Changeset 9393 for branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex
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branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex
r9392 r9393 14 14 % Old Model Output 15 15 % ================================================================ 16 \section{Old Model Output (default)}16 \section{Old model output (default)} 17 17 \label{DIA_io_old} 18 18 … … 55 55 % Diagnostics 56 56 % ================================================================ 57 \section{Standard model Output (IOM)}57 \section{Standard model output (IOM)} 58 58 \label{DIA_iom} 59 59 … … 106 106 even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server. 107 107 108 \subsection{XIOS: the IO\_SERVER}108 \subsection{XIOS: XML Inputs-Outputs Server} 109 109 110 110 \subsubsection{Attached or detached mode?} … … 148 148 \texttt{ mpirun -np 62 ./nemo.exe : -np 2 ./xios\_server.exe } 149 149 150 \subsubsection{Control of XIOS: the XIOScontext in iodef.xml}150 \subsubsection{Control of XIOS: the context in iodef.xml} 151 151 152 152 As well as the {\tt using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml. … … 216 216 you used in the f90 code (see subsequent sections for a details of the XML syntax and rules). 217 217 For example: 218 \vspace{-20pt}219 218 \begin{xmllines} 220 219 <field_definition> … … 232 231 and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in iom.F90) 233 232 or defined in the domain\_def.xml file. $e.g.$: 234 \vspace{-20pt}235 233 \begin{xmllines} 236 234 <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> 237 235 \end{xmllines} 238 Note, if your array is computed within the surface module each nn\_fsbctime\_step,236 Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step, 239 237 add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$ 240 238 which has been defined with the correct frequency of operations (iom\_set\_field\_attr in iom.F90) 241 239 242 \item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules) \\ 243 \vspace{-20pt} 240 \item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules) 244 241 \begin{xmllines} 245 242 <file id="file1" .../> … … 251 248 252 249 \end{description} 250 253 251 \subsection{XML fundamentals} 254 252 … … 262 260 See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details. 263 261 264 \subsubsection{Structure of the xmlfile used in NEMO}262 \subsubsection{Structure of the XML file used in NEMO} 265 263 266 264 The XML file used in XIOS is structured by 7 families of tags: context, axis, domain, grid, field, file and variable. … … 397 395 \\ 398 396 example 1: Direct inheritance. 399 \vspace{-20pt}400 397 \begin{xmllines} 401 398 <field_definition operation="average" > … … 410 407 \\ 411 408 example 2: Inheritance by reference. 412 \vspace{-20pt}413 409 \begin{xmllines} 414 410 <field_definition> … … 426 422 Inherit (and overwrite, if needed) the attributes of a tag you are refering to. 427 423 428 \subsubsection{Use of Groups}424 \subsubsection{Use of groups} 429 425 430 426 Groups can be used for 2 purposes. … … 432 428 In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''. 433 429 Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''. 434 \vspace{-20pt}435 430 \begin{xmllines} 436 431 <field_group id="grid_T" grid_ref="grid_T_2D"> … … 445 440 Several examples of groups of fields are proposed at the end of the file {\tt CONFIG/SHARED/field\_def.xml}. 446 441 For example, a short list of the usual variables related to the U grid: 447 \vspace{-20pt}448 442 \begin{xmllines} 449 443 <field_group id="groupU" > … … 454 448 \end{xmllines} 455 449 that can be directly included in a file through the following syntax: 456 \vspace{-20pt}457 450 \begin{xmllines} 458 451 <file id="myfile_U" output_freq="1d" /> … … 472 465 For example, in {\tt CONFIG/SHARED/domain\_def.xml}, we provide the following example of a definition 473 466 of a 5 by 5 box with the bottom left corner at point (10,10). 474 \vspace{-20pt}475 467 \begin{xmllines} 476 468 <domain_group id="grid_T"> … … 478 470 \end{xmllines} 479 471 The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. For example: 480 \vspace{-20pt}481 472 \begin{xmllines} 482 473 <file id="myfile_vzoom" output_freq="1d" > … … 490 481 for the equatorial sections and the mooring position for TAO, RAMA and PIRATA followed 491 482 by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...) 492 \vspace{-20pt}493 483 \begin{xmllines} 494 484 <file id="myfile_vzoom" output_freq="1d" > … … 500 490 \subsubsection{Define vertical zooms} 501 491 Vertical zooms are defined through the attributs zoom\_begin and zoom\_end of the tag family axis. It must therefore be done in the axis part of the XML file. For example, in NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml, we provide the following example: 502 \vspace{-20pt}503 492 \begin{xmllines} 504 493 <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" > … … 507 496 \end{xmllines} 508 497 The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. For example: 509 \vspace{-20pt}510 498 \begin{xmllines} 511 499 <file id="myfile_hzoom" output_freq="1d" > … … 517 505 518 506 The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. for example: 519 \vspace{-20pt}520 507 \begin{xmllines} 521 508 <file_group id="1d" output_freq="1d" name="myfile_1d" > … … 577 564 }} 578 565 579 \subsubsection{Other controls of the xmlattributes from NEMO}566 \subsubsection{Other controls of the XML attributes from NEMO} 580 567 581 568 The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in iom.F90). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary). … … 589 576 \hline 590 577 \hline 591 \multicolumn{2}{|c|}{field\_definition} & freq\_op & \np{rn _rdt} \\592 \hline 593 \multicolumn{2}{|c|}{SBC} & freq\_op & \np{rn _rdt} $\times$ \np{nn_fsbc} \\594 \hline 595 \multicolumn{2}{|c|}{ptrc\_T} & freq\_op & \np{rn _rdt} $\times$ \np{nn_dttrc} \\596 \hline 597 \multicolumn{2}{|c|}{diad\_T} & freq\_op & \np{rn _rdt} $\times$ \np{nn_dttrc} \\578 \multicolumn{2}{|c|}{field\_definition} & freq\_op & \np{rn\_rdt} \\ 579 \hline 580 \multicolumn{2}{|c|}{SBC} & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_fsbc} \\ 581 \hline 582 \multicolumn{2}{|c|}{ptrc\_T} & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ 583 \hline 584 \multicolumn{2}{|c|}{diad\_T} & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ 598 585 \hline 599 586 \multicolumn{2}{|c|}{EqT, EqU, EqW} & jbegin, ni, & according to the grid \\ … … 612 599 (1) Simple computation: directly define the computation when refering to the variable in the file definition. 613 600 614 \vspace{-20pt} 615 \begin{xmllines} 616 <field field\_ref="sst" name="tosK" unit="degK" > sst + 273.15 </field> 617 <field field\_ref="taum" name="taum2" unit="N2/m4" long\_name="square of wind stress module" > taum * taum </field> 618 <field field\_ref="qt" name="stupid\_check" > qt - qsr - qns </field> 601 \begin{xmllines} 602 <field field_ref="sst" name="tosK" unit="degK" > sst + 273.15 </field> 603 <field field_ref="taum" name="taum2" unit="N2/m4" long_name="square of wind stress module" > taum * taum </field> 604 <field field_ref="qt" name="stupid_check" > qt - qsr - qns </field> 619 605 \end{xmllines} 620 606 … … 622 608 623 609 in field\_definition: 624 \vspace{-20pt} 625 \begin{xmllines} 626 <field id="sst2" long\_name="square of sea surface temperature" unit="degC2" > sst * sst </field > 610 \begin{xmllines} 611 <field id="sst2" long_name="square of sea surface temperature" unit="degC2" > sst * sst </field > 627 612 \end{xmllines} 628 613 in file\_definition: 629 \vspace{-20pt} 630 \begin{xmllines} 631 <field field\_ref="sst2" > sst2 </field> 614 \begin{xmllines} 615 <field field_ref="sst2" > sst2 </field> 632 616 \end{xmllines} 633 617 Note that in this case, the following syntaxe $<$field field\_ref="sst2" /$>$ is not working as sst2 won't be evaluated. … … 635 619 (3) Change of variable precision: 636 620 637 \vspace{-20pt}638 621 \begin{xmllines} 639 622 <!-- force to keep real 8 --> 640 <field field \_ref="sst" name="tos\_r8" prec="8" />641 <!-- integer 2 with add \_offset and scale\_factor attributes -->642 <field field \_ref="sss" name="sos\_i2" prec="2" add\_offset="20." scale\_factor="1.e-3" />623 <field field_ref="sst" name="tos_r8" prec="8" /> 624 <!-- integer 2 with add_offset and scale_factor attributes --> 625 <field field_ref="sss" name="sos_i2" prec="2" add_offset="20." scale_factor="1.e-3" /> 643 626 \end{xmllines} 644 627 Note that, then the code is crashing, writting real4 variables forces a numerical convection from real8 to real4 which will create an internal error in NetCDF and will avoid the creation of the output files. Forcing double precision outputs with prec="8" (for example in the field\_definition) will avoid this problem. … … 646 629 (4) add user defined attributes: 647 630 648 \vspace{-20pt} 649 \begin{xmllines} 650 <file\_group id="1d" output\_freq="1d" output\_level="10" enabled=".TRUE."> <!-- 1d files --> 651 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 652 <field field\_ref="sst" name="tos" > 653 <variable id="my\_attribute1" type="string" > blabla </variable> 654 <variable id="my\_attribute2" type="integer" > 3 </variable> 655 <variable id="my\_attribute3" type="float" > 5.0 </variable> 631 \begin{xmllines} 632 <file_group id="1d" output_freq="1d" output_level="10" enabled=".true."> <!-- 1d files --> 633 <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > 634 <field field_ref="sst" name="tos" > 635 <variable id="my_attribute1" type="string" > blabla </variable> 636 <variable id="my_attribute2" type="integer" > 3 </variable> 637 <variable id="my_attribute3" type="float" > 5.0 </variable> 656 638 </field> 657 <variable id="my \_global\_attribute" type="string" > blabla\_global </variable>639 <variable id="my_global_attribute" type="string" > blabla_global </variable> 658 640 </file> 659 </file \_group>641 </file_group> 660 642 \end{xmllines} 661 643 … … 663 645 664 646 - define a new variable in field\_definition 665 \vspace{-20pt} 666 \begin{xmllines} 667 <field id="toce\_e3t" long\_name="temperature * e3t" unit="degC*m" grid\_ref="grid\_T\_3D" > toce * e3t </field > 647 \begin{xmllines} 648 <field id="toce_e3t" long_name="temperature * e3t" unit="degC*m" grid_ref="grid_T_3D" > toce * e3t </field > 668 649 \end{xmllines} 669 650 - use it when defining your file. 670 \vspace{-20pt} 671 \begin{xmllines} 672 <file\_group id="5d" output\_freq="5d" output\_level="10" enabled=".TRUE." > <!-- 5d files --> 673 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 674 <field field\_ref="toce" operation="instant" freq\_op="5d" > @toce\_e3t / @e3t </field> 651 \begin{xmllines} 652 <file_group id="5d" output_freq="5d" output_level="10" enabled=".true." > <!-- 5d files --> 653 <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > 654 <field field_ref="toce" operation="instant" freq_op="5d" > @toce_e3t / @e3t </field> 675 655 </file> 676 </file \_group>656 </file_group> 677 657 \end{xmllines} 678 658 The freq\_op="5d" attribute is used to define the operation frequency of the ``@'' function: here 5 day. The temporal operation done by the ``@'' is the one defined in the field definition: here we use the default, average. So, in the above case, @toce\_e3t will do the 5-day mean of toce*e3t. Operation="instant" refers to the temporal operation to be performed on the field''@toce\_e3t / @e3t'': here the temporal average is alreday done by the ``@'' function so we just use instant to do the ratio of the 2 mean values. field\_ref="toce" means that attributes not explicitely defined, are inherited from toce field. Note that in this case, freq\_op must be equal to the file output\_freq. … … 681 661 682 662 - define a new variable in field\_definition 683 \vspace{-20pt} 684 \begin{xmllines} 685 <field id="ssh2" long\_name="square of sea surface temperature" unit="degC2" > ssh * ssh </field > 663 \begin{xmllines} 664 <field id="ssh2" long_name="square of sea surface temperature" unit="degC2" > ssh * ssh </field > 686 665 \end{xmllines} 687 666 - use it when defining your file. 688 \vspace{-20pt} 689 \begin{xmllines} 690 <file\_group id="1m" output\_freq="1m" output\_level="10" enabled=".TRUE." > <!-- 1m files --> 691 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 692 <field field\_ref="ssh" name="sshstd" long\_name="sea\_surface\_temperature\_standard\_deviation" operation="instant" freq\_op="1m" > sqrt( @ssh2 - @ssh * @ssh ) </field> 667 \begin{xmllines} 668 <file_group id="1m" output_freq="1m" output_level="10" enabled=".true." > <!-- 1m files --> 669 <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > 670 <field field_ref="ssh" name="sshstd" long_name="sea_surface_temperature_standard_deviation" operation="instant" freq_op="1m" > sqrt( @ssh2 - @ssh * @ssh ) </field> 693 671 </file> 694 </file \_group>672 </file_group> 695 673 \end{xmllines} 696 674 The freq\_op="1m" attribute is used to define the operation frequency of the ``@'' function: here 1 month. The temporal operation done by the ``@'' is the one defined in the field definition: here we use the default, average. So, in the above case, @ssh2 will do the monthly mean of ssh*ssh. Operation="instant" refers to the temporal operation to be performed on the field ''sqrt( @ssh2 - @ssh * @ssh )'': here the temporal average is alreday done by the ``@'' function so we just use instant. field\_ref="ssh" means that attributes not explicitely defined, are inherited from ssh field. Note that in this case, freq\_op must be equal to the file output\_freq. … … 699 677 700 678 - define 2 new variables in field\_definition 701 \vspace{-20pt} 702 \begin{xmllines} 703 <field id="sstmax" field\_ref="sst" long\_name="max of sea surface temperature" operation="maximum" /> 704 <field id="sstmin" field\_ref="sst" long\_name="min of sea surface temperature" operation="minimum" /> 679 \begin{xmllines} 680 <field id="sstmax" field_ref="sst" long_name="max of sea surface temperature" operation="maximum" /> 681 <field id="sstmin" field_ref="sst" long_name="min of sea surface temperature" operation="minimum" /> 705 682 \end{xmllines} 706 683 - use these 2 new variables when defining your file. 707 \vspace{-20pt} 708 \begin{xmllines} 709 <file\_group id="1m" output\_freq="1m" output\_level="10" enabled=".TRUE." > <!-- 1m files --> 710 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 711 <field field\_ref="sst" name="sstdcy" long\_name="amplitude of sst diurnal cycle" operation="average" freq\_op="1d" > @sstmax - @sstmin </field> 684 \begin{xmllines} 685 <file_group id="1m" output_freq="1m" output_level="10" enabled=".true." > <!-- 1m files --> 686 <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > 687 <field field_ref="sst" name="sstdcy" long_name="amplitude of sst diurnal cycle" operation="average" freq_op="1d" > @sstmax - @sstmin </field> 712 688 </file> 713 </file \_group>689 </file_group> 714 690 \end{xmllines} 715 691 The freq\_op="1d" attribute is used to define the operation frequency of the ``@'' function: here 1 day. The temporal operation done by the ``@'' is the one defined in the field definition: here maximum for sstmax and minimum for sstmin. So, in the above case, @sstmax will do the daily max and @sstmin the daily min. Operation="average" refers to the temporal operation to be performed on the field ``@sstmax - @sstmin'': here monthly mean (of daily max - daily min of the sst). field\_ref="sst" means that attributes not explicitely defined, are inherited from sst field. … … 852 828 enabled & 853 829 switch on/off the output of a field or a file & 854 enabled=". TRUE." &830 enabled=".true." & 855 831 field, file families \\ 856 832 \hline … … 1024 1000 Output from the XIOS-1.0 IO server is compliant with \href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of the CF metadata standard. Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of section \ref{IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard. 1025 1001 1026 Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by the namelist parameter \np{ln _cfmeta} in the \ngn{namrun} namelist. This must be set to true if these metadata are to be included in the output files.1002 Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by the namelist parameter \np{ln\_cfmeta} in the \ngn{namrun} namelist. This must be set to true if these metadata are to be included in the output files. 1027 1003 1028 1004 … … 1030 1006 % NetCDF4 support 1031 1007 % ================================================================ 1032 \section{NetCDF4 Support (\protect\key{netcdf4})}1008 \section{NetCDF4 support (\protect\key{netcdf4})} 1033 1009 \label{DIA_iom} 1034 1010 … … 1048 1024 new libraries and will then read both NetCDF3 and NetCDF4 files. NEMO 1049 1025 executables linked with NetCDF4 libraries can be made to produce NetCDF3 1050 files by setting the \np{ln _nc4zip} logical to false in the \textit{namnc4}1026 files by setting the \np{ln\_nc4zip} logical to false in the \textit{namnc4} 1051 1027 namelist: 1052 1028 … … 1056 1032 1057 1033 If \key{netcdf4} has not been defined, these namelist parameters are not read. 1058 In this case, \np{ln _nc4zip} is set false and dummy routines for a few1034 In this case, \np{ln\_nc4zip} is set false and dummy routines for a few 1059 1035 NetCDF4-specific functions are defined. These functions will not be used but 1060 1036 need to be included so that compilation is possible with NetCDF3 libraries. … … 1079 1055 domain size in any dimension. The algorithm used is: 1080 1056 1081 \vspace{-20pt}1082 1057 \begin{forlines} 1083 1058 ichunksz(1) = MIN( idomain_size,MAX( (idomain_size-1)/nn_nchunks_i + 1 ,16 ) ) … … 1088 1063 1089 1064 \noindent As an example, setting: 1090 \vspace{-20pt}1091 1065 \begin{forlines} 1092 1066 nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31 … … 1106 1080 &filesize & filesize & \% \\ 1107 1081 &(KB) & (KB) & \\ 1108 \ifile{ORCA2\_restart\_0000}& 16420 & 8860 & 47\%\\1109 \ifile{ORCA2\_restart\_0001}& 16064 & 11456 & 29\%\\1110 \ifile{ORCA2\_restart\_0002}& 16064 & 9744 & 40\%\\1111 \ifile{ORCA2\_restart\_0003}& 16420 & 9404 & 43\%\\1112 \ifile{ORCA2\_restart\_0004}& 16200 & 5844 & 64\%\\1113 \ifile{ORCA2\_restart\_0005}& 15848 & 8172 & 49\%\\1114 \ifile{ORCA2\_restart\_0006}& 15848 & 8012 & 50\%\\1115 \ifile{ORCA2\_restart\_0007}& 16200 & 5148 & 69\%\\1116 \ifile{ORCA2\_2d\_grid\_T\_0000}& 2200 & 1504 & 32\%\\1117 \ifile{ORCA2\_2d\_grid\_T\_0001}& 2200 & 1748 & 21\%\\1118 \ifile{ORCA2\_2d\_grid\_T\_0002}& 2200 & 1592 & 28\%\\1119 \ifile{ORCA2\_2d\_grid\_T\_0003}& 2200 & 1540 & 30\%\\1120 \ifile{ORCA2\_2d\_grid\_T\_0004}& 2200 & 1204 & 46\%\\1121 \ifile{ORCA2\_2d\_grid\_T\_0005}& 2200 & 1444 & 35\%\\1122 \ifile{ORCA2\_2d\_grid\_T\_0006}& 2200 & 1428 & 36\%\\1123 \ifile{ORCA2\_2d\_grid\_T\_0007}& 2200 & 1148 & 48\%\\1124 1125 \ifile{ORCA2\_2d\_grid\_W\_0000}& 4416 & 2240 & 50\%\\1126 \ifile{ORCA2\_2d\_grid\_W\_0001}& 4416 & 2924 & 34\%\\1127 \ifile{ORCA2\_2d\_grid\_W\_0002}& 4416 & 2512 & 44\%\\1128 \ifile{ORCA2\_2d\_grid\_W\_0003}& 4416 & 2368 & 47\%\\1129 \ifile{ORCA2\_2d\_grid\_W\_0004}& 4416 & 1432 & 68\%\\1130 \ifile{ORCA2\_2d\_grid\_W\_0005}& 4416 & 1972 & 56\%\\1131 \ifile{ORCA2\_2d\_grid\_W\_0006}& 4416 & 2028 & 55\%\\1132 \ifile{ORCA2\_2d\_grid\_W\_0007}& 4416 & 1368 & 70\%\\1082 ORCA2\_restart\_0000.nc & 16420 & 8860 & 47\%\\ 1083 ORCA2\_restart\_0001.nc & 16064 & 11456 & 29\%\\ 1084 ORCA2\_restart\_0002.nc & 16064 & 9744 & 40\%\\ 1085 ORCA2\_restart\_0003.nc & 16420 & 9404 & 43\%\\ 1086 ORCA2\_restart\_0004.nc & 16200 & 5844 & 64\%\\ 1087 ORCA2\_restart\_0005.nc & 15848 & 8172 & 49\%\\ 1088 ORCA2\_restart\_0006.nc & 15848 & 8012 & 50\%\\ 1089 ORCA2\_restart\_0007.nc & 16200 & 5148 & 69\%\\ 1090 ORCA2\_2d\_grid\_T\_0000.nc & 2200 & 1504 & 32\%\\ 1091 ORCA2\_2d\_grid\_T\_0001.nc & 2200 & 1748 & 21\%\\ 1092 ORCA2\_2d\_grid\_T\_0002.nc & 2200 & 1592 & 28\%\\ 1093 ORCA2\_2d\_grid\_T\_0003.nc & 2200 & 1540 & 30\%\\ 1094 ORCA2\_2d\_grid\_T\_0004.nc & 2200 & 1204 & 46\%\\ 1095 ORCA2\_2d\_grid\_T\_0005.nc & 2200 & 1444 & 35\%\\ 1096 ORCA2\_2d\_grid\_T\_0006.nc & 2200 & 1428 & 36\%\\ 1097 ORCA2\_2d\_grid\_T\_0007.nc & 2200 & 1148 & 48\%\\ 1098 ... & ... & ... & ... \\ 1099 ORCA2\_2d\_grid\_W\_0000.nc & 4416 & 2240 & 50\%\\ 1100 ORCA2\_2d\_grid\_W\_0001.nc & 4416 & 2924 & 34\%\\ 1101 ORCA2\_2d\_grid\_W\_0002.nc & 4416 & 2512 & 44\%\\ 1102 ORCA2\_2d\_grid\_W\_0003.nc & 4416 & 2368 & 47\%\\ 1103 ORCA2\_2d\_grid\_W\_0004.nc & 4416 & 1432 & 68\%\\ 1104 ORCA2\_2d\_grid\_W\_0005.nc & 4416 & 1972 & 56\%\\ 1105 ORCA2\_2d\_grid\_W\_0006.nc & 4416 & 2028 & 55\%\\ 1106 ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\%\\ 1133 1107 \end{tabular} 1134 1108 \caption{ \protect\label{Tab_NC4} … … 1138 1112 1139 1113 When \key{iomput} is activated with \key{netcdf4} chunking and 1140 compression parameters for fields produced via \np{iom _put} calls are1114 compression parameters for fields produced via \np{iom\_put} calls are 1141 1115 set via an equivalent and identically named namelist to \textit{namnc4} 1142 1116 in \np{xmlio\_server.def}. Typically this namelist serves the mean files … … 1151 1125 % Tracer/Dynamics Trends 1152 1126 % ------------------------------------------------------------------------------------------------------------- 1153 \section[Tracer/Dynamics Trends (TRD)] 1154 {Tracer/Dynamics Trends (\protect\ngn{namtrd})} 1127 \section{Tracer/Dynamics trends (\protect\ngn{namtrd})} 1155 1128 \label{DIA_trd} 1156 1129 … … 1165 1138 Note that the output are done with xIOS, and therefore the \key{IOM} is required. 1166 1139 1167 What is done depends on the \ngn{namtrd} logical set to \ textit{true}:1140 What is done depends on the \ngn{namtrd} logical set to \forcode{.true.}: 1168 1141 \begin{description} 1169 \item[\np{ln _glo_trd}] : at each \np{nn_trd} time-step a check of the basin averaged properties1142 \item[\np{ln\_glo\_trd}] : at each \np{nn\_trd} time-step a check of the basin averaged properties 1170 1143 of the momentum and tracer equations is performed. This also includes a check of $T^2$, $S^2$, 1171 1144 $\tfrac{1}{2} (u^2+v2)$, and potential energy time evolution equations properties ; 1172 \item[\np{ln _dyn_trd}] : each 3D trend of the evolution of the two momentum components is output ;1173 \item[\np{ln _dyn_mxl}] : each 3D trend of the evolution of the two momentum components averaged1145 \item[\np{ln\_dyn\_trd}] : each 3D trend of the evolution of the two momentum components is output ; 1146 \item[\np{ln\_dyn\_mxl}] : each 3D trend of the evolution of the two momentum components averaged 1174 1147 over the mixed layer is output ; 1175 \item[\np{ln _vor_trd}] : a vertical summation of the moment tendencies is performed,1148 \item[\np{ln\_vor\_trd}] : a vertical summation of the moment tendencies is performed, 1176 1149 then the curl is computed to obtain the barotropic vorticity tendencies which are output ; 1177 \item[\np{ln _KE_trd}] : each 3D trend of the Kinetic Energy equation is output ;1178 \item[\np{ln _tra_trd}] : each 3D trend of the evolution of temperature and salinity is output ;1179 \item[\np{ln _tra_mxl}] : each 2D trend of the evolution of temperature and salinity averaged1150 \item[\np{ln\_KE\_trd}] : each 3D trend of the Kinetic Energy equation is output ; 1151 \item[\np{ln\_tra\_trd}] : each 3D trend of the evolution of temperature and salinity is output ; 1152 \item[\np{ln\_tra\_mxl}] : each 2D trend of the evolution of temperature and salinity averaged 1180 1153 over the mixed layer is output ; 1181 1154 \end{description} … … 1185 1158 1186 1159 \textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested. 1187 In particular, options associated with \np{ln _dyn_mxl}, \np{ln_vor_trd}, and \np{ln_tra_mxl}1160 In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} 1188 1161 are not working, and none of the option have been tested with variable volume ($i.e.$ \key{vvl} defined). 1189 1162 … … 1192 1165 % On-line Floats trajectories 1193 1166 % ------------------------------------------------------------------------------------------------------------- 1194 \section{ On-line Floats trajectories (FLO)(\protect\key{floats})}1167 \section{FLO: On-Line Floats trajectories (\protect\key{floats})} 1195 1168 \label{FLO} 1196 1169 %--------------------------------------------namflo------------------------------------------------------- … … 1203 1176 namelis variables. The algorithm used is based 1204 1177 either on the work of \cite{Blanke_Raynaud_JPO97} (default option), or on a $4^th$ 1205 Runge-Hutta algorithm (\ forcode{ln_flork4= .true.}). Note that the \cite{Blanke_Raynaud_JPO97}1178 Runge-Hutta algorithm (\np{ln\_flork4}\forcode{ = .true.}). Note that the \cite{Blanke_Raynaud_JPO97} 1206 1179 algorithm have the advantage of providing trajectories which are consistent with the 1207 1180 numeric of the code, so that the trajectories never intercept the bathymetry. … … 1209 1182 \subsubsection{ Input data: initial coordinates } 1210 1183 1211 Initial coordinates can be given with Ariane Tools convention ( IJK coordinates ,(\ forcode{ln_ariane= .true.}) )1184 Initial coordinates can be given with Ariane Tools convention ( IJK coordinates ,(\np{ln\_ariane}\forcode{ = .true.}) ) 1212 1185 or with longitude and latitude. 1213 1186 1214 1187 1215 In case of Ariane convention, input filename is \np{init _float_ariane}. Its format is:1188 In case of Ariane convention, input filename is \np{init\_float\_ariane}. Its format is: 1216 1189 1217 1190 \texttt{ I J K nisobfl itrash itrash } … … 1258 1231 1259 1232 \np{jpnfl} is the total number of floats during the run. 1260 When initial positions are read in a restart file ( \np{ln_rstflo}= .TRUE.), \np{jpnflnewflo}1233 When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{ = .true.} ), \np{jpnflnewflo} 1261 1234 can be added in the initialization file. 1262 1235 1263 \subsubsection{ Output data}1264 1265 \np{nn _writefl} is the frequency of writing in float output file and \np{nn_stockfl}1236 \subsubsection{Output data} 1237 1238 \np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} 1266 1239 is the frequency of creation of the float restart file. 1267 1240 1268 Output data can be written in ascii files (\np{ln _flo_ascii} = .TRUE.). In that case,1241 Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{ = .true.}). In that case, 1269 1242 output filename is trajec\_float. 1270 1243 1271 Another possiblity of writing format is Netcdf (\np{ln _flo_ascii} = .FALSE.). There are 2 possibilities:1244 Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{ = .false.}). There are 2 possibilities: 1272 1245 1273 1246 - if (\key{iomput}) is used, outputs are selected in iodef.xml. Here it is an example of specification 1274 1247 to put in files description section: 1275 1248 1276 \vspace{-30pt} 1277 \begin{xmllines} 1278 <group id="1d\_grid\_T" name="auto" description="ocean T grid variables" > } 1249 \begin{xmllines} 1250 <group id="1d_grid_T" name="auto" description="ocean T grid variables" > } 1279 1251 <file id="floats" description="floats variables"> }\\ 1280 <field ref="traj \_lon" name="floats\_longitude" freq\_op="86400" />}1281 <field ref="traj \_lat" name="floats\_latitude" freq\_op="86400" />}1282 <field ref="traj \_dep" name="floats\_depth" freq\_op="86400" />}1283 <field ref="traj \_temp" name="floats\_temperature" freq\_op="86400" />}1284 <field ref="traj \_salt" name="floats\_salinity" freq\_op="86400" />}1285 <field ref="traj \_dens" name="floats\_density" freq\_op="86400" />}1286 <field ref="traj \_group" name="floats\_group" freq\_op="86400" />}1252 <field ref="traj_lon" name="floats_longitude" freq_op="86400" />} 1253 <field ref="traj_lat" name="floats_latitude" freq_op="86400" />} 1254 <field ref="traj_dep" name="floats_depth" freq_op="86400" />} 1255 <field ref="traj_temp" name="floats_temperature" freq_op="86400" />} 1256 <field ref="traj_salt" name="floats_salinity" freq_op="86400" />} 1257 <field ref="traj_dens" name="floats_density" freq_op="86400" />} 1258 <field ref="traj_group" name="floats_group" freq_op="86400" />} 1287 1259 </file>} 1288 1260 </group>} … … 1312 1284 Some parameters are available in namelist \ngn{namdia\_harm} : 1313 1285 1314 - \np{nit000 _han} is the first time step used for harmonic analysis1315 1316 - \np{nitend _han} is the last time step used for harmonic analysis1317 1318 - \np{nstep _han} is the time step frequency for harmonic analysis1319 1320 - \np{nb _ana} is the number of harmonics to analyse1286 - \np{nit000\_han} is the first time step used for harmonic analysis 1287 1288 - \np{nitend\_han} is the last time step used for harmonic analysis 1289 1290 - \np{nstep\_han} is the time step frequency for harmonic analysis 1291 1292 - \np{nb\_ana} is the number of harmonics to analyse 1321 1293 1322 1294 - \np{tname} is an array with names of tidal constituents to analyse 1323 1295 1324 \np{nit000 _han} and \np{nitend_han} must be between \np{nit000} and \np{nitend} of the simulation.1296 \np{nit000\_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation. 1325 1297 The restart capability is not implemented. 1326 1298 … … 1369 1341 and the time scales over which they are averaged, as well as the level of output for debugging: 1370 1342 1371 \np{nn _dct}: frequency of instantaneous transports computing1372 1373 \np{nn _dctwri}: frequency of writing ( mean of instantaneous transports )1374 1375 \np{nn _debug}: debugging of the section1376 1377 \subsubsection{ Creating a binary file containing the pathway of each section}1343 \np{nn\_dct}: frequency of instantaneous transports computing 1344 1345 \np{nn\_dctwri}: frequency of writing ( mean of instantaneous transports ) 1346 1347 \np{nn\_debug}: debugging of the section 1348 1349 \subsubsection{Creating a binary file containing the pathway of each section} 1378 1350 1379 1351 In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run}, the file \textit{ {list\_sections.ascii\_global}} … … 1460 1432 1461 1433 1462 \subsubsection{ To read the output files}1434 \subsubsection{To read the output files} 1463 1435 1464 1436 The output format is : … … 1494 1466 % Steric effect in sea surface height 1495 1467 % ================================================================ 1496 \section{Diagnosing the Steric effect in sea surface height}1468 \section{Diagnosing the steric effect in sea surface height} 1497 1469 \label{DIA_steric} 1498 1470 … … 1649 1621 % Other Diagnostics 1650 1622 % ------------------------------------------------------------------------------------------------------------- 1651 \section{Other Diagnostics (\protect\key{diahth}, \protect\key{diaar5})}1623 \section{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})} 1652 1624 \label{DIA_diag_others} 1653 1625 … … 1681 1653 The poleward heat and salt transports, their advective and diffusive component, and 1682 1654 the meriodional stream function can be computed on-line in \mdl{diaptr} 1683 \np{ln _diaptr} to true (see the \textit{\ngn{namptr} } namelist below).1684 When \np{ln _subbas}~=~true, transports and stream function are computed1655 \np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below). 1656 When \np{ln\_subbas}\forcode{ = .true.}, transports and stream function are computed 1685 1657 for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S) 1686 1658 as well as for the World Ocean. The sub-basin decomposition requires an input file … … 1716 1688 % 25 hour mean and hourly Surface, Mid and Bed 1717 1689 % ----------------------------------------------------------- 1718 \subsection{25 hour mean output for tidal models 1690 \subsection{25 hour mean output for tidal models} 1719 1691 1720 1692 %------------------------------------------nam_dia25h------------------------------------- … … 1731 1703 % Top Middle and Bed hourly output 1732 1704 % ----------------------------------------------------------- 1733 \subsection{Top Middle and Bed hourly output}1705 \subsection{Top middle and bed hourly output} 1734 1706 1735 1707 %------------------------------------------nam_diatmb----------------------------------------------------- … … 1756 1728 in the zonal, meridional and vertical directions respectively. The vertical component is included although it is not strictly valid as the vertical velocity is calculated from the continuity equation rather than as a prognostic variable. Physically this represents the rate at which information is propogated across a grid cell. Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step. 1757 1729 1758 The variables can be activated by setting the \np{nn _diacfl} namelist parameter to 1 in the \ngn{namctl} namelist. The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of where the maximum value occurs. 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 with the coordinates of each. The maximum values from the run are also copied to the ocean.output file.1730 The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist. The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of where the maximum value occurs. 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 with the coordinates of each. The maximum values from the run are also copied to the ocean.output file. 1759 1731 1760 1732
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