Changeset 9392 for branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex
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- 2018-03-09T16:57:00+01:00 (6 years ago)
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branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex
r9389 r9392 217 217 For example: 218 218 \vspace{-20pt} 219 \begin{xml code}219 \begin{xmllines} 220 220 <field_definition> 221 221 <!-- T grid --> … … 226 226 ... 227 227 </field_definition> 228 \end{xml code}228 \end{xmllines} 229 229 Note your definition must be added to the field\_group whose reference grid is consistent 230 230 with the size of the array passed to iomput. … … 233 233 or defined in the domain\_def.xml file. $e.g.$: 234 234 \vspace{-20pt} 235 \begin{xml code}235 \begin{xmllines} 236 236 <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> 237 \end{xml code}237 \end{xmllines} 238 238 Note, if your array is computed within the surface module each nn\_fsbc time\_step, 239 239 add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$ … … 242 242 \item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules) \\ 243 243 \vspace{-20pt} 244 \begin{xml code}244 \begin{xmllines} 245 245 <file id="file1" .../> 246 246 ... … … 248 248 ... 249 249 </file> 250 \end{xml code}250 \end{xmllines} 251 251 252 252 \end{description} … … 398 398 example 1: Direct inheritance. 399 399 \vspace{-20pt} 400 \begin{xml code}400 \begin{xmllines} 401 401 <field_definition operation="average" > 402 402 <field id="sst" /> <!-- averaged sst --> 403 403 <field id="sss" operation="instant"/> <!-- instantaneous sss --> 404 404 </field_definition> 405 \end{xml code}405 \end{xmllines} 406 406 The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average'' 407 407 of the attribute ''operation'' from its parent. Note that a child can overwrite … … 411 411 example 2: Inheritance by reference. 412 412 \vspace{-20pt} 413 \begin{xml code}413 \begin{xmllines} 414 414 <field_definition> 415 415 <field id="sst" long_name="sea surface temperature" /> … … 423 423 </file> 424 424 </file_definition> 425 \end{xml code}425 \end{xmllines} 426 426 Inherit (and overwrite, if needed) the attributes of a tag you are refering to. 427 427 … … 433 433 Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''. 434 434 \vspace{-20pt} 435 \begin{xml code}435 \begin{xmllines} 436 436 <field_group id="grid_T" grid_ref="grid_T_2D"> 437 437 <field id="toce" long_name="temperature" unit="degC" grid_ref="grid_T_3D"/> … … 440 440 <field id="ssh" long_name="sea surface height" unit="m" /> 441 441 ... 442 \end{xml code}442 \end{xmllines} 443 443 444 444 Secondly, the group can be used to replace a list of elements. … … 446 446 For example, a short list of the usual variables related to the U grid: 447 447 \vspace{-20pt} 448 \begin{xml code}448 \begin{xmllines} 449 449 <field_group id="groupU" > 450 450 <field field_ref="uoce" /> … … 452 452 <field field_ref="utau" /> 453 453 </field_group> 454 \end{xml code}454 \end{xmllines} 455 455 that can be directly included in a file through the following syntax: 456 456 \vspace{-20pt} 457 \begin{xml code}457 \begin{xmllines} 458 458 <file id="myfile_U" output_freq="1d" /> 459 459 <field_group group_ref="groupU"/> 460 460 <field field_ref="uocetr_eff" /> <!-- add another field --> 461 461 </file> 462 \end{xml code}462 \end{xmllines} 463 463 464 464 \subsection{Detailed functionalities } … … 473 473 of a 5 by 5 box with the bottom left corner at point (10,10). 474 474 \vspace{-20pt} 475 \begin{xml code}475 \begin{xmllines} 476 476 <domain_group id="grid_T"> 477 477 <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" /> 478 \end{xml code}478 \end{xmllines} 479 479 The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. For example: 480 480 \vspace{-20pt} 481 \begin{xml code}481 \begin{xmllines} 482 482 <file id="myfile_vzoom" output_freq="1d" > 483 483 <field field_ref="toce" domain_ref="myzoom"/> 484 484 </file> 485 \end{xml code}485 \end{xmllines} 486 486 Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain. 487 487 The Equatorial section, the TAO, RAMA and PIRATA moorings are alredy registered in the code … … 491 491 by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...) 492 492 \vspace{-20pt} 493 \begin{xml code}493 \begin{xmllines} 494 494 <file id="myfile_vzoom" output_freq="1d" > 495 495 <field field_ref="toce" domain_ref="0n180wT"/> 496 496 </file> 497 \end{xml code}497 \end{xmllines} 498 498 Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if you use the ''multiple\_file'' type for your output files, you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat, \href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}). We are therefore advising to use the ''one\_file'' type in this case. 499 499 … … 501 501 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: 502 502 \vspace{-20pt} 503 \begin{xml code}503 \begin{xmllines} 504 504 <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" > 505 505 <axis id="deptht" /> 506 506 <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" /> 507 \end{xml code}507 \end{xmllines} 508 508 The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. For example: 509 509 \vspace{-20pt} 510 \begin{xml code}510 \begin{xmllines} 511 511 <file id="myfile_hzoom" output_freq="1d" > 512 512 <field field_ref="toce" axis_ref="deptht_myzoom"/> 513 513 </file> 514 \end{xml code}514 \end{xmllines} 515 515 516 516 \subsubsection{Control of the output file names} … … 518 518 The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. for example: 519 519 \vspace{-20pt} 520 \begin{xml code}520 \begin{xmllines} 521 521 <file_group id="1d" output_freq="1d" name="myfile_1d" > 522 522 <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA" --> … … 527 527 </file> 528 528 </file_group> 529 \end{xml code}529 \end{xmllines} 530 530 However it is often very convienent to define the file name with the name of the experiment, the output file frequency and the date of the beginning and the end of the simulation (which are informations stored either in the namelist or in the XML file). To do so, we added the following rule: if the id of the tag file is ''fileN''(where N = 1 to 999 on 1 to 3 digits) or one of the predefined sections or moorings (see next subsection), the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by:\\ 531 531 \\ … … 589 589 \hline 590 590 \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} \\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} \\ 598 598 \hline 599 599 \multicolumn{2}{|c|}{EqT, EqU, EqW} & jbegin, ni, & according to the grid \\ … … 613 613 614 614 \vspace{-20pt} 615 \begin{xml code}615 \begin{xmllines} 616 616 <field field\_ref="sst" name="tosK" unit="degK" > sst + 273.15 </field> 617 617 <field field\_ref="taum" name="taum2" unit="N2/m4" long\_name="square of wind stress module" > taum * taum </field> 618 618 <field field\_ref="qt" name="stupid\_check" > qt - qsr - qns </field> 619 \end{xml code}619 \end{xmllines} 620 620 621 621 (2) Simple computation: define a new variable and use it in the file definition. … … 623 623 in field\_definition: 624 624 \vspace{-20pt} 625 \begin{xml code}625 \begin{xmllines} 626 626 <field id="sst2" long\_name="square of sea surface temperature" unit="degC2" > sst * sst </field > 627 \end{xml code}627 \end{xmllines} 628 628 in file\_definition: 629 629 \vspace{-20pt} 630 \begin{xml code}630 \begin{xmllines} 631 631 <field field\_ref="sst2" > sst2 </field> 632 \end{xml code}632 \end{xmllines} 633 633 Note that in this case, the following syntaxe $<$field field\_ref="sst2" /$>$ is not working as sst2 won't be evaluated. 634 634 … … 636 636 637 637 \vspace{-20pt} 638 \begin{xml code}638 \begin{xmllines} 639 639 <!-- force to keep real 8 --> 640 640 <field field\_ref="sst" name="tos\_r8" prec="8" /> 641 641 <!-- integer 2 with add\_offset and scale\_factor attributes --> 642 642 <field field\_ref="sss" name="sos\_i2" prec="2" add\_offset="20." scale\_factor="1.e-3" /> 643 \end{xml code}643 \end{xmllines} 644 644 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. 645 645 … … 647 647 648 648 \vspace{-20pt} 649 \begin{xml code}649 \begin{xmllines} 650 650 <file\_group id="1d" output\_freq="1d" output\_level="10" enabled=".TRUE."> <!-- 1d files --> 651 651 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > … … 658 658 </file> 659 659 </file\_group> 660 \end{xml code}660 \end{xmllines} 661 661 662 662 (5) use of the ``@'' function: example 1, weighted temporal average … … 664 664 - define a new variable in field\_definition 665 665 \vspace{-20pt} 666 \begin{xml code}666 \begin{xmllines} 667 667 <field id="toce\_e3t" long\_name="temperature * e3t" unit="degC*m" grid\_ref="grid\_T\_3D" > toce * e3t </field > 668 \end{xml code}668 \end{xmllines} 669 669 - use it when defining your file. 670 670 \vspace{-20pt} 671 \begin{xml code}671 \begin{xmllines} 672 672 <file\_group id="5d" output\_freq="5d" output\_level="10" enabled=".TRUE." > <!-- 5d files --> 673 673 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > … … 675 675 </file> 676 676 </file\_group> 677 \end{xml code}677 \end{xmllines} 678 678 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. 679 679 … … 682 682 - define a new variable in field\_definition 683 683 \vspace{-20pt} 684 \begin{xml code}684 \begin{xmllines} 685 685 <field id="ssh2" long\_name="square of sea surface temperature" unit="degC2" > ssh * ssh </field > 686 \end{xml code}686 \end{xmllines} 687 687 - use it when defining your file. 688 688 \vspace{-20pt} 689 \begin{xml code}689 \begin{xmllines} 690 690 <file\_group id="1m" output\_freq="1m" output\_level="10" enabled=".TRUE." > <!-- 1m files --> 691 691 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > … … 693 693 </file> 694 694 </file\_group> 695 \end{xml code}695 \end{xmllines} 696 696 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. 697 697 … … 700 700 - define 2 new variables in field\_definition 701 701 \vspace{-20pt} 702 \begin{xml code}702 \begin{xmllines} 703 703 <field id="sstmax" field\_ref="sst" long\_name="max of sea surface temperature" operation="maximum" /> 704 704 <field id="sstmin" field\_ref="sst" long\_name="min of sea surface temperature" operation="minimum" /> 705 \end{xml code}705 \end{xmllines} 706 706 - use these 2 new variables when defining your file. 707 707 \vspace{-20pt} 708 \begin{xml code}708 \begin{xmllines} 709 709 <file\_group id="1m" output\_freq="1m" output\_level="10" enabled=".TRUE." > <!-- 1m files --> 710 710 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > … … 712 712 </file> 713 713 </file\_group> 714 \end{xml code}714 \end{xmllines} 715 715 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. 716 716 … … 1024 1024 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 1025 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.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. 1027 1027 1028 1028 … … 1048 1048 new libraries and will then read both NetCDF3 and NetCDF4 files. NEMO 1049 1049 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}1050 files by setting the \np{ln_nc4zip} logical to false in the \textit{namnc4} 1051 1051 namelist: 1052 1052 … … 1056 1056 1057 1057 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 few1058 In this case, \np{ln_nc4zip} is set false and dummy routines for a few 1059 1059 NetCDF4-specific functions are defined. These functions will not be used but 1060 1060 need to be included so that compilation is possible with NetCDF3 libraries. … … 1106 1106 &filesize & filesize & \% \\ 1107 1107 &(KB) & (KB) & \\ 1108 ORCA2\_restart\_0000.nc& 16420 & 8860 & 47\%\\1109 ORCA2\_restart\_0001.nc& 16064 & 11456 & 29\%\\1110 ORCA2\_restart\_0002.nc& 16064 & 9744 & 40\%\\1111 ORCA2\_restart\_0003.nc& 16420 & 9404 & 43\%\\1112 ORCA2\_restart\_0004.nc& 16200 & 5844 & 64\%\\1113 ORCA2\_restart\_0005.nc& 15848 & 8172 & 49\%\\1114 ORCA2\_restart\_0006.nc& 15848 & 8012 & 50\%\\1115 ORCA2\_restart\_0007.nc& 16200 & 5148 & 69\%\\1116 ORCA2\_2d\_grid\_T\_0000.nc& 2200 & 1504 & 32\%\\1117 ORCA2\_2d\_grid\_T\_0001.nc& 2200 & 1748 & 21\%\\1118 ORCA2\_2d\_grid\_T\_0002.nc& 2200 & 1592 & 28\%\\1119 ORCA2\_2d\_grid\_T\_0003.nc& 2200 & 1540 & 30\%\\1120 ORCA2\_2d\_grid\_T\_0004.nc& 2200 & 1204 & 46\%\\1121 ORCA2\_2d\_grid\_T\_0005.nc& 2200 & 1444 & 35\%\\1122 ORCA2\_2d\_grid\_T\_0006.nc& 2200 & 1428 & 36\%\\1123 ORCA2\_2d\_grid\_T\_0007.nc& 2200 & 1148 & 48\%\\1124 ... & ... & ... &.. \\1125 ORCA2\_2d\_grid\_W\_0000.nc& 4416 & 2240 & 50\%\\1126 ORCA2\_2d\_grid\_W\_0001.nc& 4416 & 2924 & 34\%\\1127 ORCA2\_2d\_grid\_W\_0002.nc& 4416 & 2512 & 44\%\\1128 ORCA2\_2d\_grid\_W\_0003.nc& 4416 & 2368 & 47\%\\1129 ORCA2\_2d\_grid\_W\_0004.nc& 4416 & 1432 & 68\%\\1130 ORCA2\_2d\_grid\_W\_0005.nc& 4416 & 1972 & 56\%\\1131 ORCA2\_2d\_grid\_W\_0006.nc& 4416 & 2028 & 55\%\\1132 ORCA2\_2d\_grid\_W\_0007.nc& 4416 & 1368 & 70\%\\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\%\\ 1133 1133 \end{tabular} 1134 1134 \caption{ \protect\label{Tab_NC4} … … 1138 1138 1139 1139 When \key{iomput} is activated with \key{netcdf4} chunking and 1140 compression parameters for fields produced via \np{iom \_put} calls are1140 compression parameters for fields produced via \np{iom_put} calls are 1141 1141 set via an equivalent and identically named namelist to \textit{namnc4} 1142 1142 in \np{xmlio\_server.def}. Typically this namelist serves the mean files … … 1167 1167 What is done depends on the \ngn{namtrd} logical set to \textit{true}: 1168 1168 \begin{description} 1169 \item[\np{ln \_glo\_trd}] : at each \np{nn\_trd} time-step a check of the basin averaged properties1169 \item[\np{ln_glo_trd}] : at each \np{nn_trd} time-step a check of the basin averaged properties 1170 1170 of the momentum and tracer equations is performed. This also includes a check of $T^2$, $S^2$, 1171 1171 $\tfrac{1}{2} (u^2+v2)$, 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 averaged1172 \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 averaged 1174 1174 over the mixed layer is output ; 1175 \item[\np{ln \_vor\_trd}] : a vertical summation of the moment tendencies is performed,1175 \item[\np{ln_vor_trd}] : a vertical summation of the moment tendencies is performed, 1176 1176 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 averaged1177 \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 averaged 1180 1180 over the mixed layer is output ; 1181 1181 \end{description} … … 1185 1185 1186 1186 \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}1187 In particular, options associated with \np{ln_dyn_mxl}, \np{ln_vor_trd}, and \np{ln_tra_mxl} 1188 1188 are not working, and none of the option have been tested with variable volume ($i.e.$ \key{vvl} defined). 1189 1189 … … 1203 1203 namelis variables. The algorithm used is based 1204 1204 either on the work of \cite{Blanke_Raynaud_JPO97} (default option), or on a $4^th$ 1205 Runge-Hutta algorithm (\ np{ln\_flork4}=true). Note that the \cite{Blanke_Raynaud_JPO97}1205 Runge-Hutta algorithm (\forcode{ln_flork4 = .true.}). Note that the \cite{Blanke_Raynaud_JPO97} 1206 1206 algorithm have the advantage of providing trajectories which are consistent with the 1207 1207 numeric of the code, so that the trajectories never intercept the bathymetry. … … 1209 1209 \subsubsection{ Input data: initial coordinates } 1210 1210 1211 Initial coordinates can be given with Ariane Tools convention ( IJK coordinates ,(\ np{ln\_ariane}=true) )1211 Initial coordinates can be given with Ariane Tools convention ( IJK coordinates ,(\forcode{ln_ariane = .true.}) ) 1212 1212 or with longitude and latitude. 1213 1213 1214 1214 1215 In case of Ariane convention, input filename is \np{init \_float\_ariane}. Its format is:1215 In case of Ariane convention, input filename is \np{init_float_ariane}. Its format is: 1216 1216 1217 1217 \texttt{ I J K nisobfl itrash itrash } … … 1258 1258 1259 1259 \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}1260 When initial positions are read in a restart file ( \np{ln_rstflo}= .TRUE. ), \np{jpnflnewflo} 1261 1261 can be added in the initialization file. 1262 1262 1263 1263 \subsubsection{ Output data } 1264 1264 1265 \np{nn \_writefl} is the frequency of writing in float output file and \np{nn\_stockfl}1265 \np{nn_writefl} is the frequency of writing in float output file and \np{nn_stockfl} 1266 1266 is the frequency of creation of the float restart file. 1267 1267 1268 Output data can be written in ascii files (\np{ln \_flo\_ascii} = .TRUE. ). In that case,1268 Output data can be written in ascii files (\np{ln_flo_ascii} = .TRUE. ). In that case, 1269 1269 output filename is trajec\_float. 1270 1270 1271 Another possiblity of writing format is Netcdf (\np{ln \_flo\_ascii} = .FALSE. ). There are 2 possibilities:1271 Another possiblity of writing format is Netcdf (\np{ln_flo_ascii} = .FALSE. ). There are 2 possibilities: 1272 1272 1273 1273 - if (\key{iomput}) is used, outputs are selected in iodef.xml. Here it is an example of specification … … 1275 1275 1276 1276 \vspace{-30pt} 1277 \begin{xml code}1277 \begin{xmllines} 1278 1278 <group id="1d\_grid\_T" name="auto" description="ocean T grid variables" > } 1279 1279 <file id="floats" description="floats variables"> }\\ … … 1287 1287 </file>} 1288 1288 </group>} 1289 \end{xml code}1290 1291 1292 - if (\key{iomput}) is not used, a file called trajec\_float.ncwill be created by IOIPSL library.1289 \end{xmllines} 1290 1291 1292 - if (\key{iomput}) is not used, a file called \ifile{trajec\_float} will be created by IOIPSL library. 1293 1293 1294 1294 … … 1312 1312 Some parameters are available in namelist \ngn{namdia\_harm} : 1313 1313 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 analyse1314 - \np{nit000_han} is the first time step used for harmonic analysis 1315 1316 - \np{nitend_han} is the last time step used for harmonic analysis 1317 1318 - \np{nstep_han} is the time step frequency for harmonic analysis 1319 1320 - \np{nb_ana} is the number of harmonics to analyse 1321 1321 1322 1322 - \np{tname} is an array with names of tidal constituents to analyse 1323 1323 1324 \np{nit000 \_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation.1324 \np{nit000_han} and \np{nitend_han} must be between \np{nit000} and \np{nitend} of the simulation. 1325 1325 The restart capability is not implemented. 1326 1326 … … 1369 1369 and the time scales over which they are averaged, as well as the level of output for debugging: 1370 1370 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 section1371 \np{nn_dct}: frequency of instantaneous transports computing 1372 1373 \np{nn_dctwri}: frequency of writing ( mean of instantaneous transports ) 1374 1375 \np{nn_debug}: debugging of the section 1376 1376 1377 1377 \subsubsection{ Creating a binary file containing the pathway of each section } … … 1681 1681 The poleward heat and salt transports, their advective and diffusive component, and 1682 1682 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 computed1683 \np{ln_diaptr} to true (see the \textit{\ngn{namptr} } namelist below). 1684 When \np{ln_subbas}~=~true, transports and stream function are computed 1685 1685 for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S) 1686 1686 as well as for the World Ocean. The sub-basin decomposition requires an input file … … 1756 1756 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 1757 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.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. 1759 1759 1760 1760
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