Changeset 10414 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex
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r10354 r10414 1 \documentclass[../tex_main/NEMO_manual]{subfiles} 1 \documentclass[../main/NEMO_manual]{subfiles} 2 2 3 \begin{document} 3 4 % ================================================================ … … 6 7 \chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)} 7 8 \label{chap:DIA} 9 8 10 \minitoc 9 11 10 12 \newpage 11 $\ $\newline % force a new line12 13 13 14 % ================================================================ … … 168 169 See the XML basics section below for more details on XML syntax and rules. 169 170 170 \begin{table} \scriptsize 171 \begin{tabularx}{\textwidth}{|lXl|} \hline 172 variable name & 173 description & 174 example \\ \hline \hline 175 buffer\_size & 176 buffer size used by XIOS to send data from NEMO to XIOS. 177 Larger is more efficient. 178 Note that needed/used buffer sizes are summarized at the end of the job & 179 25000000 \\ \hline 180 buffer\_server\_factor\_size & 181 ratio between NEMO and XIOS buffer size. 182 Should be 2. & 183 2 \\ \hline 184 info\_level & 185 verbosity level (0 to 100) & 186 0 \\ \hline 187 using\_server & 188 activate attached(false) or detached(true) mode & 189 true \\ \hline 190 using\_oasis & 191 XIOS is used with OASIS(true) or not (false) & 192 false \\ \hline 193 oasis\_codes\_id & 194 when using oasis, define the identifier of NEMO in the namcouple. 195 Note that the identifier of XIOS is xios.x & 196 oceanx \\ \hline 197 \end{tabularx} 171 \begin{table} 172 \scriptsize 173 \begin{tabularx}{\textwidth}{|lXl|} 174 \hline 175 variable name & 176 description & 177 example \\ 178 \hline 179 \hline 180 buffer\_size & 181 buffer size used by XIOS to send data from NEMO to XIOS. 182 Larger is more efficient. 183 Note that needed/used buffer sizes are summarized at the end of the job & 184 25000000 \\ 185 \hline 186 buffer\_server\_factor\_size & 187 ratio between NEMO and XIOS buffer size. 188 Should be 2. & 189 2 \\ 190 \hline 191 info\_level & 192 verbosity level (0 to 100) & 193 0 \\ 194 \hline 195 using\_server & 196 activate attached(false) or detached(true) mode & 197 true \\ 198 \hline 199 using\_oasis & 200 XIOS is used with OASIS(true) or not (false) & 201 false \\ 202 \hline 203 oasis\_codes\_id & 204 when using oasis, define the identifier of NEMO in the namcouple. 205 Note that the identifier of XIOS is xios.x & 206 oceanx \\ 207 \hline 208 \end{tabularx} 198 209 \end{table} 199 210 … … 281 292 Each tag family has hierarchy of three flavors (except for context): 282 293 283 \begin{table} \scriptsize 284 \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} \hline 285 flavor & description & 286 example \\ \hline \hline 287 root & declaration of the root element that can contain element groups or elements & 288 \xmlcode{<file_definition ... >} \\ \hline 289 group & declaration of a group element that can contain element groups or elements & 290 \xmlcode{<file_group ... >} \\ \hline 291 element & declaration of an element that can contain elements & 292 \xmlcode{<file ... >} \\ \hline 293 \end{tabular*} 294 \begin{table} 295 \scriptsize 296 \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 297 \hline 298 flavor & description & 299 example \\ 300 \hline 301 \hline 302 root & declaration of the root element that can contain element groups or elements & 303 \xmlcode{<file_definition ... >} \\ 304 \hline 305 group & declaration of a group element that can contain element groups or elements & 306 \xmlcode{<file_group ... >} \\ 307 \hline 308 element & declaration of an element that can contain elements & 309 \xmlcode{<file ... >} \\ 310 \hline 311 \end{tabular*} 294 312 \end{table} 295 313 … … 306 324 In \NEMO, we used the following contexts (that can be defined in any order): 307 325 308 \begin{table} \scriptsize 309 \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} \hline 310 context & description & 311 example \\ \hline \hline 312 context xios & context containing information for XIOS & 313 \xmlcode{<context id="xios" ... >} \\ \hline 314 context nemo & context containing IO information for NEMO (mother grid when using AGRIF) & 315 \xmlcode{<context id="nemo" ... >} \\ \hline 316 context 1\_nemo & context containing IO information for NEMO child grid 1 (when using AGRIF) & 317 \xmlcode{<context id="1_nemo" ... >} \\ \hline 318 context n\_nemo & context containing IO information for NEMO child grid n (when using AGRIF) & 319 \xmlcode{<context id="n_nemo" ... >} \\ \hline 326 \begin{table} 327 \scriptsize 328 \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 329 \hline 330 context & description & 331 example \\ 332 \hline 333 \hline 334 context xios & context containing information for XIOS & 335 \xmlcode{<context id="xios" ... >} \\ 336 \hline 337 context nemo & context containing IO information for NEMO (mother grid when using AGRIF) & 338 \xmlcode{<context id="nemo" ... >} \\ 339 \hline 340 context 1\_nemo & context containing IO information for NEMO child grid 1 (when using AGRIF) & 341 \xmlcode{<context id="1_nemo" ... >} \\ 342 \hline 343 context n\_nemo & context containing IO information for NEMO child grid n (when using AGRIF) & 344 \xmlcode{<context id="n_nemo" ... >} \\ 345 \hline 346 \end{tabular} 347 \end{table} 348 349 \noindent The xios context contains only 1 tag: 350 351 \begin{table} 352 \scriptsize 353 \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 354 \hline 355 context tag & 356 description & 357 example \\ 358 \hline 359 \hline 360 variable\_definition & 361 define variables needed by XIOS. 362 This can be seen as a kind of namelist for XIOS. & 363 \xmlcode{<variable_definition ... >} \\ 364 \hline 320 365 \end{tabular} 321 366 \end{table} 322 367 323 \noindent The xios context contains only 1 tag:324 325 \begin{table} \scriptsize326 \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} \hline327 context tag &328 description &329 example \\ \hline \hline330 variable\_definition &331 define variables needed by XIOS.332 This can be seen as a kind of namelist for XIOS. &333 \xmlcode{<variable_definition ... >} \\ \hline334 \end{tabular}335 \end{table}336 337 368 \noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts 338 369 (that can be defined in any order): 339 370 340 \begin{table} \scriptsize 341 \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} \hline 342 context tag & description & 343 example \\ \hline \hline 344 field\_definition & define all variables that can potentially be outputted & 345 \xmlcode{<field_definition ... >} \\ \hline 346 file\_definition & define the netcdf files to be created and the variables they will contain & 347 \xmlcode{<file_definition ... >} \\ \hline 348 axis\_definition & define vertical axis & 349 \xmlcode{<axis_definition ... >} \\ \hline 350 domain\_definition & define the horizontal grids & 351 \xmlcode{<domain_definition ... >} \\ \hline 352 grid\_definition & define the 2D and 3D grids (association of an axis and a domain) & 353 \xmlcode{<grid_definition ... >} \\ \hline 354 \end{tabular} 371 \begin{table} 372 \scriptsize 373 \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 374 \hline 375 context tag & description & 376 example \\ 377 \hline 378 \hline 379 field\_definition & define all variables that can potentially be outputted & 380 \xmlcode{<field_definition ... >} \\ 381 \hline 382 file\_definition & define the netcdf files to be created and the variables they will contain & 383 \xmlcode{<file_definition ... >} \\ 384 \hline 385 axis\_definition & define vertical axis & 386 \xmlcode{<axis_definition ... >} \\ 387 \hline 388 domain\_definition & define the horizontal grids & 389 \xmlcode{<domain_definition ... >} \\ 390 \hline 391 grid\_definition & define the 2D and 3D grids (association of an axis and a domain) & 392 \xmlcode{<grid_definition ... >} \\ 393 \hline 394 \end{tabular} 355 395 \end{table} 356 396 … … 538 578 the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by: 539 579 540 \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} 580 \begin{table} 581 \scriptsize 582 \begin{tabularx}{\textwidth}{|lX|} 583 \hline 584 \centering placeholder string & 585 automatically replaced by \\ 586 \hline 587 \hline 588 \centering @expname@ & 589 the experiment name (from cn\_exp in the namelist) \\ 590 \hline 591 \centering @freq@ & 592 output frequency (from attribute output\_freq) \\ 593 \hline 594 \centering @startdate@ & 595 starting date of the simulation (from nn\_date0 in the restart or the namelist). 596 \newline 597 \verb?yyyymmdd? format \\ 598 \hline 599 \centering @startdatefull@ & 600 starting date of the simulation (from nn\_date0 in the restart or the namelist). 601 \newline 602 \verb?yyyymmdd_hh:mm:ss? format \\ 603 \hline 604 \centering @enddate@ & 605 ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). 606 \newline 607 \verb?yyyymmdd? format \\ 608 \hline 609 \centering @enddatefull@ & 610 ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). 611 \newline 612 \verb?yyyymmdd_hh:mm:ss? format \\ 613 \hline 614 \end{tabularx} 561 615 \end{table} 562 616 … … 585 639 \\ 586 640 587 \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} 641 \begin{table} 642 \scriptsize 643 \begin{tabularx}{\textwidth}{|X|c|c|c|} 644 \hline 645 tag ids affected by automatic definition of some of their attributes & 646 name attribute & 647 attribute value \\ 648 \hline 649 \hline 650 field\_definition & 651 freq\_op & 652 \np{rn\_rdt} \\ 653 \hline 654 SBC & 655 freq\_op & 656 \np{rn\_rdt} $\times$ \np{nn\_fsbc} \\ 657 \hline 658 ptrc\_T & 659 freq\_op & 660 \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ 661 \hline 662 diad\_T & 663 freq\_op & 664 \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ 665 \hline 666 EqT, EqU, EqW & 667 jbegin, ni, & 668 according to the grid \\ 669 & 670 name\_suffix & 671 \\ 672 \hline 673 TAO, RAMA and PIRATA moorings & 674 zoom\_ibegin, zoom\_jbegin, & 675 according to the grid \\ 676 & 677 name\_suffix & 678 \\ 679 \hline 680 \end{tabularx} 617 681 \end{table} 618 682 … … 774 838 \subsubsection{Tag list per family} 775 839 776 \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} 840 \begin{table} 841 \scriptsize 842 \begin{tabularx}{\textwidth}{|l|X|X|l|X|} 843 \hline 844 tag name & 845 description & 846 accepted attribute & 847 child of & 848 parent of \\ 849 \hline 850 \hline 851 simulation & 852 this tag is the root tag which encapsulates all the content of the XML file & 853 none & 854 none & 855 context \\ 856 \hline 857 context & 858 encapsulates parts of the XML file dedicated to different codes or different parts of a code & 859 id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin & 860 simulation & 861 all root tags: ... \_definition \\ 862 \hline 863 \end{tabularx} 864 \caption{Context tags} 795 865 \end{table} 796 866 797 \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\_*}")} 867 \begin{table} 868 \scriptsize 869 \begin{tabularx}{\textwidth}{|l|X|X|X|l|} 870 \hline 871 tag name & 872 description & 873 accepted attribute & 874 child of & 875 parent of \\ 876 \hline 877 \hline 878 field\_definition & 879 encapsulates the definition of all the fields that can potentially be outputted & 880 axis\_ref, default\_value, domain\_ref, enabled, grid\_ref, level, operation, prec, src & 881 context & 882 field or field\_group \\ 883 \hline 884 field\_group & 885 encapsulates a group of fields & 886 axis\_ref, default\_value, domain\_ref, enabled, group\_ref, grid\_ref, 887 id, level, operation, prec, src & 888 field\_definition, field\_group, file & 889 field or field\_group \\ 890 \hline 891 field & 892 define a specific field & 893 axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref, 894 id, level, long\_name, name, operation, prec, standard\_name, unit & 895 field\_definition, field\_group, file & 896 none \\ 897 \hline 898 \end{tabularx} 899 \caption{Field tags ("\tt{field\_*}")} 823 900 \end{table} 824 901 825 \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\_*}")} 902 \begin{table} 903 \scriptsize 904 \begin{tabularx}{\textwidth}{|l|X|X|X|l|} 905 \hline 906 tag name & 907 description & 908 accepted attribute & 909 child of & 910 parent of \\ 911 \hline 912 \hline 913 file\_definition & 914 encapsulates the definition of all the files that will be outputted & 915 enabled, min\_digits, name, name\_suffix, output\_level, 916 split\_freq\_format, split\_freq, sync\_freq, type, src & 917 context & 918 file or file\_group \\ 919 \hline 920 file\_group & 921 encapsulates a group of files that will be outputted & 922 enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, 923 split\_freq\_format, split\_freq, sync\_freq, type, src & 924 file\_definition, file\_group & 925 file or file\_group \\ 926 \hline 927 file & 928 define the contents of a file to be outputted & 929 enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, 930 split\_freq\_format, split\_freq, sync\_freq, type, src & 931 file\_definition, file\_group & 932 field \\ 933 \hline 934 \end{tabularx} 935 \caption{File tags ("\tt{file\_*}")} 852 936 \end{table} 853 937 854 \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\_*}")} 938 \begin{table} 939 \scriptsize 940 \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 941 \hline 942 tag name & 943 description & 944 accepted attribute & 945 child of & 946 parent of \\ 947 \hline 948 \hline 949 axis\_definition & 950 define all the vertical axis potentially used by the variables & 951 src & 952 context & 953 axis\_group, axis \\ 954 \hline 955 axis\_group & 956 encapsulates a group of vertical axis & 957 id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size & 958 axis\_definition, axis\_group & 959 axis\_group, axis \\ 960 \hline 961 axis & 962 define a vertical axis & 963 id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size & 964 axis\_definition, axis\_group & 965 none \\ 966 \hline 967 \end{tabularx} 968 \caption{Axis tags ("\tt{axis\_*}")} 878 969 \end{table} 879 970 880 \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\_*)}"} 971 \begin{table} 972 \scriptsize 973 \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 974 \hline 975 tag name & 976 description & 977 accepted attribute & 978 child of & 979 parent of \\ 980 \hline 981 \hline 982 domain\_\-definition & 983 define all the horizontal domains potentially used by the variables & 984 src & 985 context & 986 domain\_\-group, domain \\ 987 \hline 988 domain\_group & 989 encapsulates a group of horizontal domains & 990 id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & 991 domain\_\-definition, domain\_group & 992 domain\_\-group, domain \\ 993 \hline 994 domain & 995 define an horizontal domain & 996 id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & 997 domain\_\-definition, domain\_group & 998 none \\ 999 \hline 1000 \end{tabularx} 1001 \caption{Domain tags ("\tt{domain\_*)}"} 904 1002 \end{table} 905 1003 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\_*}")} 1004 \begin{table} 1005 \scriptsize 1006 \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 1007 \hline 1008 tag name & 1009 description & 1010 accepted attribute & 1011 child of & 1012 parent of \\ 1013 \hline 1014 \hline 1015 grid\_definition & 1016 define all the grid (association of a domain and/or an axis) potentially used by the variables & 1017 src & 1018 context & 1019 grid\_group, grid \\ 1020 \hline 1021 grid\_group & 1022 encapsulates a group of grids & 1023 id, domain\_ref,axis\_ref & 1024 grid\_definition, grid\_group & 1025 grid\_group, grid \\ 1026 \hline 1027 grid & 1028 define a grid & 1029 id, domain\_ref,axis\_ref & 1030 grid\_definition, grid\_group & 1031 none \\ 1032 \hline 1033 \end{tabularx} 1034 \caption{Grid tags ("\tt{grid\_*}")} 930 1035 \end{table} 931 1036 932 1037 \subsubsection{Attributes list per family} 933 1038 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}")} 1039 \begin{table} 1040 \scriptsize 1041 \begin{tabularx}{\textwidth}{|l|X|l|l|} 1042 \hline 1043 attribute name & 1044 description & 1045 example & 1046 accepted by \\ 1047 \hline 1048 \hline 1049 axis\_ref & 1050 refers to the id of a vertical axis & 1051 axis\_ref="deptht" & 1052 field, grid families \\ 1053 \hline 1054 domain\_ref & 1055 refers to the id of a domain & 1056 domain\_ref="grid\_T" & 1057 field or grid families \\ 1058 \hline 1059 field\_ref & 1060 id of the field we want to add in a file & 1061 field\_ref="toce" & 1062 field \\ 1063 \hline 1064 grid\_ref & 1065 refers to the id of a grid & 1066 grid\_ref="grid\_T\_2D" & 1067 field family \\ 1068 \hline 1069 group\_ref & 1070 refer to a group of variables & 1071 group\_ref="mooring" & 1072 field\_group \\ 1073 \hline 1074 \end{tabularx} 1075 \caption{Reference attributes ("\tt{*\_ref}")} 962 1076 \end{table} 963 1077 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\_*}")} 1078 \begin{table} 1079 \scriptsize 1080 \begin{tabularx}{\textwidth}{|l|X|l|l|} 1081 \hline 1082 attribute name & 1083 description & 1084 example & 1085 accepted by \\ 1086 \hline 1087 \hline 1088 zoom\_ibegin & 1089 starting point along x direction of the zoom. 1090 Automatically defined for TAO/RAMA/PIRATA moorings & 1091 zoom\_ibegin="1" & 1092 domain family \\ 1093 \hline 1094 zoom\_jbegin & 1095 starting point along y direction of the zoom. 1096 Automatically defined for TAO/RAMA/PIRATA moorings & 1097 zoom\_jbegin="1" & 1098 domain family \\ 1099 \hline 1100 zoom\_ni & 1101 zoom extent along x direction & 1102 zoom\_ni="1" & 1103 domain family \\ 1104 \hline 1105 zoom\_nj & 1106 zoom extent along y direction & 1107 zoom\_nj="1" & 1108 domain family \\ 1109 \hline 1110 \end{tabularx} 1111 \caption{Domain attributes ("\tt{zoom\_*}")} 990 1112 \end{table} 991 1113 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} 1114 \begin{table} 1115 \scriptsize 1116 \begin{tabularx}{\textwidth}{|l|X|l|l|} 1117 \hline 1118 attribute name & 1119 description & 1120 example & 1121 accepted by \\ 1122 \hline 1123 \hline 1124 min\_digits & 1125 specify the minimum of digits used in the core number in the name of the NetCDF file & 1126 min\_digits="4" & 1127 file family \\ 1128 \hline 1129 name\_suffix & 1130 suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file & 1131 name\_suffix="\_myzoom" & 1132 file family \\ 1133 \hline 1134 output\_level & 1135 output priority of variables in a file: 0 (high) to 10 (low). 1136 All variables listed in the file with a level smaller or equal to output\_level will be output. 1137 Other variables won't be output even if they are listed in the file. & 1138 output\_level="10" & 1139 file family \\ 1140 \hline 1141 split\_freq & 1142 frequency at which to temporally split output files. 1143 Units can be ts (timestep), y, mo, d, h, mi, s. 1144 Useful for long runs to prevent over-sized output files. & 1145 split\_freq="1mo" & 1146 file family \\ 1147 \hline 1148 split\_freq\-\_format & 1149 date format used in the name of temporally split output files. 1150 Can be specified using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s & 1151 split\_freq\_format= "\%y\%mo\%d" & 1152 file family \\ 1153 \hline 1154 sync\_freq & 1155 NetCDF file synchronization frequency (update of the time\_counter). 1156 Units can be ts (timestep), y, mo, d, h, mi, s. & 1157 sync\_freq="10d" & 1158 file family \\ 1159 \hline 1160 type (1) & 1161 specify if the output files are to be split spatially (multiple\_file) or not (one\_file) & 1162 type="multiple\_file" & 1163 file familly \\ 1164 \hline 1165 \end{tabularx} 1166 \caption{File attributes} 1034 1167 \end{table} 1035 1168 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} 1169 \begin{table} 1170 \scriptsize 1171 \begin{tabularx}{\textwidth}{|l|X|l|l|} 1172 \hline 1173 attribute name & 1174 description & 1175 example & 1176 accepted by \\ 1177 \hline 1178 \hline 1179 default\_value & 1180 missing\_value definition & 1181 default\_value="1.e20" & 1182 field family \\ 1183 \hline 1184 level & 1185 output priority of a field: 0 (high) to 10 (low) & 1186 level="1" & 1187 field family \\ 1188 \hline 1189 operation & 1190 type of temporal operation: average, accumulate, instantaneous, min, max and once & 1191 operation="average" & 1192 field family \\ 1193 \hline 1194 output\_freq & 1195 operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. & 1196 output\_freq="1d12h" & 1197 field family \\ 1198 \hline 1199 prec & 1200 output precision: real 4 or real 8 & 1201 prec="4" & 1202 field family \\ 1203 \hline 1204 long\_name & 1205 define the long\_name attribute in the NetCDF file & 1206 long\_name="Vertical T levels" & 1207 field \\ 1208 \hline 1209 standard\_name & 1210 define the standard\_name attribute in the NetCDF file & 1211 standard\_name= "Eastward\_Sea\_Ice\_Transport" & 1212 field \\ 1213 \hline 1214 \end{tabularx} 1215 \caption{Field attributes} 1072 1216 \end{table} 1073 1217 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} 1218 \begin{table} 1219 \scriptsize 1220 \begin{tabularx}{\textwidth}{|l|X|X|X|} 1221 \hline 1222 attribute name & 1223 description & 1224 example & 1225 accepted by \\ 1226 \hline 1227 \hline 1228 enabled & 1229 switch on/off the output of a field or a file & 1230 enabled=".true." & 1231 field, file families \\ 1232 \hline 1233 description & 1234 just for information, not used & 1235 description="ocean T grid variables" & 1236 all tags \\ 1237 \hline 1238 id & 1239 allow to identify a tag & 1240 id="nemo" & 1241 accepted by all tags except simulation \\ 1242 \hline 1243 name & 1244 name of a variable or a file. If the name of a file is undefined, its id is used as a name & 1245 name="tos" & 1246 field or file families \\ 1247 \hline 1248 positive & 1249 convention used for the orientation of vertival axis (positive downward in \NEMO). & 1250 positive="down" & 1251 axis family \\ 1252 \hline 1253 src & 1254 allow to include a file & 1255 src="./field\_def.xml" & 1256 accepted by all tags except simulation \\ 1257 \hline 1258 time\_origin & 1259 specify the origin of the time counter & 1260 time\_origin="1900-01-01 00:00:00" & 1261 context \\ 1262 \hline 1263 type (2) & 1264 define the type of a variable tag & 1265 type="boolean" & 1266 variable \\ 1267 \hline 1268 unit & 1269 unit of a variable or the vertical axis & 1270 unit="m" & 1271 field and axis families \\ 1272 \hline 1273 \end{tabularx} 1274 \caption{Miscellaneous attributes} 1118 1275 \end{table} 1119 1276 … … 1200 1357 1201 1358 %------------------------------------------TABLE---------------------------------------------------- 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} 1359 \begin{table} 1360 \scriptsize 1361 \centering 1362 \begin{tabular}{lrrr} 1363 Filename & NetCDF3 & NetCDF4 & Reduction \\ 1364 & filesize & filesize & \% \\ 1365 & (KB) & (KB) & \\ 1366 ORCA2\_restart\_0000.nc & 16420 & 8860 & 47\% \\ 1367 ORCA2\_restart\_0001.nc & 16064 & 11456 & 29\% \\ 1368 ORCA2\_restart\_0002.nc & 16064 & 9744 & 40\% \\ 1369 ORCA2\_restart\_0003.nc & 16420 & 9404 & 43\% \\ 1370 ORCA2\_restart\_0004.nc & 16200 & 5844 & 64\% \\ 1371 ORCA2\_restart\_0005.nc & 15848 & 8172 & 49\% \\ 1372 ORCA2\_restart\_0006.nc & 15848 & 8012 & 50\% \\ 1373 ORCA2\_restart\_0007.nc & 16200 & 5148 & 69\% \\ 1374 ORCA2\_2d\_grid\_T\_0000.nc & 2200 & 1504 & 32\% \\ 1375 ORCA2\_2d\_grid\_T\_0001.nc & 2200 & 1748 & 21\% \\ 1376 ORCA2\_2d\_grid\_T\_0002.nc & 2200 & 1592 & 28\% \\ 1377 ORCA2\_2d\_grid\_T\_0003.nc & 2200 & 1540 & 30\% \\ 1378 ORCA2\_2d\_grid\_T\_0004.nc & 2200 & 1204 & 46\% \\ 1379 ORCA2\_2d\_grid\_T\_0005.nc & 2200 & 1444 & 35\% \\ 1380 ORCA2\_2d\_grid\_T\_0006.nc & 2200 & 1428 & 36\% \\ 1381 ORCA2\_2d\_grid\_T\_0007.nc & 2200 & 1148 & 48\% \\ 1382 ... & ... & ... & ... \\ 1383 ORCA2\_2d\_grid\_W\_0000.nc & 4416 & 2240 & 50\% \\ 1384 ORCA2\_2d\_grid\_W\_0001.nc & 4416 & 2924 & 34\% \\ 1385 ORCA2\_2d\_grid\_W\_0002.nc & 4416 & 2512 & 44\% \\ 1386 ORCA2\_2d\_grid\_W\_0003.nc & 4416 & 2368 & 47\% \\ 1387 ORCA2\_2d\_grid\_W\_0004.nc & 4416 & 1432 & 68\% \\ 1388 ORCA2\_2d\_grid\_W\_0005.nc & 4416 & 1972 & 56\% \\ 1389 ORCA2\_2d\_grid\_W\_0006.nc & 4416 & 2028 & 55\% \\ 1390 ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\% \\ 1391 \end{tabular} 1392 \caption{ 1393 \protect\label{tab:NC4} 1394 Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression 1395 } 1236 1396 \end{table} 1237 1397 %---------------------------------------------------------------------------------------------------- … … 1329 1489 1330 1490 \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}} \\ 1491 \noindent 1492 {\scriptsize 1493 \texttt{ 1494 100.00000 90.00000 -1.50000 1.00000 0.00000 \\ 1495 102.00000 90.00000 -1.50000 1.00000 0.00000 \\ 1496 104.00000 90.00000 -1.50000 1.00000 0.00000 \\ 1497 106.00000 90.00000 -1.50000 1.00000 0.00000 \\ 1498 108.00000 90.00000 -1.50000 1.00000 0.00000} 1499 } \\ 1337 1500 1338 1501 In the other case (longitude and latitude), input filename is init\_float. … … 1351 1514 1352 1515 \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 }} \\ 1516 \noindent 1517 {\scriptsize 1518 \texttt{ 1519 20.0 0.0 0.0 0 1 1 \\ 1520 -21.0 0.0 0.0 0 1 1 \\ 1521 -22.0 0.0 0.0 0 1 1 \\ 1522 -23.0 0.0 0.0 0 1 1 \\ 1523 -24.0 0.0 0.0 0 1 1 } 1524 } \\ 1359 1525 1360 1526 \np{jpnfl} is the total number of floats during the run. … … 1426 1592 The Harmonic analysis solve the following equation: 1427 1593 1428 \[h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i}\] 1594 \[ 1595 h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i} 1596 \] 1429 1597 1430 1598 With $A_{j}$, $\nu_{j}$, $\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error. … … 1432 1600 We can rewrite this equation: 1433 1601 1434 \[h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i}\] 1602 \[ 1603 h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i} 1604 \] 1435 1605 1436 1606 with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ and $\phi_{j}=arctan(S_{j}/C_{j})$. … … 1497 1667 1498 1668 \noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\ 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}} 1669 {\scriptsize 1670 \texttt{ 1671 long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\ 1672 classtype \\ 1673 zbound1 \\ 1674 zbound2 \\ 1675 . \\ 1676 . \\ 1677 nclass-1 \\ 1678 nclass} 1679 } 1508 1680 1509 1681 \noindent where \texttt{classtype} can be: … … 1527 1699 Examples of two sections, the ACC\_Drake\_Passage with no classes, 1528 1700 and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\ 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}} 1701 \noindent 1702 {\scriptsize 1703 \texttt{ 1704 -68. -54.5 -60. -64.7 00 okstrpond noice ACC\_Drake\_Passage \\ 1705 -80.5 22.5 -80.5 25.5 05 nostrpond noice ATL\_Cuba\_Florida \\ 1706 ztem \\ 1707 -2.0 \\ 1708 4.5 \\ 1709 7.0 \\ 1710 12.0 \\ 1711 40.0} 1712 } 1538 1713 1539 1714 \subsubsection{To read the output files} 1540 1715 1541 1716 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}} \\ 1717 {\scriptsize 1718 \texttt{ 1719 date, time-step number, section number, \\ 1720 section name, section slope coefficient, class number, \\ 1721 class name, class bound 1 , classe bound2, \\ 1722 transport\_direction1, transport\_direction2, \\ 1723 transport\_total} 1724 } \\ 1548 1725 1549 1726 For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class and … … 1559 1736 direction: \\ 1560 1737 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} 1738 \begin{table} 1739 \scriptsize 1740 \begin{tabular}{|l|l|l|l|l|} 1741 \hline 1742 section slope coefficient & section type & direction 1 & direction 2 & total transport \\ 1743 \hline 1744 0. & horizontal & northward & southward & postive: northward \\ 1745 \hline 1746 1000. & vertical & eastward & westward & postive: eastward \\ 1747 \hline 1748 \texttt{$\neq$ 0, $\neq$ 1000.} & diagonal & eastward & westward & postive: eastward \\ 1749 \hline 1750 \end{tabular} 1572 1751 \end{table} 1573 1752 … … 1609 1788 A non-Boussinesq fluid conserves mass. It satisfies the following relations: 1610 1789 1611 \[ \begin{split} 1612 \mathcal{M} &= \mathcal{V} \;\bar{\rho} \\ 1613 \mathcal{V} &= \mathcal{A} \;\bar{\eta} 1614 \end{split} \label{eq:MV_nBq} 1615 \] 1790 \begin{equation} 1791 \begin{split} 1792 \mathcal{M} &= \mathcal{V} \;\bar{\rho} \\ 1793 \mathcal{V} &= \mathcal{A} \;\bar{\eta} 1794 \end{split} 1795 \label{eq:MV_nBq} 1796 \end{equation} 1616 1797 1617 1798 Temporal changes in total mass is obtained from the density conservation equation: 1618 1799 1619 \[ \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} ) 1620 = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface} 1621 \label{eq:Co_nBq} \] 1800 \begin{equation} 1801 \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} ) 1802 = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface} 1803 \label{eq:Co_nBq} 1804 \end{equation} 1622 1805 1623 1806 where $\rho$ is the \textit{in situ} density, and \textit{emp} the surface mass exchanges with the other media of … … 1625 1808 Its global averaged leads to the total mass change 1626 1809 1627 \[ \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}} 1628 \label{eq:Mass_nBq} \] 1810 \begin{equation} 1811 \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}} 1812 \label{eq:Mass_nBq} 1813 \end{equation} 1629 1814 1630 1815 where $\overline{\textit{emp}} = \int_S \textit{emp}\,ds$ is the net mass flux through the ocean surface. … … 1632 1817 the evolution equation of the mean sea level 1633 1818 1634 \[ \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}} 1635 - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}} 1636 \label{eq:ssh_nBq} \] 1819 \begin{equation} 1820 \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}} 1821 - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}} 1822 \label{eq:ssh_nBq} 1823 \end{equation} 1637 1824 1638 1825 The first term in equation \autoref{eq:ssh_nBq} alters sea level by adding or subtracting mass from the ocean. … … 1643 1830 In particular, the mass conservation equation, \autoref{eq:Co_nBq}, degenerates into the incompressibility equation: 1644 1831 1645 \[ \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) 1646 = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface} 1647 \label{eq:Co_Bq} \] 1832 \[ 1833 \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface} 1834 % \label{eq:Co_Bq} 1835 \] 1648 1836 1649 1837 and the global average of this equation now gives the temporal change of the total volume, 1650 1838 1651 \[ \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o} 1652 \label{eq:V_Bq} \] 1839 \[ 1840 \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o} 1841 % \label{eq:V_Bq} 1842 \] 1653 1843 1654 1844 Only the volume is conserved, not mass, or, more precisely, the mass which is conserved is the Boussinesq mass, … … 1666 1856 $\eta_s$, a spatially uniform variable, as follows: 1667 1857 1668 \[ \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A} 1669 \label{eq:M_Bq} \] 1858 \begin{equation} 1859 \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A} 1860 \label{eq:M_Bq} 1861 \end{equation} 1670 1862 1671 1863 Any change in $\mathcal{M}$ which cannot be explained by the net mass flux through the ocean surface … … 1675 1867 in \autoref{eq:M_Bq} leads to a very simple form for the steric height: 1676 1868 1677 \[ \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D} 1678 \label{eq:steric_Bq} \] 1869 \begin{equation} 1870 \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D} 1871 \label{eq:steric_Bq} 1872 \end{equation} 1679 1873 1680 1874 The above formulation of the steric height of a Boussinesq ocean requires four remarks. … … 1698 1892 In the non linear free surface case, $i.e.$ \key{vvl} defined, it is given by 1699 1893 1700 \[ \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} } 1701 { \sum_{i,\,j,\,k} e_{1t} e_{2t} e_{3t} } 1702 \label{eq:discrete_steric_Bq_nfs} \] 1894 \[ 1895 \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} }{ \sum_{i,\,j,\,k} e_{1t} e_{2t} e_{3t} } 1896 % \label{eq:discrete_steric_Bq_nfs} 1897 \] 1703 1898 1704 1899 whereas in the linear free surface, … … 1706 1901 better approximate the total ocean mass and thus the steric sea level: 1707 1902 1708 \[ \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta } 1709 { \sum_{i,\,j,\,k} e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} e_{1t}e_{2t} \eta } 1710 \label{eq:discrete_steric_Bq_fs} \] 1903 \[ 1904 \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta } 1905 { \sum_{i,\,j,\,k} e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} e_{1t}e_{2t} \eta } 1906 % \label{eq:discrete_steric_Bq_fs} 1907 \] 1711 1908 1712 1909 The fourth and last remark concerns the effective sea level and the presence of sea-ice. … … 1725 1922 It is given by: 1726 1923 1727 \[ \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv 1728 \label{eq:thermosteric_Bq} \] 1924 \[ 1925 \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv 1926 % \label{eq:thermosteric_Bq} 1927 \] 1729 1928 1730 1929 where $S_o$ and $p_o$ are the initial salinity and pressure, respectively. … … 1777 1976 \begin{center} 1778 1977 \includegraphics[width=1.0\textwidth]{Fig_mask_subasins} 1779 \caption{ \protect\label{fig:mask_subasins} 1978 \caption{ 1979 \protect\label{fig:mask_subasins} 1780 1980 Decomposition of the World Ocean (here ORCA2) into sub-basin used in to 1781 1981 compute the heat and salt transports as well as the meridional stream-function: 1782 1982 Atlantic basin (red), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green). 1783 1983 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.} 1785 \end{center} \end{figure} 1984 Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line. 1985 } 1986 \end{center} 1987 \end{figure} 1786 1988 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1787 1989 … … 1835 2037 The advective Courant numbers can be calculated according to 1836 2038 1837 \[ C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}} 1838 \label{eq:CFL} \] 2039 \[ 2040 C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}} 2041 % \label{eq:CFL} 2042 \] 1839 2043 1840 2044 in the zonal, meridional and vertical directions respectively. … … 1854 2058 % ================================================================ 1855 2059 2060 \biblio 2061 1856 2062 \end{document}
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