_eff" /> <!-- add another field --> |
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| 446 | </file> |
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[9392] | 447 | \end{xmllines} |
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[4148] | 448 | |
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[9413] | 449 | \subsection{Detailed functionalities} |
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[4148] | 450 | |
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[10368] | 451 | The file \path{NEMOGCM/CONFIG/ORCA2_LIM/iodef_demo.xml} provides several examples of the use of |
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[9413] | 452 | the new functionalities offered by the XML interface of XIOS. |
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[4148] | 453 | |
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| 454 | \subsubsection{Define horizontal subdomains} |
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[9413] | 455 | |
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[10368] | 456 | Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of |
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[9413] | 457 | the tag family domain. |
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[6289] | 458 | It must therefore be done in the domain part of the XML file. |
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[9413] | 459 | For example, in \path{CONFIG/SHARED/domain_def.xml}, we provide the following example of a definition of |
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| 460 | a 5 by 5 box with the bottom left corner at point (10,10). |
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| 461 | |
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[9392] | 462 | \begin{xmllines} |
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[9413] | 463 | <domain_group id="grid_T"> |
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| 464 | <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" /> |
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[9392] | 465 | \end{xmllines} |
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[9413] | 466 | |
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[10368] | 467 | The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. |
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[9413] | 468 | For example: |
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| 469 | |
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[9392] | 470 | \begin{xmllines} |
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[9413] | 471 | <file id="myfile_vzoom" output_freq="1d" > |
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| 472 | <field field_ref="toce" domain_ref="myzoom"/> |
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| 473 | </file> |
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[9392] | 474 | \end{xmllines} |
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[9413] | 475 | |
---|
[6289] | 476 | Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain. |
---|
[10368] | 477 | The Equatorial section, the TAO, RAMA and PIRATA moorings are already registered in the code and |
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[9413] | 478 | can therefore be outputted without taking care of their (i,j) position in the grid. |
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| 479 | These predefined domains can be activated by the use of specific domain\_ref: |
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[10368] | 480 | ''EqT'', ''EqU'' or ''EqW'' for the equatorial sections and |
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| 481 | the mooring position for TAO, RAMA and PIRATA followed by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...) |
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[9413] | 482 | |
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[9392] | 483 | \begin{xmllines} |
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[9413] | 484 | <file id="myfile_vzoom" output_freq="1d" > |
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| 485 | <field field_ref="toce" domain_ref="0n180wT"/> |
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| 486 | </file> |
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[9392] | 487 | \end{xmllines} |
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[4148] | 488 | |
---|
[9413] | 489 | Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if |
---|
| 490 | you use the ''multiple\_file'' type for your output files, |
---|
| 491 | you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat, |
---|
| 492 | \href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}). |
---|
| 493 | We are therefore advising to use the ''one\_file'' type in this case. |
---|
| 494 | |
---|
[4148] | 495 | \subsubsection{Define vertical zooms} |
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[9413] | 496 | |
---|
[10368] | 497 | Vertical zooms are defined through the attributs zoom\_begin and zoom\_end of the tag family axis. |
---|
| 498 | It must therefore be done in the axis part of the XML file. |
---|
[9413] | 499 | For example, in \path{NEMOGCM/CONFIG/ORCA2_LIM/iodef_demo.xml}, we provide the following example: |
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| 500 | |
---|
[9392] | 501 | \begin{xmllines} |
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[9413] | 502 | <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" > |
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| 503 | <axis id="deptht" /> |
---|
| 504 | <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" /> |
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[9392] | 505 | \end{xmllines} |
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[9413] | 506 | |
---|
[10368] | 507 | The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. |
---|
[9413] | 508 | For example: |
---|
| 509 | |
---|
[9392] | 510 | \begin{xmllines} |
---|
[9413] | 511 | <file id="myfile_hzoom" output_freq="1d" > |
---|
| 512 | <field field_ref="toce" axis_ref="deptht_myzoom"/> |
---|
| 513 | </file> |
---|
[9392] | 514 | \end{xmllines} |
---|
[4148] | 515 | |
---|
| 516 | \subsubsection{Control of the output file names} |
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| 517 | |
---|
[9413] | 518 | The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. |
---|
| 519 | For example: |
---|
| 520 | |
---|
[9392] | 521 | \begin{xmllines} |
---|
[9413] | 522 | <file_group id="1d" output_freq="1d" name="myfile_1d" > |
---|
| 523 | <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA" --> |
---|
| 524 | ... |
---|
| 525 | </file> |
---|
| 526 | <file id="myfileB" name_suffix="_BBB" > <!-- will create file "myfile_1d_BBB" --> |
---|
| 527 | ... |
---|
| 528 | </file> |
---|
| 529 | </file_group> |
---|
[9392] | 530 | \end{xmllines} |
---|
[2541] | 531 | |
---|
[10368] | 532 | However it is often very convienent to define the file name with the name of the experiment, |
---|
| 533 | the output file frequency and the date of the beginning and the end of the simulation |
---|
[9413] | 534 | (which are informations stored either in the namelist or in the XML file). |
---|
[10368] | 535 | To do so, we added the following rule: |
---|
| 536 | if the id of the tag file is ''fileN'' (where N = 1 to 999 on 1 to 3 digits) or |
---|
| 537 | one of the predefined sections or moorings (see next subsection), |
---|
| 538 | the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by: |
---|
[9413] | 539 | |
---|
| 540 | \begin{table} \scriptsize |
---|
| 541 | \begin{tabularx}{\textwidth}{|lX|} \hline |
---|
| 542 | \centering placeholder string & |
---|
| 543 | automatically replaced by \\ \hline \hline |
---|
| 544 | \centering @expname@ & |
---|
| 545 | the experiment name (from cn\_exp in the namelist) \\ \hline |
---|
| 546 | \centering @freq@ & |
---|
| 547 | output frequency (from attribute output\_freq) \\ \hline |
---|
| 548 | \centering @startdate@ & |
---|
| 549 | starting date of the simulation (from nn\_date0 in the restart or the namelist). \newline |
---|
| 550 | \verb?yyyymmdd? format \\ \hline |
---|
| 551 | \centering @startdatefull@ & |
---|
| 552 | starting date of the simulation (from nn\_date0 in the restart or the namelist). \newline |
---|
| 553 | \verb?yyyymmdd_hh:mm:ss? format \\ \hline |
---|
| 554 | \centering @enddate@ & |
---|
| 555 | ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \newline |
---|
| 556 | \verb?yyyymmdd? format \\ \hline |
---|
| 557 | \centering @enddatefull@ & |
---|
| 558 | ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \newline |
---|
| 559 | \verb?yyyymmdd_hh:mm:ss? format \\ \hline |
---|
| 560 | \end{tabularx} |
---|
| 561 | \end{table} |
---|
| 562 | |
---|
[4153] | 563 | \noindent For example, |
---|
[9413] | 564 | \xmlline|<file id="myfile_hzoom" name="myfile_@expname@_@startdate@_freq@freq@" output_freq="1d" >| |
---|
| 565 | |
---|
[4153] | 566 | \noindent with the namelist: |
---|
[9413] | 567 | \begin{forlines} |
---|
| 568 | cn_exp = "ORCA2" |
---|
| 569 | nn_date0 = 19891231 |
---|
| 570 | ln_rstart = .false. |
---|
| 571 | \end{forlines} |
---|
| 572 | |
---|
[10368] | 573 | \noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d} |
---|
[4148] | 574 | |
---|
[9393] | 575 | \subsubsection{Other controls of the XML attributes from NEMO} |
---|
[4148] | 576 | |
---|
[9413] | 577 | The values of some attributes are defined by subroutine calls within NEMO |
---|
[10368] | 578 | (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in \mdl{iom}). |
---|
| 579 | Any definition given in the XML file will be overwritten. |
---|
| 580 | By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the XML file |
---|
| 581 | (but this is not necessary). |
---|
| 582 | \\ |
---|
[4148] | 583 | |
---|
[10368] | 584 | Here is the list of these attributes: |
---|
| 585 | \\ |
---|
[2541] | 586 | |
---|
[9413] | 587 | \begin{table} \scriptsize |
---|
| 588 | \begin{tabularx}{\textwidth}{|X|c|c|c|} \hline |
---|
| 589 | tag ids affected by automatic definition of some of their attributes & |
---|
| 590 | name attribute & |
---|
| 591 | attribute value \\ \hline \hline |
---|
| 592 | field\_definition & |
---|
| 593 | freq\_op & |
---|
| 594 | \np{rn\_rdt} \\ \hline |
---|
| 595 | SBC & |
---|
| 596 | freq\_op & |
---|
| 597 | \np{rn\_rdt} $\times$ \np{nn\_fsbc} \\ \hline |
---|
| 598 | ptrc\_T & |
---|
| 599 | freq\_op & |
---|
| 600 | \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ \hline |
---|
| 601 | diad\_T & |
---|
| 602 | freq\_op & |
---|
| 603 | \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ \hline |
---|
| 604 | EqT, EqU, EqW & |
---|
| 605 | jbegin, ni, & |
---|
| 606 | according to the grid \\ |
---|
| 607 | & |
---|
| 608 | name\_suffix & |
---|
| 609 | \\ \hline |
---|
| 610 | TAO, RAMA and PIRATA moorings & |
---|
| 611 | zoom\_ibegin, zoom\_jbegin, & |
---|
| 612 | according to the grid \\ |
---|
| 613 | & |
---|
| 614 | name\_suffix & |
---|
| 615 | \\ \hline |
---|
| 616 | \end{tabularx} |
---|
| 617 | \end{table} |
---|
| 618 | |
---|
[5107] | 619 | \subsubsection{Advanced use of XIOS functionalities} |
---|
[2541] | 620 | |
---|
[4153] | 621 | \subsection{XML reference tables} |
---|
[9407] | 622 | \label{subsec:IOM_xmlref} |
---|
[4153] | 623 | |
---|
[9413] | 624 | \begin{enumerate} |
---|
[10368] | 625 | \item |
---|
| 626 | Simple computation: directly define the computation when refering to the variable in the file definition. |
---|
[5107] | 627 | |
---|
[9392] | 628 | \begin{xmllines} |
---|
[9413] | 629 | <field field_ref="sst" name="tosK" unit="degK" > sst + 273.15 </field> |
---|
| 630 | <field field_ref="taum" name="taum2" unit="N2/m4" long_name="square of wind stress module" > taum * taum </field> |
---|
| 631 | <field field_ref="qt" name="stupid_check" > qt - qsr - qns </field> |
---|
[9392] | 632 | \end{xmllines} |
---|
[5107] | 633 | |
---|
[10368] | 634 | \item |
---|
| 635 | Simple computation: define a new variable and use it in the file definition. |
---|
[5107] | 636 | |
---|
| 637 | in field\_definition: |
---|
[9413] | 638 | |
---|
[9392] | 639 | \begin{xmllines} |
---|
[9413] | 640 | <field id="sst2" long_name="square of sea surface temperature" unit="degC2" > sst * sst </field > |
---|
[9392] | 641 | \end{xmllines} |
---|
[9413] | 642 | |
---|
[5107] | 643 | in file\_definition: |
---|
[9413] | 644 | |
---|
[9392] | 645 | \begin{xmllines} |
---|
[9413] | 646 | <field field_ref="sst2" > sst2 </field> |
---|
[9392] | 647 | \end{xmllines} |
---|
[5107] | 648 | |
---|
[10368] | 649 | Note that in this case, the following syntaxe \xmlcode{<field field_ref="sst2" />} is not working as |
---|
[9413] | 650 | sst2 won't be evaluated. |
---|
[5107] | 651 | |
---|
[10368] | 652 | \item |
---|
| 653 | Change of variable precision: |
---|
[9413] | 654 | |
---|
[9392] | 655 | \begin{xmllines} |
---|
[9413] | 656 | <!-- force to keep real 8 --> |
---|
| 657 | <field field_ref="sst" name="tos_r8" prec="8" /> |
---|
| 658 | <!-- integer 2 with add_offset and scale_factor attributes --> |
---|
| 659 | <field field_ref="sss" name="sos_i2" prec="2" add_offset="20." scale_factor="1.e-3" /> |
---|
[9392] | 660 | \end{xmllines} |
---|
[5107] | 661 | |
---|
[9413] | 662 | Note that, then the code is crashing, writting real4 variables forces a numerical convection from |
---|
[10368] | 663 | real8 to real4 which will create an internal error in NetCDF and will avoid the creation of the output files. |
---|
| 664 | Forcing double precision outputs with prec="8" (for example in the field\_definition) will avoid this problem. |
---|
[5107] | 665 | |
---|
[10368] | 666 | \item |
---|
| 667 | add user defined attributes: |
---|
[9413] | 668 | |
---|
[9392] | 669 | \begin{xmllines} |
---|
[9413] | 670 | <file_group id="1d" output_freq="1d" output_level="10" enabled=".true."> <!-- 1d files --> |
---|
[9393] | 671 | <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > |
---|
[9413] | 672 | <field field_ref="sst" name="tos" > |
---|
| 673 | <variable id="my_attribute1" type="string" > blabla </variable> |
---|
| 674 | <variable id="my_attribute2" type="integer" > 3 </variable> |
---|
| 675 | <variable id="my_attribute3" type="float" > 5.0 </variable> |
---|
| 676 | </field> |
---|
| 677 | <variable id="my_global_attribute" type="string" > blabla_global </variable> |
---|
| 678 | </file> |
---|
| 679 | </file_group> |
---|
[9392] | 680 | \end{xmllines} |
---|
[5107] | 681 | |
---|
[10368] | 682 | \item |
---|
| 683 | use of the ``@'' function: example 1, weighted temporal average |
---|
[5107] | 684 | |
---|
| 685 | - define a new variable in field\_definition |
---|
[9413] | 686 | |
---|
[9392] | 687 | \begin{xmllines} |
---|
[9413] | 688 | <field id="toce_e3t" long_name="temperature * e3t" unit="degC*m" grid_ref="grid_T_3D" >toce * e3t</field> |
---|
[9392] | 689 | \end{xmllines} |
---|
[9413] | 690 | |
---|
| 691 | - use it when defining your file. |
---|
| 692 | |
---|
[9392] | 693 | \begin{xmllines} |
---|
[9393] | 694 | <file_group id="5d" output_freq="5d" output_level="10" enabled=".true." > <!-- 5d files --> |
---|
[9413] | 695 | <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > |
---|
| 696 | <field field_ref="toce" operation="instant" freq_op="5d" > @toce_e3t / @e3t </field> |
---|
| 697 | </file> |
---|
[9393] | 698 | </file_group> |
---|
[9392] | 699 | \end{xmllines} |
---|
[5107] | 700 | |
---|
[9413] | 701 | The freq\_op="5d" attribute is used to define the operation frequency of the ``@'' function: here 5 day. |
---|
[10368] | 702 | The temporal operation done by the ``@'' is the one defined in the field definition: |
---|
[9413] | 703 | here we use the default, average. |
---|
| 704 | So, in the above case, @toce\_e3t will do the 5-day mean of toce*e3t. |
---|
[10368] | 705 | Operation="instant" refers to the temporal operation to be performed on the field''@toce\_e3t / @e3t'': |
---|
| 706 | here the temporal average is alreday done by the ``@'' function so we just use instant to do the ratio of |
---|
[9413] | 707 | the 2 mean values. |
---|
| 708 | field\_ref="toce" means that attributes not explicitely defined, are inherited from toce field. |
---|
| 709 | Note that in this case, freq\_op must be equal to the file output\_freq. |
---|
[5107] | 710 | |
---|
[10368] | 711 | \item |
---|
| 712 | use of the ``@'' function: example 2, monthly SSH standard deviation |
---|
[9413] | 713 | |
---|
[5107] | 714 | - define a new variable in field\_definition |
---|
[9413] | 715 | |
---|
[9392] | 716 | \begin{xmllines} |
---|
[9413] | 717 | <field id="ssh2" long_name="square of sea surface temperature" unit="degC2" > ssh * ssh </field > |
---|
[9392] | 718 | \end{xmllines} |
---|
[9413] | 719 | |
---|
| 720 | - use it when defining your file. |
---|
| 721 | |
---|
[9392] | 722 | \begin{xmllines} |
---|
[9393] | 723 | <file_group id="1m" output_freq="1m" output_level="10" enabled=".true." > <!-- 1m files --> |
---|
[9413] | 724 | <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > |
---|
| 725 | <field field_ref="ssh" name="sshstd" long_name="sea_surface_temperature_standard_deviation" |
---|
| 726 | operation="instant" freq_op="1m" > |
---|
| 727 | sqrt( @ssh2 - @ssh * @ssh ) |
---|
| 728 | </field> |
---|
| 729 | </file> |
---|
[9393] | 730 | </file_group> |
---|
[9392] | 731 | \end{xmllines} |
---|
[5107] | 732 | |
---|
[9413] | 733 | The freq\_op="1m" attribute is used to define the operation frequency of the ``@'' function: here 1 month. |
---|
[10368] | 734 | The temporal operation done by the ``@'' is the one defined in the field definition: |
---|
[9413] | 735 | here we use the default, average. |
---|
| 736 | So, in the above case, @ssh2 will do the monthly mean of ssh*ssh. |
---|
[10368] | 737 | Operation="instant" refers to the temporal operation to be performed on the field ''sqrt( @ssh2 - @ssh * @ssh )'': |
---|
[9413] | 738 | here the temporal average is alreday done by the ``@'' function so we just use instant. |
---|
| 739 | field\_ref="ssh" means that attributes not explicitely defined, are inherited from ssh field. |
---|
| 740 | Note that in this case, freq\_op must be equal to the file output\_freq. |
---|
[5107] | 741 | |
---|
[10368] | 742 | \item |
---|
| 743 | use of the ``@'' function: example 3, monthly average of SST diurnal cycle |
---|
[9413] | 744 | |
---|
[5107] | 745 | - define 2 new variables in field\_definition |
---|
[9413] | 746 | |
---|
[9392] | 747 | \begin{xmllines} |
---|
[9413] | 748 | <field id="sstmax" field_ref="sst" long_name="max of sea surface temperature" operation="maximum" /> |
---|
| 749 | <field id="sstmin" field_ref="sst" long_name="min of sea surface temperature" operation="minimum" /> |
---|
[9392] | 750 | \end{xmllines} |
---|
[9413] | 751 | |
---|
| 752 | - use these 2 new variables when defining your file. |
---|
| 753 | |
---|
[9392] | 754 | \begin{xmllines} |
---|
[9393] | 755 | <file_group id="1m" output_freq="1m" output_level="10" enabled=".true." > <!-- 1m files --> |
---|
[9413] | 756 | <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > |
---|
| 757 | <field field_ref="sst" name="sstdcy" long_name="amplitude of sst diurnal cycle" operation="average" freq_op="1d" > |
---|
| 758 | @sstmax - @sstmin |
---|
| 759 | </field> |
---|
| 760 | </file> |
---|
[9393] | 761 | </file_group> |
---|
[9392] | 762 | \end{xmllines} |
---|
[5107] | 763 | |
---|
[9413] | 764 | \end{enumerate} |
---|
[5107] | 765 | |
---|
[9413] | 766 | The freq\_op="1d" attribute is used to define the operation frequency of the ``@'' function: here 1 day. |
---|
[10368] | 767 | The temporal operation done by the ``@'' is the one defined in the field definition: |
---|
| 768 | here maximum for sstmax and minimum for sstmin. |
---|
[9413] | 769 | So, in the above case, @sstmax will do the daily max and @sstmin the daily min. |
---|
[10368] | 770 | Operation="average" refers to the temporal operation to be performed on the field ``@sstmax - @sstmin'': |
---|
[9413] | 771 | here monthly mean (of daily max - daily min of the sst). |
---|
| 772 | field\_ref="sst" means that attributes not explicitely defined, are inherited from sst field. |
---|
[5107] | 773 | |
---|
[9413] | 774 | \subsubsection{Tag list per family} |
---|
[2541] | 775 | |
---|
[9413] | 776 | \begin{table} \scriptsize |
---|
| 777 | \begin{tabularx}{\textwidth}{|l|X|X|l|X|} \hline |
---|
| 778 | tag name & |
---|
| 779 | description & |
---|
| 780 | accepted attribute & |
---|
| 781 | child of & |
---|
| 782 | parent of \\ \hline \hline |
---|
| 783 | simulation & |
---|
| 784 | this tag is the root tag which encapsulates all the content of the XML file & |
---|
| 785 | none & |
---|
| 786 | none & |
---|
| 787 | context \\ \hline |
---|
| 788 | context & |
---|
| 789 | encapsulates parts of the XML file dedicated to different codes or different parts of a code & |
---|
| 790 | id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin & |
---|
| 791 | simulation & |
---|
| 792 | all root tags: ... \_definition \\ \hline |
---|
| 793 | \end{tabularx} |
---|
| 794 | \caption{Context tags} |
---|
| 795 | \end{table} |
---|
[2541] | 796 | |
---|
[9413] | 797 | \begin{table} \scriptsize |
---|
| 798 | \begin{tabularx}{\textwidth}{|l|X|X|X|l|} \hline |
---|
| 799 | tag name & |
---|
| 800 | description & |
---|
| 801 | accepted attribute & |
---|
| 802 | child of & |
---|
| 803 | parent of \\ \hline \hline |
---|
| 804 | field\_definition & |
---|
| 805 | encapsulates the definition of all the fields that can potentially be outputted & |
---|
| 806 | axis\_ref, default\_value, domain\_ref, enabled, grid\_ref, level, operation, prec, src & |
---|
| 807 | context & |
---|
| 808 | field or field\_group \\ \hline |
---|
| 809 | field\_group & |
---|
| 810 | encapsulates a group of fields & |
---|
| 811 | axis\_ref, default\_value, domain\_ref, enabled, group\_ref, grid\_ref, |
---|
| 812 | id, level, operation, prec, src & |
---|
| 813 | field\_definition, field\_group, file & |
---|
| 814 | field or field\_group \\ \hline |
---|
| 815 | field & |
---|
| 816 | define a specific field & |
---|
| 817 | axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref, |
---|
| 818 | id, level, long\_name, name, operation, prec, standard\_name, unit & |
---|
| 819 | field\_definition, field\_group, file & |
---|
| 820 | none \\ \hline |
---|
| 821 | \end{tabularx} |
---|
| 822 | \caption{Field tags ("\tt{field\_*}")} |
---|
| 823 | \end{table} |
---|
[2541] | 824 | |
---|
[9413] | 825 | \begin{table} \scriptsize |
---|
| 826 | \begin{tabularx}{\textwidth}{|l|X|X|X|l|} \hline |
---|
| 827 | tag name & |
---|
| 828 | description & |
---|
| 829 | accepted attribute & |
---|
| 830 | child of & |
---|
| 831 | parent of \\ \hline \hline |
---|
| 832 | file\_definition & |
---|
| 833 | encapsulates the definition of all the files that will be outputted & |
---|
| 834 | enabled, min\_digits, name, name\_suffix, output\_level, |
---|
| 835 | split\_freq\_format, split\_freq, sync\_freq, type, src & |
---|
| 836 | context & |
---|
| 837 | file or file\_group \\ \hline |
---|
| 838 | file\_group & |
---|
| 839 | encapsulates a group of files that will be outputted & |
---|
| 840 | enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, |
---|
| 841 | split\_freq\_format, split\_freq, sync\_freq, type, src & |
---|
| 842 | file\_definition, file\_group & |
---|
| 843 | file or file\_group \\ \hline |
---|
| 844 | file & |
---|
| 845 | define the contents of a file to be outputted & |
---|
| 846 | enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, |
---|
| 847 | split\_freq\_format, split\_freq, sync\_freq, type, src & |
---|
| 848 | file\_definition, file\_group & |
---|
| 849 | field \\ \hline |
---|
| 850 | \end{tabularx} |
---|
| 851 | \caption{File tags ("\tt{file\_*}")} |
---|
| 852 | \end{table} |
---|
[2541] | 853 | |
---|
[9413] | 854 | \begin{table} \scriptsize |
---|
| 855 | \begin{tabularx}{\textwidth}{|l|X|X|X|X|} \hline |
---|
| 856 | tag name & |
---|
| 857 | description & |
---|
| 858 | accepted attribute & |
---|
| 859 | child of & |
---|
| 860 | parent of \\ \hline \hline |
---|
| 861 | axis\_definition & |
---|
| 862 | define all the vertical axis potentially used by the variables & |
---|
| 863 | src & |
---|
| 864 | context & |
---|
| 865 | axis\_group, axis \\ \hline |
---|
| 866 | axis\_group & |
---|
| 867 | encapsulates a group of vertical axis & |
---|
| 868 | id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size & |
---|
| 869 | axis\_definition, axis\_group & |
---|
| 870 | axis\_group, axis \\ \hline |
---|
| 871 | axis & |
---|
| 872 | define a vertical axis & |
---|
| 873 | id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size & |
---|
| 874 | axis\_definition, axis\_group & |
---|
| 875 | none \\ \hline |
---|
| 876 | \end{tabularx} |
---|
| 877 | \caption{Axis tags ("\tt{axis\_*}")} |
---|
| 878 | \end{table} |
---|
[2541] | 879 | |
---|
[9413] | 880 | \begin{table} \scriptsize |
---|
| 881 | \begin{tabularx}{\textwidth}{|l|X|X|X|X|} \hline |
---|
| 882 | tag name & |
---|
| 883 | description & |
---|
| 884 | accepted attribute & |
---|
| 885 | child of & |
---|
| 886 | parent of \\ \hline \hline |
---|
| 887 | domain\_\-definition & |
---|
| 888 | define all the horizontal domains potentially used by the variables & |
---|
| 889 | src & |
---|
| 890 | context & |
---|
| 891 | domain\_\-group, domain \\ \hline |
---|
| 892 | domain\_group & |
---|
| 893 | encapsulates a group of horizontal domains & |
---|
| 894 | id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & |
---|
| 895 | domain\_\-definition, domain\_group & |
---|
| 896 | domain\_\-group, domain \\ \hline |
---|
| 897 | domain & |
---|
| 898 | define an horizontal domain & |
---|
| 899 | id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & |
---|
| 900 | domain\_\-definition, domain\_group & |
---|
| 901 | none \\ \hline |
---|
| 902 | \end{tabularx} |
---|
| 903 | \caption{Domain tags ("\tt{domain\_*)}"} |
---|
| 904 | \end{table} |
---|
| 905 | |
---|
| 906 | \begin{table} \scriptsize |
---|
| 907 | \begin{tabularx}{\textwidth}{|l|X|X|X|X|} \hline |
---|
| 908 | tag name & |
---|
| 909 | description & |
---|
| 910 | accepted attribute & |
---|
| 911 | child of & |
---|
| 912 | parent of \\ \hline \hline |
---|
| 913 | grid\_definition & |
---|
| 914 | define all the grid (association of a domain and/or an axis) potentially used by the variables & |
---|
| 915 | src & |
---|
| 916 | context & |
---|
| 917 | grid\_group, grid \\ \hline |
---|
| 918 | grid\_group & |
---|
| 919 | encapsulates a group of grids & |
---|
| 920 | id, domain\_ref,axis\_ref & |
---|
| 921 | grid\_definition, grid\_group & |
---|
| 922 | grid\_group, grid \\ \hline |
---|
| 923 | grid & |
---|
| 924 | define a grid & |
---|
| 925 | id, domain\_ref,axis\_ref & |
---|
| 926 | grid\_definition, grid\_group & |
---|
| 927 | none \\ \hline |
---|
| 928 | \end{tabularx} |
---|
| 929 | \caption{Grid tags ("\tt{grid\_*}")} |
---|
| 930 | \end{table} |
---|
| 931 | |
---|
| 932 | \subsubsection{Attributes list per family} |
---|
| 933 | |
---|
| 934 | \begin{table} \scriptsize |
---|
| 935 | \begin{tabularx}{\textwidth}{|l|X|l|l|} \hline |
---|
| 936 | attribute name & |
---|
| 937 | description & |
---|
| 938 | example & |
---|
| 939 | accepted by \\ \hline \hline |
---|
| 940 | axis\_ref & |
---|
| 941 | refers to the id of a vertical axis & |
---|
| 942 | axis\_ref="deptht" & |
---|
| 943 | field, grid families \\ \hline |
---|
| 944 | domain\_ref & |
---|
| 945 | refers to the id of a domain & |
---|
| 946 | domain\_ref="grid\_T" & |
---|
| 947 | field or grid families \\ \hline |
---|
| 948 | field\_ref & |
---|
| 949 | id of the field we want to add in a file & |
---|
| 950 | field\_ref="toce" & |
---|
| 951 | field \\ \hline |
---|
| 952 | grid\_ref & |
---|
| 953 | refers to the id of a grid & |
---|
| 954 | grid\_ref="grid\_T\_2D" & |
---|
| 955 | field family \\ \hline |
---|
| 956 | group\_ref & |
---|
| 957 | refer to a group of variables & |
---|
| 958 | group\_ref="mooring" & |
---|
| 959 | field\_group \\ \hline |
---|
| 960 | \end{tabularx} |
---|
| 961 | \caption{Reference attributes ("\tt{*\_ref}")} |
---|
| 962 | \end{table} |
---|
| 963 | |
---|
| 964 | \begin{table} \scriptsize |
---|
| 965 | \begin{tabularx}{\textwidth}{|l|X|l|l|} \hline |
---|
| 966 | attribute name & |
---|
| 967 | description & |
---|
| 968 | example & |
---|
| 969 | accepted by \\ \hline \hline |
---|
| 970 | zoom\_ibegin & |
---|
| 971 | starting point along x direction of the zoom. |
---|
| 972 | Automatically defined for TAO/RAMA/PIRATA moorings & |
---|
| 973 | zoom\_ibegin="1" & |
---|
| 974 | domain family \\ \hline |
---|
| 975 | zoom\_jbegin & |
---|
| 976 | starting point along y direction of the zoom. |
---|
| 977 | Automatically defined for TAO/RAMA/PIRATA moorings & |
---|
| 978 | zoom\_jbegin="1" & |
---|
| 979 | domain family \\ \hline |
---|
| 980 | zoom\_ni & |
---|
| 981 | zoom extent along x direction & |
---|
| 982 | zoom\_ni="1" & |
---|
| 983 | domain family \\ \hline |
---|
| 984 | zoom\_nj & |
---|
| 985 | zoom extent along y direction & |
---|
| 986 | zoom\_nj="1" & |
---|
| 987 | domain family \\ \hline |
---|
| 988 | \end{tabularx} |
---|
| 989 | \caption{Domain attributes ("\tt{zoom\_*}")} |
---|
| 990 | \end{table} |
---|
| 991 | |
---|
| 992 | \begin{table} \scriptsize |
---|
| 993 | \begin{tabularx}{\textwidth}{|l|X|l|l|} \hline |
---|
| 994 | attribute name & |
---|
| 995 | description & |
---|
| 996 | example & |
---|
| 997 | accepted by \\ \hline \hline |
---|
| 998 | min\_digits & |
---|
| 999 | specify the minimum of digits used in the core number in the name of the NetCDF file & |
---|
| 1000 | min\_digits="4" & |
---|
| 1001 | file family \\ \hline |
---|
| 1002 | name\_suffix & |
---|
| 1003 | suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file & |
---|
| 1004 | name\_suffix="\_myzoom" & |
---|
| 1005 | file family \\ \hline |
---|
| 1006 | output\_level & |
---|
| 1007 | output priority of variables in a file: 0 (high) to 10 (low). |
---|
| 1008 | All variables listed in the file with a level smaller or equal to output\_level will be output. |
---|
| 1009 | Other variables won't be output even if they are listed in the file. & |
---|
| 1010 | output\_level="10" & |
---|
| 1011 | file family \\ \hline |
---|
| 1012 | split\_freq & |
---|
| 1013 | frequency at which to temporally split output files. |
---|
| 1014 | Units can be ts (timestep), y, mo, d, h, mi, s. |
---|
| 1015 | Useful for long runs to prevent over-sized output files. & |
---|
| 1016 | split\_freq="1mo" & |
---|
| 1017 | file family \\ \hline |
---|
| 1018 | split\_freq\-\_format & |
---|
| 1019 | date format used in the name of temporally split output files. |
---|
| 1020 | Can be specified using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s & |
---|
| 1021 | split\_freq\_format= "\%y\%mo\%d" & |
---|
| 1022 | file family \\ \hline |
---|
| 1023 | sync\_freq & |
---|
| 1024 | NetCDF file synchronization frequency (update of the time\_counter). |
---|
| 1025 | Units can be ts (timestep), y, mo, d, h, mi, s. & |
---|
| 1026 | sync\_freq="10d" & |
---|
| 1027 | file family \\ \hline |
---|
| 1028 | type (1) & |
---|
| 1029 | specify if the output files are to be split spatially (multiple\_file) or not (one\_file) & |
---|
| 1030 | type="multiple\_file" & |
---|
| 1031 | file familly \\ \hline |
---|
| 1032 | \end{tabularx} |
---|
| 1033 | \caption{File attributes} |
---|
| 1034 | \end{table} |
---|
| 1035 | |
---|
| 1036 | \begin{table} \scriptsize |
---|
| 1037 | \begin{tabularx}{\textwidth}{|l|X|l|l|} \hline |
---|
| 1038 | attribute name & |
---|
| 1039 | description & |
---|
| 1040 | example & |
---|
| 1041 | accepted by \\ \hline \hline |
---|
| 1042 | default\_value & |
---|
| 1043 | missing\_value definition & |
---|
| 1044 | default\_value="1.e20" & |
---|
| 1045 | field family \\ \hline |
---|
| 1046 | level & |
---|
| 1047 | output priority of a field: 0 (high) to 10 (low) & |
---|
| 1048 | level="1" & |
---|
| 1049 | field family \\ \hline |
---|
| 1050 | operation & |
---|
| 1051 | type of temporal operation: average, accumulate, instantaneous, min, max and once & |
---|
| 1052 | operation="average" & |
---|
| 1053 | field family \\ \hline |
---|
| 1054 | output\_freq & |
---|
| 1055 | operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. & |
---|
| 1056 | output\_freq="1d12h" & |
---|
| 1057 | field family \\ \hline |
---|
| 1058 | prec & |
---|
| 1059 | output precision: real 4 or real 8 & |
---|
| 1060 | prec="4" & |
---|
| 1061 | field family \\ \hline |
---|
| 1062 | long\_name & |
---|
| 1063 | define the long\_name attribute in the NetCDF file & |
---|
| 1064 | long\_name="Vertical T levels" & |
---|
| 1065 | field \\ \hline |
---|
| 1066 | standard\_name & |
---|
| 1067 | define the standard\_name attribute in the NetCDF file & |
---|
| 1068 | standard\_name= "Eastward\_Sea\_Ice\_Transport" & |
---|
| 1069 | field \\ \hline |
---|
| 1070 | \end{tabularx} |
---|
| 1071 | \caption{Field attributes} |
---|
| 1072 | \end{table} |
---|
| 1073 | |
---|
| 1074 | \begin{table} \scriptsize |
---|
| 1075 | \begin{tabularx}{\textwidth}{|l|X|X|X|} \hline |
---|
| 1076 | attribute name & |
---|
| 1077 | description & |
---|
| 1078 | example & |
---|
| 1079 | accepted by \\ \hline \hline |
---|
| 1080 | enabled & |
---|
| 1081 | switch on/off the output of a field or a file & |
---|
| 1082 | enabled=".true." & |
---|
| 1083 | field, file families \\ \hline |
---|
| 1084 | description & |
---|
| 1085 | just for information, not used & |
---|
| 1086 | description="ocean T grid variables" & |
---|
| 1087 | all tags \\ \hline |
---|
| 1088 | id & |
---|
| 1089 | allow to identify a tag & |
---|
| 1090 | id="nemo" & |
---|
| 1091 | accepted by all tags except simulation \\ \hline |
---|
| 1092 | name & |
---|
| 1093 | name of a variable or a file. If the name of a file is undefined, its id is used as a name & |
---|
| 1094 | name="tos" & |
---|
| 1095 | field or file families \\ \hline |
---|
| 1096 | positive & |
---|
| 1097 | convention used for the orientation of vertival axis (positive downward in \NEMO). & |
---|
| 1098 | positive="down" & |
---|
| 1099 | axis family \\ \hline |
---|
| 1100 | src & |
---|
| 1101 | allow to include a file & |
---|
| 1102 | src="./field\_def.xml" & |
---|
| 1103 | accepted by all tags except simulation \\ \hline |
---|
| 1104 | time\_origin & |
---|
| 1105 | specify the origin of the time counter & |
---|
| 1106 | time\_origin="1900-01-01 00:00:00" & |
---|
| 1107 | context \\ \hline |
---|
| 1108 | type (2) & |
---|
| 1109 | define the type of a variable tag & |
---|
| 1110 | type="boolean" & |
---|
| 1111 | variable \\ \hline |
---|
| 1112 | unit & |
---|
| 1113 | unit of a variable or the vertical axis & |
---|
| 1114 | unit="m" & |
---|
| 1115 | field and axis families \\ \hline |
---|
| 1116 | \end{tabularx} |
---|
| 1117 | \caption{Miscellaneous attributes} |
---|
| 1118 | \end{table} |
---|
| 1119 | |
---|
[5515] | 1120 | \subsection{CF metadata standard compliance} |
---|
[2541] | 1121 | |
---|
[9413] | 1122 | Output from the XIOS-1.0 IO server is compliant with |
---|
[10368] | 1123 | \href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of |
---|
| 1124 | the CF metadata standard. |
---|
| 1125 | Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of |
---|
| 1126 | section \autoref{subsec:IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard. |
---|
[2541] | 1127 | |
---|
[10368] | 1128 | Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by |
---|
| 1129 | the namelist parameter \np{ln\_cfmeta} in the \ngn{namrun} namelist. |
---|
[9413] | 1130 | This must be set to true if these metadata are to be included in the output files. |
---|
[5515] | 1131 | |
---|
| 1132 | |
---|
[2541] | 1133 | % ================================================================ |
---|
| 1134 | % NetCDF4 support |
---|
| 1135 | % ================================================================ |
---|
[9393] | 1136 | \section{NetCDF4 support (\protect\key{netcdf4})} |
---|
[9413] | 1137 | \label{sec:DIA_nc4} |
---|
[2541] | 1138 | |
---|
[9413] | 1139 | Since version 3.3, support for NetCDF4 chunking and (loss-less) compression has been included. |
---|
[10368] | 1140 | These options build on the standard NetCDF output and allow the user control over the size of the chunks via |
---|
| 1141 | namelist settings. |
---|
[9413] | 1142 | Chunking and compression can lead to significant reductions in file sizes for a small runtime overhead. |
---|
[10368] | 1143 | For a fuller discussion on chunking and other performance issues the reader is referred to |
---|
| 1144 | the NetCDF4 documentation found \href{http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.html#Chunking}{here}. |
---|
[2541] | 1145 | |
---|
[10368] | 1146 | The new features are only available when the code has been linked with a NetCDF4 library |
---|
| 1147 | (version 4.1 onwards, recommended) which has been built with HDF5 support (version 1.8.4 onwards, recommended). |
---|
| 1148 | Datasets created with chunking and compression are not backwards compatible with NetCDF3 "classic" format but |
---|
| 1149 | most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files. |
---|
| 1150 | NEMO executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by |
---|
[9413] | 1151 | setting the \np{ln\_nc4zip} logical to false in the \textit{namnc4} namelist: |
---|
[2541] | 1152 | |
---|
| 1153 | %------------------------------------------namnc4---------------------------------------------------- |
---|
[10146] | 1154 | |
---|
| 1155 | \nlst{namnc4} |
---|
[2541] | 1156 | %------------------------------------------------------------------------------------------------------------- |
---|
| 1157 | |
---|
[9413] | 1158 | If \key{netcdf4} has not been defined, these namelist parameters are not read. |
---|
[10368] | 1159 | In this case, \np{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined. |
---|
| 1160 | These functions will not be used but need to be included so that compilation is possible with NetCDF3 libraries. |
---|
[2541] | 1161 | |
---|
[10368] | 1162 | When using NetCDF4 libraries, \key{netcdf4} should be defined even if the intention is to |
---|
[9413] | 1163 | create only NetCDF3-compatible files. |
---|
[10368] | 1164 | This is necessary to avoid duplication between the dummy routines and the actual routines present in the library. |
---|
[9413] | 1165 | Most compilers will fail at compile time when faced with such duplication. |
---|
[10368] | 1166 | Thus when linking with NetCDF4 libraries the user must define \key{netcdf4} and |
---|
[9413] | 1167 | control the type of NetCDF file produced via the namelist parameter. |
---|
[2541] | 1168 | |
---|
[10368] | 1169 | Chunking and compression is applied only to 4D fields and |
---|
| 1170 | there is no advantage in chunking across more than one time dimension since |
---|
| 1171 | previously written chunks would have to be read back and decompressed before being added to. |
---|
[9413] | 1172 | Therefore, user control over chunk sizes is provided only for the three space dimensions. |
---|
| 1173 | The user sets an approximate number of chunks along each spatial axis. |
---|
[10368] | 1174 | The actual size of the chunks will depend on global domain size for mono-processors or, more likely, |
---|
| 1175 | the local processor domain size for distributed processing. |
---|
| 1176 | The derived values are subject to practical minimum values (to avoid wastefully small chunk sizes) and |
---|
[9413] | 1177 | cannot be greater than the domain size in any dimension. |
---|
| 1178 | The algorithm used is: |
---|
[2541] | 1179 | |
---|
[9388] | 1180 | \begin{forlines} |
---|
[9413] | 1181 | ichunksz(1) = MIN(idomain_size, MAX((idomain_size-1) / nn_nchunks_i + 1 ,16 )) |
---|
| 1182 | ichunksz(2) = MIN(jdomain_size, MAX((jdomain_size-1) / nn_nchunks_j + 1 ,16 )) |
---|
| 1183 | ichunksz(3) = MIN(kdomain_size, MAX((kdomain_size-1) / nn_nchunks_k + 1 , 1 )) |
---|
| 1184 | ichunksz(4) = 1 |
---|
[9388] | 1185 | \end{forlines} |
---|
[2541] | 1186 | |
---|
| 1187 | \noindent As an example, setting: |
---|
[9413] | 1188 | |
---|
[9388] | 1189 | \begin{forlines} |
---|
[9413] | 1190 | nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31 |
---|
[9388] | 1191 | \end{forlines} |
---|
[2541] | 1192 | |
---|
[10368] | 1193 | \noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1} respectively in |
---|
[9413] | 1194 | the mono-processor case (i.e. global domain of {\small\tt 182x149x31}). |
---|
| 1195 | An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in |
---|
[10368] | 1196 | table \autoref{tab:NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with |
---|
| 1197 | a 4x2 mpi partitioning. |
---|
| 1198 | Note the variation in the compression ratio achieved which reflects chiefly the dry to wet volume ratio of |
---|
| 1199 | each processing region. |
---|
[2541] | 1200 | |
---|
| 1201 | %------------------------------------------TABLE---------------------------------------------------- |
---|
[9413] | 1202 | \begin{table} \scriptsize \centering |
---|
| 1203 | \begin{tabular}{lrrr} |
---|
| 1204 | Filename & NetCDF3 & NetCDF4 & Reduction \\ |
---|
| 1205 | & filesize & filesize & \% \\ |
---|
| 1206 | & (KB) & (KB) & \\ |
---|
| 1207 | ORCA2\_restart\_0000.nc & 16420 & 8860 & 47\% \\ |
---|
| 1208 | ORCA2\_restart\_0001.nc & 16064 & 11456 & 29\% \\ |
---|
| 1209 | ORCA2\_restart\_0002.nc & 16064 & 9744 & 40\% \\ |
---|
| 1210 | ORCA2\_restart\_0003.nc & 16420 & 9404 & 43\% \\ |
---|
| 1211 | ORCA2\_restart\_0004.nc & 16200 & 5844 & 64\% \\ |
---|
| 1212 | ORCA2\_restart\_0005.nc & 15848 & 8172 & 49\% \\ |
---|
| 1213 | ORCA2\_restart\_0006.nc & 15848 & 8012 & 50\% \\ |
---|
| 1214 | ORCA2\_restart\_0007.nc & 16200 & 5148 & 69\% \\ |
---|
| 1215 | ORCA2\_2d\_grid\_T\_0000.nc & 2200 & 1504 & 32\% \\ |
---|
| 1216 | ORCA2\_2d\_grid\_T\_0001.nc & 2200 & 1748 & 21\% \\ |
---|
| 1217 | ORCA2\_2d\_grid\_T\_0002.nc & 2200 & 1592 & 28\% \\ |
---|
| 1218 | ORCA2\_2d\_grid\_T\_0003.nc & 2200 & 1540 & 30\% \\ |
---|
| 1219 | ORCA2\_2d\_grid\_T\_0004.nc & 2200 & 1204 & 46\% \\ |
---|
| 1220 | ORCA2\_2d\_grid\_T\_0005.nc & 2200 & 1444 & 35\% \\ |
---|
| 1221 | ORCA2\_2d\_grid\_T\_0006.nc & 2200 & 1428 & 36\% \\ |
---|
| 1222 | ORCA2\_2d\_grid\_T\_0007.nc & 2200 & 1148 & 48\% \\ |
---|
| 1223 | ... & ... & ... & ... \\ |
---|
| 1224 | ORCA2\_2d\_grid\_W\_0000.nc & 4416 & 2240 & 50\% \\ |
---|
| 1225 | ORCA2\_2d\_grid\_W\_0001.nc & 4416 & 2924 & 34\% \\ |
---|
| 1226 | ORCA2\_2d\_grid\_W\_0002.nc & 4416 & 2512 & 44\% \\ |
---|
| 1227 | ORCA2\_2d\_grid\_W\_0003.nc & 4416 & 2368 & 47\% \\ |
---|
| 1228 | ORCA2\_2d\_grid\_W\_0004.nc & 4416 & 1432 & 68\% \\ |
---|
| 1229 | ORCA2\_2d\_grid\_W\_0005.nc & 4416 & 1972 & 56\% \\ |
---|
| 1230 | ORCA2\_2d\_grid\_W\_0006.nc & 4416 & 2028 & 55\% \\ |
---|
| 1231 | ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\% \\ |
---|
| 1232 | \end{tabular} |
---|
| 1233 | \caption{ |
---|
| 1234 | \protect\label{tab:NC4} |
---|
| 1235 | Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression} |
---|
[2541] | 1236 | \end{table} |
---|
| 1237 | %---------------------------------------------------------------------------------------------------- |
---|
| 1238 | |
---|
[10368] | 1239 | When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via |
---|
| 1240 | \np{iom\_put} calls are set via an equivalent and identically named namelist to \textit{namnc4} in |
---|
| 1241 | \np{xmlio\_server.def}. |
---|
| 1242 | Typically this namelist serves the mean files whilst the \ngn{ namnc4} in the main namelist file continues to |
---|
| 1243 | serve the restart files. |
---|
| 1244 | This duplication is unfortunate but appropriate since, if using io\_servers, the domain sizes of |
---|
| 1245 | the individual files produced by the io\_server processes may be different to those produced by |
---|
[9413] | 1246 | the invidual processing regions and different chunking choices may be desired. |
---|
[2541] | 1247 | |
---|
| 1248 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 1249 | % Tracer/Dynamics Trends |
---|
| 1250 | % ------------------------------------------------------------------------------------------------------------- |
---|
[9393] | 1251 | \section{Tracer/Dynamics trends (\protect\ngn{namtrd})} |
---|
[9407] | 1252 | \label{sec:DIA_trd} |
---|
[2541] | 1253 | |
---|
| 1254 | %------------------------------------------namtrd---------------------------------------------------- |
---|
[10146] | 1255 | |
---|
| 1256 | \nlst{namtrd} |
---|
[2541] | 1257 | %------------------------------------------------------------------------------------------------------------- |
---|
| 1258 | |
---|
[10368] | 1259 | Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to |
---|
| 1260 | \mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation |
---|
| 1261 | ($i.e.$ at the end of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines). |
---|
[9413] | 1262 | This capability is controlled by options offered in \ngn{namtrd} namelist. |
---|
[6289] | 1263 | Note that the output are done with xIOS, and therefore the \key{IOM} is required. |
---|
[2541] | 1264 | |
---|
[9393] | 1265 | What is done depends on the \ngn{namtrd} logical set to \forcode{.true.}: |
---|
[9413] | 1266 | |
---|
[2541] | 1267 | \begin{description} |
---|
[10368] | 1268 | \item[\np{ln\_glo\_trd}]: |
---|
| 1269 | at each \np{nn\_trd} time-step a check of the basin averaged properties of |
---|
| 1270 | the momentum and tracer equations is performed. |
---|
| 1271 | This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$, |
---|
| 1272 | and potential energy time evolution equations properties; |
---|
| 1273 | \item[\np{ln\_dyn\_trd}]: |
---|
| 1274 | each 3D trend of the evolution of the two momentum components is output; |
---|
| 1275 | \item[\np{ln\_dyn\_mxl}]: |
---|
| 1276 | each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output; |
---|
| 1277 | \item[\np{ln\_vor\_trd}]: |
---|
| 1278 | a vertical summation of the moment tendencies is performed, |
---|
| 1279 | then the curl is computed to obtain the barotropic vorticity tendencies which are output; |
---|
| 1280 | \item[\np{ln\_KE\_trd}] : |
---|
| 1281 | each 3D trend of the Kinetic Energy equation is output; |
---|
| 1282 | \item[\np{ln\_tra\_trd}]: |
---|
| 1283 | each 3D trend of the evolution of temperature and salinity is output; |
---|
| 1284 | \item[\np{ln\_tra\_mxl}]: |
---|
| 1285 | each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output; |
---|
[2541] | 1286 | \end{description} |
---|
| 1287 | |
---|
[9413] | 1288 | Note that the mixed layer tendency diagnostic can also be used on biogeochemical models via |
---|
| 1289 | the \key{trdtrc} and \key{trdmld\_trc} CPP keys. |
---|
[2541] | 1290 | |
---|
[9413] | 1291 | \textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested. |
---|
[10368] | 1292 | In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} are not working, |
---|
| 1293 | and none of the options have been tested with variable volume ($i.e.$ \key{vvl} defined). |
---|
[2541] | 1294 | |
---|
| 1295 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 1296 | % On-line Floats trajectories |
---|
| 1297 | % ------------------------------------------------------------------------------------------------------------- |
---|
[9393] | 1298 | \section{FLO: On-Line Floats trajectories (\protect\key{floats})} |
---|
[9407] | 1299 | \label{sec:FLO} |
---|
[2541] | 1300 | %--------------------------------------------namflo------------------------------------------------------- |
---|
[10146] | 1301 | |
---|
| 1302 | \nlst{namflo} |
---|
[2541] | 1303 | %-------------------------------------------------------------------------------------------------------------- |
---|
| 1304 | |
---|
[10368] | 1305 | The on-line computation of floats advected either by the three dimensional velocity field or constraint to |
---|
| 1306 | remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project. |
---|
[9413] | 1307 | Options are defined by \ngn{namflo} namelis variables. |
---|
[10368] | 1308 | The algorithm used is based either on the work of \cite{Blanke_Raynaud_JPO97} (default option), |
---|
| 1309 | or on a $4^th$ Runge-Hutta algorithm (\np{ln\_flork4}\forcode{ = .true.}). |
---|
| 1310 | Note that the \cite{Blanke_Raynaud_JPO97} algorithm have the advantage of providing trajectories which |
---|
[9413] | 1311 | are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry. |
---|
[2541] | 1312 | |
---|
[9413] | 1313 | \subsubsection{Input data: initial coordinates} |
---|
[3294] | 1314 | |
---|
[10368] | 1315 | Initial coordinates can be given with Ariane Tools convention |
---|
| 1316 | (IJK coordinates, (\np{ln\_ariane}\forcode{ = .true.}) ) or with longitude and latitude. |
---|
[3294] | 1317 | |
---|
[9413] | 1318 | In case of Ariane convention, input filename is \np{init\_float\_ariane}. |
---|
| 1319 | Its format is: \\ |
---|
| 1320 | {\scriptsize \texttt{I J K nisobfl itrash itrash}} |
---|
[3294] | 1321 | |
---|
[9413] | 1322 | \noindent with: |
---|
[3294] | 1323 | |
---|
| 1324 | - I,J,K : indexes of initial position |
---|
| 1325 | |
---|
| 1326 | - nisobfl: 0 for an isobar float, 1 for a float following the w velocity |
---|
| 1327 | |
---|
| 1328 | - itrash : set to zero; it is a dummy variable to respect Ariane Tools convention |
---|
| 1329 | |
---|
[9413] | 1330 | \noindent Example: \\ |
---|
| 1331 | \noindent {\scriptsize \texttt{ |
---|
| 1332 | 100.00000 90.00000 -1.50000 1.00000 0.00000 \\ |
---|
| 1333 | 102.00000 90.00000 -1.50000 1.00000 0.00000 \\ |
---|
| 1334 | 104.00000 90.00000 -1.50000 1.00000 0.00000 \\ |
---|
| 1335 | 106.00000 90.00000 -1.50000 1.00000 0.00000 \\ |
---|
| 1336 | 108.00000 90.00000 -1.50000 1.00000 0.00000}} \\ |
---|
[3294] | 1337 | |
---|
[9413] | 1338 | In the other case (longitude and latitude), input filename is init\_float. |
---|
| 1339 | Its format is: \\ |
---|
| 1340 | {\scriptsize \texttt{Long Lat depth nisobfl ngrpfl itrash}} |
---|
[3294] | 1341 | |
---|
| 1342 | \noindent with: |
---|
| 1343 | |
---|
| 1344 | - Long, Lat, depth : Longitude, latitude, depth |
---|
| 1345 | |
---|
| 1346 | - nisobfl: 0 for an isobar float, 1 for a float following the w velocity |
---|
| 1347 | |
---|
| 1348 | - ngrpfl : number to identify searcher group |
---|
| 1349 | |
---|
| 1350 | - itrash :set to 1; it is a dummy variable. |
---|
| 1351 | |
---|
[9413] | 1352 | \noindent Example: \\ |
---|
| 1353 | \noindent {\scriptsize \texttt{ |
---|
| 1354 | 20.0 0.0 0.0 0 1 1 \\ |
---|
| 1355 | -21.0 0.0 0.0 0 1 1 \\ |
---|
| 1356 | -22.0 0.0 0.0 0 1 1 \\ |
---|
| 1357 | -23.0 0.0 0.0 0 1 1 \\ |
---|
| 1358 | -24.0 0.0 0.0 0 1 1 }} \\ |
---|
[3294] | 1359 | |
---|
| 1360 | \np{jpnfl} is the total number of floats during the run. |
---|
[10368] | 1361 | When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{ = .true.} ), |
---|
[9413] | 1362 | \np{jpnflnewflo} can be added in the initialization file. |
---|
[3294] | 1363 | |
---|
[9393] | 1364 | \subsubsection{Output data} |
---|
[3294] | 1365 | |
---|
[10368] | 1366 | \np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} is the frequency of |
---|
| 1367 | creation of the float restart file. |
---|
[3294] | 1368 | |
---|
[9413] | 1369 | Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{ = .true.}). |
---|
| 1370 | In that case, output filename is trajec\_float. |
---|
[3294] | 1371 | |
---|
[9413] | 1372 | Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{ = .false.}). |
---|
| 1373 | There are 2 possibilities: |
---|
[3294] | 1374 | |
---|
[10368] | 1375 | - if (\key{iomput}) is used, outputs are selected in iodef.xml. |
---|
| 1376 | Here it is an example of specification to put in files description section: |
---|
[3294] | 1377 | |
---|
[9392] | 1378 | \begin{xmllines} |
---|
[9413] | 1379 | <group id="1d_grid_T" name="auto" description="ocean T grid variables" > } |
---|
| 1380 | <file id="floats" description="floats variables"> } |
---|
| 1381 | <field ref="traj_lon" name="floats_longitude" freq_op="86400" />} |
---|
| 1382 | <field ref="traj_lat" name="floats_latitude" freq_op="86400" />} |
---|
| 1383 | <field ref="traj_dep" name="floats_depth" freq_op="86400" />} |
---|
| 1384 | <field ref="traj_temp" name="floats_temperature" freq_op="86400" />} |
---|
| 1385 | <field ref="traj_salt" name="floats_salinity" freq_op="86400" />} |
---|
| 1386 | <field ref="traj_dens" name="floats_density" freq_op="86400" />} |
---|
| 1387 | <field ref="traj_group" name="floats_group" freq_op="86400" />} |
---|
| 1388 | </file>} |
---|
| 1389 | </group>} |
---|
[9392] | 1390 | \end{xmllines} |
---|
[3294] | 1391 | |
---|
[9392] | 1392 | - if (\key{iomput}) is not used, a file called \ifile{trajec\_float} will be created by IOIPSL library. |
---|
[3294] | 1393 | |
---|
[10368] | 1394 | See also \href{http://stockage.univ-brest.fr/~grima/Ariane/}{here} the web site describing the off-line use of |
---|
| 1395 | this marvellous diagnostic tool. |
---|
[2541] | 1396 | |
---|
| 1397 | % ------------------------------------------------------------------------------------------------------------- |
---|
[3294] | 1398 | % Harmonic analysis of tidal constituents |
---|
| 1399 | % ------------------------------------------------------------------------------------------------------------- |
---|
[9363] | 1400 | \section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) } |
---|
[9407] | 1401 | \label{sec:DIA_diag_harm} |
---|
[3294] | 1402 | |
---|
| 1403 | %------------------------------------------namdia_harm---------------------------------------------------- |
---|
[10146] | 1404 | % |
---|
| 1405 | \nlst{nam_diaharm} |
---|
[3294] | 1406 | %---------------------------------------------------------------------------------------------------------- |
---|
| 1407 | |
---|
[9413] | 1408 | A module is available to compute the amplitude and phase of tidal waves. |
---|
[6289] | 1409 | This on-line Harmonic analysis is actived with \key{diaharm}. |
---|
[9413] | 1410 | |
---|
[10368] | 1411 | Some parameters are available in namelist \ngn{namdia\_harm}: |
---|
[3294] | 1412 | |
---|
[9413] | 1413 | - \np{nit000\_han} is the first time step used for harmonic analysis |
---|
[3294] | 1414 | |
---|
[9413] | 1415 | - \np{nitend\_han} is the last time step used for harmonic analysis |
---|
[3294] | 1416 | |
---|
[9413] | 1417 | - \np{nstep\_han} is the time step frequency for harmonic analysis |
---|
[3294] | 1418 | |
---|
[9413] | 1419 | - \np{nb\_ana} is the number of harmonics to analyse |
---|
[3294] | 1420 | |
---|
[9413] | 1421 | - \np{tname} is an array with names of tidal constituents to analyse |
---|
[3294] | 1422 | |
---|
[10368] | 1423 | \np{nit000\_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation. |
---|
| 1424 | The restart capability is not implemented. |
---|
[3294] | 1425 | |
---|
[10368] | 1426 | The Harmonic analysis solve the following equation: |
---|
[3294] | 1427 | |
---|
[9413] | 1428 | \[h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i}\] |
---|
| 1429 | |
---|
[10368] | 1430 | With $A_{j}$, $\nu_{j}$, $\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error. |
---|
[3294] | 1431 | $h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\ |
---|
| 1432 | We can rewrite this equation: |
---|
| 1433 | |
---|
[9413] | 1434 | \[h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i}\] |
---|
| 1435 | |
---|
| 1436 | with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ and $\phi_{j}=arctan(S_{j}/C_{j})$. |
---|
| 1437 | |
---|
[3294] | 1438 | We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave. |
---|
| 1439 | |
---|
| 1440 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 1441 | % Sections transports |
---|
| 1442 | % ------------------------------------------------------------------------------------------------------------- |
---|
[9363] | 1443 | \section{Transports across sections (\protect\key{diadct}) } |
---|
[9407] | 1444 | \label{sec:DIA_diag_dct} |
---|
[3294] | 1445 | |
---|
[6497] | 1446 | %------------------------------------------namdct---------------------------------------------------- |
---|
[10146] | 1447 | |
---|
| 1448 | \nlst{namdct} |
---|
[6497] | 1449 | %------------------------------------------------------------------------------------------------------------- |
---|
| 1450 | |
---|
[10368] | 1451 | A module is available to compute the transport of volume, heat and salt through sections. |
---|
[6289] | 1452 | This diagnostic is actived with \key{diadct}. |
---|
[3294] | 1453 | |
---|
[9413] | 1454 | Each section is defined by the coordinates of its 2 extremities. |
---|
[10368] | 1455 | The pathways between them are contructed using tools which can be found in \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT} |
---|
| 1456 | and are written in a binary file \texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is later read in by |
---|
| 1457 | NEMO to compute on-line transports. |
---|
[3294] | 1458 | |
---|
[9413] | 1459 | The on-line transports module creates three output ascii files: |
---|
[3294] | 1460 | |
---|
[9413] | 1461 | - \texttt{volume\_transport} for volume transports (unit: $10^{6} m^{3} s^{-1}$) |
---|
[3294] | 1462 | |
---|
[9413] | 1463 | - \texttt{heat\_transport} for heat transports (unit: $10^{15} W$) |
---|
[3294] | 1464 | |
---|
[9413] | 1465 | - \texttt{salt\_transport} for salt transports (unit: $10^{9}Kg s^{-1}$) \\ |
---|
[3294] | 1466 | |
---|
[10368] | 1467 | Namelist variables in \ngn{namdct} control how frequently the flows are summed and the time scales over which |
---|
| 1468 | they are averaged, as well as the level of output for debugging: |
---|
[9413] | 1469 | \np{nn\_dct} : frequency of instantaneous transports computing |
---|
[9393] | 1470 | \np{nn\_dctwri}: frequency of writing ( mean of instantaneous transports ) |
---|
[9413] | 1471 | \np{nn\_debug} : debugging of the section |
---|
[3294] | 1472 | |
---|
[9393] | 1473 | \subsubsection{Creating a binary file containing the pathway of each section} |
---|
[3294] | 1474 | |
---|
[10368] | 1475 | In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run}, |
---|
| 1476 | the file \textit{ {list\_sections.ascii\_global}} contains a list of all the sections that are to be computed |
---|
| 1477 | (this list of sections is based on MERSEA project metrics). |
---|
[3294] | 1478 | |
---|
[9413] | 1479 | Another file is available for the GYRE configuration (\texttt{ {list\_sections.ascii\_GYRE}}). |
---|
[3294] | 1480 | |
---|
[9413] | 1481 | Each section is defined by: \\ |
---|
| 1482 | \noindent {\scriptsize \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\ |
---|
[3294] | 1483 | with: |
---|
| 1484 | |
---|
[9413] | 1485 | - \texttt{long1 lat1}, coordinates of the first extremity of the section; |
---|
[3294] | 1486 | |
---|
[9413] | 1487 | - \texttt{long2 lat2}, coordinates of the second extremity of the section; |
---|
[3294] | 1488 | |
---|
[9413] | 1489 | - \texttt{nclass} the number of bounds of your classes (e.g. 3 bounds for 2 classes); |
---|
[3294] | 1490 | |
---|
[9413] | 1491 | - \texttt{okstrpond} to compute heat and salt transports, \texttt{nostrpond} if no; |
---|
[3294] | 1492 | |
---|
[9413] | 1493 | - \texttt{ice} to compute surface and volume ice transports, \texttt{noice} if no. \\ |
---|
[3294] | 1494 | |
---|
[10368] | 1495 | \noindent The results of the computing of transports, and the directions of positive and |
---|
| 1496 | negative flow do not depend on the order of the 2 extremities in this file. \\ |
---|
[3294] | 1497 | |
---|
[10368] | 1498 | \noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\ |
---|
[9413] | 1499 | {\scriptsize \texttt{ |
---|
| 1500 | long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\ |
---|
| 1501 | classtype \\ |
---|
| 1502 | zbound1 \\ |
---|
| 1503 | zbound2 \\ |
---|
| 1504 | . \\ |
---|
| 1505 | . \\ |
---|
| 1506 | nclass-1 \\ |
---|
| 1507 | nclass}} |
---|
[3294] | 1508 | |
---|
| 1509 | \noindent where \texttt{classtype} can be: |
---|
| 1510 | |
---|
[9413] | 1511 | - \texttt{zsal} for salinity classes |
---|
[3294] | 1512 | |
---|
[9413] | 1513 | - \texttt{ztem} for temperature classes |
---|
[3294] | 1514 | |
---|
[9413] | 1515 | - \texttt{zlay} for depth classes |
---|
[3294] | 1516 | |
---|
[9413] | 1517 | - \texttt{zsigi} for insitu density classes |
---|
[3294] | 1518 | |
---|
[9413] | 1519 | - \texttt{zsigp} for potential density classes \\ |
---|
[3294] | 1520 | |
---|
[10368] | 1521 | The script \texttt{job.ksh} computes the pathway for each section and creates a binary file |
---|
| 1522 | \texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is read by NEMO. \\ |
---|
[3294] | 1523 | |
---|
[10368] | 1524 | It is possible to use this tools for new configuations: \texttt{job.ksh} has to be updated with |
---|
| 1525 | the coordinates file name and path. \\ |
---|
[3294] | 1526 | |
---|
[10368] | 1527 | Examples of two sections, the ACC\_Drake\_Passage with no classes, |
---|
| 1528 | and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\ |
---|
[9413] | 1529 | \noindent {\scriptsize \texttt{ |
---|
| 1530 | -68. -54.5 -60. -64.7 00 okstrpond noice ACC\_Drake\_Passage \\ |
---|
| 1531 | -80.5 22.5 -80.5 25.5 05 nostrpond noice ATL\_Cuba\_Florida \\ |
---|
| 1532 | ztem \\ |
---|
| 1533 | -2.0 \\ |
---|
| 1534 | 4.5 \\ |
---|
| 1535 | 7.0 \\ |
---|
| 1536 | 12.0 \\ |
---|
| 1537 | 40.0}} |
---|
[3294] | 1538 | |
---|
[9393] | 1539 | \subsubsection{To read the output files} |
---|
[3294] | 1540 | |
---|
[9413] | 1541 | The output format is: \\ |
---|
| 1542 | {\scriptsize \texttt{ |
---|
| 1543 | date, time-step number, section number, \\ |
---|
| 1544 | section name, section slope coefficient, class number, \\ |
---|
| 1545 | class name, class bound 1 , classe bound2, \\ |
---|
| 1546 | transport\_direction1, transport\_direction2, \\ |
---|
| 1547 | transport\_total}} \\ |
---|
[3294] | 1548 | |
---|
[10368] | 1549 | For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class and |
---|
| 1550 | the last line corresponds to the total transport summed over all classes. |
---|
| 1551 | For sections with no classes, class number \texttt{1} corresponds to \texttt{total class} and |
---|
[9413] | 1552 | this class is called \texttt{N}, meaning \texttt{none}. |
---|
[3294] | 1553 | |
---|
[9413] | 1554 | - \texttt{transport\_direction1} is the positive part of the transport ($\geq$ 0). |
---|
[3294] | 1555 | |
---|
[9413] | 1556 | - \texttt{transport\_direction2} is the negative part of the transport ($\leq$ 0). \\ |
---|
[3294] | 1557 | |
---|
[10368] | 1558 | \noindent The \texttt{section slope coefficient} gives information about the significance of transports signs and |
---|
| 1559 | direction: \\ |
---|
[3294] | 1560 | |
---|
[9413] | 1561 | \begin{table} \scriptsize |
---|
| 1562 | \begin{tabular}{|l|l|l|l|l|} \hline |
---|
| 1563 | section slope coefficient & section type & direction 1 & direction 2 & total transport |
---|
| 1564 | \\ \hline |
---|
| 1565 | 0. & horizontal & northward & southward & postive: northward |
---|
| 1566 | \\ \hline |
---|
| 1567 | 1000. & vertical & eastward & westward & postive: eastward |
---|
| 1568 | \\ \hline |
---|
| 1569 | \texttt{$\neq$ 0, $\neq$ 1000.} & diagonal & eastward & westward & postive: eastward |
---|
| 1570 | \\ \hline |
---|
| 1571 | \end{tabular} |
---|
| 1572 | \end{table} |
---|
[3294] | 1573 | |
---|
[2541] | 1574 | % ================================================================ |
---|
| 1575 | % Steric effect in sea surface height |
---|
| 1576 | % ================================================================ |
---|
[9393] | 1577 | \section{Diagnosing the steric effect in sea surface height} |
---|
[9407] | 1578 | \label{sec:DIA_steric} |
---|
[2541] | 1579 | |
---|
| 1580 | |
---|
[10368] | 1581 | Changes in steric sea level are caused when changes in the density of the water column imply an expansion or |
---|
| 1582 | contraction of the column. |
---|
| 1583 | It is essentially produced through surface heating/cooling and to a lesser extent through non-linear effects of |
---|
| 1584 | the equation of state (cabbeling, thermobaricity...). |
---|
[9413] | 1585 | Non-Boussinesq models contain all ocean effects within the ocean acting on the sea level. |
---|
| 1586 | In particular, they include the steric effect. |
---|
[10368] | 1587 | In contrast, Boussinesq models, such as \NEMO, conserve volume, rather than mass, |
---|
[9413] | 1588 | and so do not properly represent expansion or contraction. |
---|
| 1589 | The steric effect is therefore not explicitely represented. |
---|
[10368] | 1590 | This approximation does not represent a serious error with respect to the flow field calculated by the model |
---|
| 1591 | \citep{Greatbatch_JGR94}, but extra attention is required when investigating sea level, |
---|
| 1592 | as steric changes are an important contribution to local changes in sea level on seasonal and climatic time scales. |
---|
| 1593 | This is especially true for investigation into sea level rise due to global warming. |
---|
[2541] | 1594 | |
---|
[10368] | 1595 | Fortunately, the steric contribution to the sea level consists of a spatially uniform component that |
---|
[9413] | 1596 | can be diagnosed by considering the mass budget of the world ocean \citep{Greatbatch_JGR94}. |
---|
[10368] | 1597 | In order to better understand how global mean sea level evolves and thus how the steric sea level can be diagnosed, |
---|
| 1598 | we compare, in the following, the non-Boussinesq and Boussinesq cases. |
---|
[2541] | 1599 | |
---|
[9413] | 1600 | Let denote |
---|
| 1601 | $\mathcal{M}$ the total mass of liquid seawater ($\mathcal{M} = \int_D \rho dv$), |
---|
| 1602 | $\mathcal{V}$ the total volume of seawater ($\mathcal{V} = \int_D dv$), |
---|
| 1603 | $\mathcal{A}$ the total surface of the ocean ($\mathcal{A} = \int_S ds$), |
---|
| 1604 | $\bar{\rho}$ the global mean seawater (\textit{in situ}) density |
---|
| 1605 | ($\bar{\rho} = 1/\mathcal{V} \int_D \rho \,dv$), and |
---|
| 1606 | $\bar{\eta}$ the global mean sea level |
---|
| 1607 | ($\bar{\eta} = 1/\mathcal{A} \int_S \eta \,ds$). |
---|
[2541] | 1608 | |
---|
| 1609 | A non-Boussinesq fluid conserves mass. It satisfies the following relations: |
---|
[9413] | 1610 | |
---|
[9414] | 1611 | \[ \begin{split} |
---|
[9413] | 1612 | \mathcal{M} &= \mathcal{V} \;\bar{\rho} \\ |
---|
| 1613 | \mathcal{V} &= \mathcal{A} \;\bar{\eta} |
---|
[9414] | 1614 | \end{split} \label{eq:MV_nBq} |
---|
| 1615 | \] |
---|
[9413] | 1616 | |
---|
[10368] | 1617 | Temporal changes in total mass is obtained from the density conservation equation: |
---|
[9413] | 1618 | |
---|
| 1619 | \[ \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} ) |
---|
| 1620 | = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface} |
---|
| 1621 | \label{eq:Co_nBq} \] |
---|
| 1622 | |
---|
[10368] | 1623 | where $\rho$ is the \textit{in situ} density, and \textit{emp} the surface mass exchanges with the other media of |
---|
| 1624 | the Earth system (atmosphere, sea-ice, land). |
---|
[2541] | 1625 | Its global averaged leads to the total mass change |
---|
[9413] | 1626 | |
---|
| 1627 | \[ \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}} |
---|
| 1628 | \label{eq:Mass_nBq} \] |
---|
| 1629 | |
---|
| 1630 | where $\overline{\textit{emp}} = \int_S \textit{emp}\,ds$ is the net mass flux through the ocean surface. |
---|
[10368] | 1631 | Bringing \autoref{eq:Mass_nBq} and the time derivative of \autoref{eq:MV_nBq} together leads to |
---|
[9413] | 1632 | the evolution equation of the mean sea level |
---|
| 1633 | |
---|
| 1634 | \[ \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}} |
---|
| 1635 | - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}} |
---|
| 1636 | \label{eq:ssh_nBq} \] |
---|
| 1637 | |
---|
[10368] | 1638 | The first term in equation \autoref{eq:ssh_nBq} alters sea level by adding or subtracting mass from the ocean. |
---|
| 1639 | The second term arises from temporal changes in the global mean density; $i.e.$ from steric effects. |
---|
[2541] | 1640 | |
---|
[10368] | 1641 | In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ appears multiplied by |
---|
| 1642 | the gravity ($i.e.$ in the hydrostatic balance of the primitive Equations). |
---|
| 1643 | In particular, the mass conservation equation, \autoref{eq:Co_nBq}, degenerates into the incompressibility equation: |
---|
[9413] | 1644 | |
---|
| 1645 | \[ \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) |
---|
| 1646 | = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface} |
---|
| 1647 | \label{eq:Co_Bq} \] |
---|
| 1648 | |
---|
[2541] | 1649 | and the global average of this equation now gives the temporal change of the total volume, |
---|
[9413] | 1650 | |
---|
| 1651 | \[ \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o} |
---|
| 1652 | \label{eq:V_Bq} \] |
---|
| 1653 | |
---|
[10368] | 1654 | Only the volume is conserved, not mass, or, more precisely, the mass which is conserved is the Boussinesq mass, |
---|
| 1655 | $\mathcal{M}_o = \rho_o \mathcal{V}$. |
---|
| 1656 | The total volume (or equivalently the global mean sea level) is altered only by net volume fluxes across |
---|
| 1657 | the ocean surface, not by changes in mean mass of the ocean: the steric effect is missing in a Boussinesq fluid. |
---|
[9413] | 1658 | |
---|
[10368] | 1659 | Nevertheless, following \citep{Greatbatch_JGR94}, the steric effect on the volume can be diagnosed by |
---|
[9413] | 1660 | considering the mass budget of the ocean. |
---|
[10368] | 1661 | The apparent changes in $\mathcal{M}$, mass of the ocean, which are not induced by surface mass flux |
---|
| 1662 | must be compensated by a spatially uniform change in the mean sea level due to expansion/contraction of the ocean |
---|
| 1663 | \citep{Greatbatch_JGR94}. |
---|
| 1664 | In others words, the Boussinesq mass, $\mathcal{M}_o$, can be related to $\mathcal{M}$, |
---|
| 1665 | the total mass of the ocean seen by the Boussinesq model, via the steric contribution to the sea level, |
---|
[9413] | 1666 | $\eta_s$, a spatially uniform variable, as follows: |
---|
| 1667 | |
---|
| 1668 | \[ \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A} |
---|
| 1669 | \label{eq:M_Bq} \] |
---|
| 1670 | |
---|
[10368] | 1671 | Any change in $\mathcal{M}$ which cannot be explained by the net mass flux through the ocean surface |
---|
| 1672 | is converted into a mean change in sea level. |
---|
| 1673 | Introducing the total density anomaly, $\mathcal{D}= \int_D d_a \,dv$, |
---|
| 1674 | where $d_a = (\rho -\rho_o ) / \rho_o$ is the density anomaly used in \NEMO (cf. \autoref{subsec:TRA_eos}) |
---|
| 1675 | in \autoref{eq:M_Bq} leads to a very simple form for the steric height: |
---|
[2541] | 1676 | |
---|
[9413] | 1677 | \[ \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D} |
---|
| 1678 | \label{eq:steric_Bq} \] |
---|
| 1679 | |
---|
[2541] | 1680 | The above formulation of the steric height of a Boussinesq ocean requires four remarks. |
---|
| 1681 | First, one can be tempted to define $\rho_o$ as the initial value of $\mathcal{M}/\mathcal{V}$, |
---|
[9413] | 1682 | $i.e.$ set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero. |
---|
| 1683 | We do not recommend that. |
---|
| 1684 | Indeed, in this case $\rho_o$ depends on the initial state of the ocean. |
---|
[10368] | 1685 | Since $\rho_o$ has a direct effect on the dynamics of the ocean |
---|
| 1686 | (it appears in the pressure gradient term of the momentum equation) |
---|
| 1687 | it is definitively not a good idea when inter-comparing experiments. |
---|
[9413] | 1688 | We better recommend to fixe once for all $\rho_o$ to $1035\;Kg\,m^{-3}$. |
---|
[10368] | 1689 | This value is a sensible choice for the reference density used in a Boussinesq ocean climate model since, |
---|
| 1690 | with the exception of only a small percentage of the ocean, density in the World Ocean varies by no more than |
---|
| 1691 | 2$\%$ from this value (\cite{Gill1982}, page 47). |
---|
[2541] | 1692 | |
---|
[10368] | 1693 | Second, we have assumed here that the total ocean surface, $\mathcal{A}$, |
---|
| 1694 | does not change when the sea level is changing as it is the case in all global ocean GCMs |
---|
[9413] | 1695 | (wetting and drying of grid point is not allowed). |
---|
[2541] | 1696 | |
---|
[10368] | 1697 | Third, the discretisation of \autoref{eq:steric_Bq} depends on the type of free surface which is considered. |
---|
[9413] | 1698 | In the non linear free surface case, $i.e.$ \key{vvl} defined, it is given by |
---|
[2541] | 1699 | |
---|
[9413] | 1700 | \[ \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} } |
---|
| 1701 | { \sum_{i,\,j,\,k} e_{1t} e_{2t} e_{3t} } |
---|
| 1702 | \label{eq:discrete_steric_Bq_nfs} \] |
---|
| 1703 | |
---|
[10368] | 1704 | whereas in the linear free surface, |
---|
| 1705 | the volume above the \textit{z=0} surface must be explicitly taken into account to |
---|
| 1706 | better approximate the total ocean mass and thus the steric sea level: |
---|
[9413] | 1707 | |
---|
| 1708 | \[ \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta } |
---|
| 1709 | { \sum_{i,\,j,\,k} e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} e_{1t}e_{2t} \eta } |
---|
| 1710 | \label{eq:discrete_steric_Bq_fs} \] |
---|
| 1711 | |
---|
[2541] | 1712 | The fourth and last remark concerns the effective sea level and the presence of sea-ice. |
---|
[9413] | 1713 | In the real ocean, sea ice (and snow above it) depresses the liquid seawater through its mass loading. |
---|
| 1714 | This depression is a result of the mass of sea ice/snow system acting on the liquid ocean. |
---|
[10368] | 1715 | There is, however, no dynamical effect associated with these depressions in the liquid ocean sea level, |
---|
[9413] | 1716 | so that there are no associated ocean currents. |
---|
[10368] | 1717 | Hence, the dynamically relevant sea level is the effective sea level, |
---|
| 1718 | $i.e.$ the sea level as if sea ice (and snow) were converted to liquid seawater \citep{Campin_al_OM08}. |
---|
| 1719 | However, in the current version of \NEMO the sea-ice is levitating above the ocean without mass exchanges between |
---|
| 1720 | ice and ocean. |
---|
| 1721 | Therefore the model effective sea level is always given by $\eta + \eta_s$, whether or not there is sea ice present. |
---|
[2541] | 1722 | |
---|
[9413] | 1723 | In AR5 outputs, the thermosteric sea level is demanded. |
---|
| 1724 | It is steric sea level due to changes in ocean density arising just from changes in temperature. |
---|
| 1725 | It is given by: |
---|
| 1726 | |
---|
| 1727 | \[ \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv |
---|
| 1728 | \label{eq:thermosteric_Bq} \] |
---|
| 1729 | |
---|
[2541] | 1730 | where $S_o$ and $p_o$ are the initial salinity and pressure, respectively. |
---|
| 1731 | |
---|
[10368] | 1732 | Both steric and thermosteric sea level are computed in \mdl{diaar5} which needs the \key{diaar5} defined to |
---|
| 1733 | be called. |
---|
[2541] | 1734 | |
---|
[6497] | 1735 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 1736 | % Other Diagnostics |
---|
| 1737 | % ------------------------------------------------------------------------------------------------------------- |
---|
[9393] | 1738 | \section{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})} |
---|
[9407] | 1739 | \label{sec:DIA_diag_others} |
---|
[6497] | 1740 | |
---|
[9413] | 1741 | Aside from the standard model variables, other diagnostics can be computed on-line. |
---|
| 1742 | The available ready-to-add diagnostics modules can be found in directory DIA. |
---|
[6497] | 1743 | |
---|
[9363] | 1744 | \subsection{Depth of various quantities (\protect\mdl{diahth})} |
---|
[6497] | 1745 | |
---|
[10368] | 1746 | Among the available diagnostics the following ones are obtained when defining the \key{diahth} CPP key: |
---|
[6497] | 1747 | |
---|
| 1748 | - the mixed layer depth (based on a density criterion \citep{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth}) |
---|
| 1749 | |
---|
| 1750 | - the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth}) |
---|
| 1751 | |
---|
| 1752 | - the depth of the 20\deg C isotherm (\mdl{diahth}) |
---|
| 1753 | |
---|
| 1754 | - the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) |
---|
| 1755 | |
---|
| 1756 | % ----------------------------------------------------------- |
---|
| 1757 | % Poleward heat and salt transports |
---|
| 1758 | % ----------------------------------------------------------- |
---|
| 1759 | |
---|
[9363] | 1760 | \subsection{Poleward heat and salt transports (\protect\mdl{diaptr})} |
---|
[6497] | 1761 | |
---|
| 1762 | %------------------------------------------namptr----------------------------------------- |
---|
[10146] | 1763 | |
---|
| 1764 | \nlst{namptr} |
---|
[6497] | 1765 | %----------------------------------------------------------------------------------------- |
---|
| 1766 | |
---|
[10368] | 1767 | The poleward heat and salt transports, their advective and diffusive component, |
---|
| 1768 | and the meriodional stream function can be computed on-line in \mdl{diaptr} \np{ln\_diaptr} to true |
---|
[9413] | 1769 | (see the \textit{\ngn{namptr} } namelist below). |
---|
[10368] | 1770 | When \np{ln\_subbas}\forcode{ = .true.}, transports and stream function are computed for the Atlantic, Indian, |
---|
| 1771 | Pacific and Indo-Pacific Oceans (defined north of 30\deg S) as well as for the World Ocean. |
---|
| 1772 | The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays, |
---|
| 1773 | the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:mask_subasins}). |
---|
[6497] | 1774 | |
---|
| 1775 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
[10368] | 1776 | \begin{figure}[!t] |
---|
| 1777 | \begin{center} |
---|
| 1778 | \includegraphics[width=1.0\textwidth]{Fig_mask_subasins} |
---|
| 1779 | \caption{ \protect\label{fig:mask_subasins} |
---|
| 1780 | Decomposition of the World Ocean (here ORCA2) into sub-basin used in to |
---|
| 1781 | compute the heat and salt transports as well as the meridional stream-function: |
---|
| 1782 | Atlantic basin (red), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green). |
---|
| 1783 | Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay are removed from the sub-basins. |
---|
| 1784 | Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line.} |
---|
[9413] | 1785 | \end{center} \end{figure} |
---|
[6497] | 1786 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
| 1787 | |
---|
| 1788 | % ----------------------------------------------------------- |
---|
| 1789 | % CMIP specific diagnostics |
---|
| 1790 | % ----------------------------------------------------------- |
---|
[9363] | 1791 | \subsection{CMIP specific diagnostics (\protect\mdl{diaar5})} |
---|
[6497] | 1792 | |
---|
[9413] | 1793 | A series of diagnostics has been added in the \mdl{diaar5}. |
---|
[6497] | 1794 | They corresponds to outputs that are required for AR5 simulations (CMIP5) |
---|
[9413] | 1795 | (see also \autoref{sec:DIA_steric} for one of them). |
---|
[6497] | 1796 | Activating those outputs requires to define the \key{diaar5} CPP key. |
---|
| 1797 | |
---|
| 1798 | % ----------------------------------------------------------- |
---|
| 1799 | % 25 hour mean and hourly Surface, Mid and Bed |
---|
| 1800 | % ----------------------------------------------------------- |
---|
[9393] | 1801 | \subsection{25 hour mean output for tidal models} |
---|
[6497] | 1802 | |
---|
| 1803 | %------------------------------------------nam_dia25h------------------------------------- |
---|
[10146] | 1804 | |
---|
| 1805 | \nlst{nam_dia25h} |
---|
[6497] | 1806 | %----------------------------------------------------------------------------------------- |
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| 1807 | |
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| 1808 | A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean. |
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| 1809 | The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from |
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| 1810 | midnight at the start of the day to midight at the day end. |
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[10368] | 1811 | This diagnostic is actived with the logical $ln\_dia25h$. |
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[6497] | 1812 | |
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| 1813 | % ----------------------------------------------------------- |
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| 1814 | % Top Middle and Bed hourly output |
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| 1815 | % ----------------------------------------------------------- |
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[9393] | 1816 | \subsection{Top middle and bed hourly output} |
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[6497] | 1817 | |
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| 1818 | %------------------------------------------nam_diatmb----------------------------------------------------- |
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[10146] | 1819 | |
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| 1820 | \nlst{nam_diatmb} |
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[6497] | 1821 | %---------------------------------------------------------------------------------------------------------- |
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| 1822 | |
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[10368] | 1823 | A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables. |
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| 1824 | This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs. |
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[9413] | 1825 | The tidal signal is retained but the overall data usage is cut to just three vertical levels. |
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| 1826 | Also the bottom level is calculated for each cell. |
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[10368] | 1827 | This diagnostic is actived with the logical $ln\_diatmb$. |
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[6497] | 1828 | |
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| 1829 | % ----------------------------------------------------------- |
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| 1830 | % Courant numbers |
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| 1831 | % ----------------------------------------------------------- |
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| 1832 | \subsection{Courant numbers} |
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| 1833 | |
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[9413] | 1834 | Courant numbers provide a theoretical indication of the model's numerical stability. |
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| 1835 | The advective Courant numbers can be calculated according to |
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[6497] | 1836 | |
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[9413] | 1837 | \[ C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}} |
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| 1838 | \label{eq:CFL} \] |
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[6497] | 1839 | |
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[9413] | 1840 | in the zonal, meridional and vertical directions respectively. |
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[10368] | 1841 | The vertical component is included although it is not strictly valid as the vertical velocity is calculated from |
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| 1842 | the continuity equation rather than as a prognostic variable. |
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[9413] | 1843 | Physically this represents the rate at which information is propogated across a grid cell. |
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[10368] | 1844 | Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step. |
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[2541] | 1845 | |
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[10368] | 1846 | The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist. |
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[9413] | 1847 | The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. |
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[10368] | 1848 | In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of |
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| 1849 | where the maximum value occurs. |
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| 1850 | At the end of the model run the maximum value of $C_u$, $C_v$, and $C_w$ for the whole model run is printed along |
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| 1851 | with the coordinates of each. |
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[9413] | 1852 | The maximum values from the run are also copied to the ocean.output file. |
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[2541] | 1853 | |
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[9413] | 1854 | % ================================================================ |
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[2541] | 1855 | |
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[6997] | 1856 | \end{document} |
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