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branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Biblio/Biblio.bib
r4560 r5682 271 271 volume = {326}, 272 272 pages = {677--684} 273 } 274 275 @ARTICLE{Beckmann2003, 276 author = {A. Beckmann and H. Goosse}, 277 title = {A parameterization of ice shelf-ocean interaction for climate models}, 278 journal = OM 279 year = {2003} 280 volume = {5} 281 pages = {157--170} 273 282 } 274 283 -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Chapters/Chap_DIA.tex
r5003 r5682 74 74 The second functionality targets output performance when running in parallel (\key{mpp\_mpi}). Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO processes) to collect and write the outputs. With an appropriate choice of N by the user, the bottleneck associated with the writing of the output files can be greatly reduced. 75 75 76 Since version 3.5, the iom\_put interface depends on an external code called \href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}. This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to create a single output file and therefore to bypass the rebuilding phase. Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to an HDF5 library that has been correctly compiled (i.e. with the configure option $--$enable-parallel). Note that the files created by iomput through XIOS are incompatible with NetCDF3. All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3.76 In version 3.6, the iom\_put interface depends on an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/branchs/xios-1.0}{XIOS-1.0} (use of revision 618 or higher is required). This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to create a single output file and therefore to bypass the rebuilding phase. Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to an HDF5 library that has been correctly compiled (i.e. with the configure option $--$enable-parallel). Note that the files created by iomput through XIOS are incompatible with NetCDF3. All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3. 77 77 78 78 Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers, where N is typically much less than the number of NEMO processors, will reduce the number of output files created. This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors. Note that for smaller configurations, the rebuilding phase can be avoided, even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server. … … 543 543 \end{tabular} 544 544 545 \subsubsection{Advanced use of XIOS functionalities} 545 546 546 547 \subsection{XML reference tables} 548 \label{IOM_xmlref} 549 550 (1) Simple computation: directly define the computation when refering to the variable in the file definition. 551 552 \vspace{-20pt} 553 \begin{alltt} {{\scriptsize 554 \begin{verbatim} 555 <field field\_ref="sst" name="tosK" unit="degK" > sst + 273.15 </field> 556 <field field\_ref="taum" name="taum2" unit="N2/m4" long\_name="square of wind stress module" > taum * taum </field> 557 <field field\_ref="qt" name="stupid\_check" > qt - qsr - qns </field> 558 \end{verbatim} 559 }}\end{alltt} 560 561 (2) Simple computation: define a new variable and use it in the file definition. 562 563 in field\_definition: 564 \vspace{-20pt} 565 \begin{alltt} {{\scriptsize 566 \begin{verbatim} 567 <field id="sst2" long\_name="square of sea surface temperature" unit="degC2" > sst * sst </field > 568 \end{verbatim} 569 }}\end{alltt} 570 in file\_definition: 571 \vspace{-20pt} 572 \begin{alltt} {{\scriptsize 573 \begin{verbatim} 574 <field field\_ref="sst2" > sst2 </field> 575 \end{verbatim} 576 }}\end{alltt} 577 Note that in this case, the following syntaxe $<$field field\_ref="sst2" /$>$ is not working as sst2 won't be evaluated. 578 579 (3) Change of variable precision: 580 581 \vspace{-20pt} 582 \begin{alltt} {{\scriptsize 583 \begin{verbatim} 584 <!-- force to keep real 8 --> 585 <field field\_ref="sst" name="tos\_r8" prec="8" /> 586 <!-- integer 2 with add\_offset and scale\_factor attributes --> 587 <field field\_ref="sss" name="sos\_i2" prec="2" add\_offset="20." scale\_factor="1.e-3" /> 588 \end{verbatim} 589 }}\end{alltt} 590 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. 591 592 (4) add user defined attributes: 593 594 \vspace{-20pt} 595 \begin{alltt} {{\scriptsize 596 \begin{verbatim} 597 <file\_group id="1d" output\_freq="1d" output\_level="10" enabled=".TRUE."> <!-- 1d files --> 598 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 599 <field field\_ref="sst" name="tos" > 600 <variable id="my\_attribute1" type="string" > blabla </variable> 601 <variable id="my\_attribute2" type="integer" > 3 </variable> 602 <variable id="my\_attribute3" type="float" > 5.0 </variable> 603 </field> 604 <variable id="my\_global\_attribute" type="string" > blabla\_global </variable> 605 </file> 606 </file\_group> 607 \end{verbatim} 608 }}\end{alltt} 609 610 (5) use of the ``@'' function: example 1, weighted temporal average 611 612 - define a new variable in field\_definition 613 \vspace{-20pt} 614 \begin{alltt} {{\scriptsize 615 \begin{verbatim} 616 <field id="toce\_e3t" long\_name="temperature * e3t" unit="degC*m" grid\_ref="grid\_T\_3D" > toce * e3t </field > 617 \end{verbatim} 618 }}\end{alltt} 619 - use it when defining your file. 620 \vspace{-20pt} 621 \begin{alltt} {{\scriptsize 622 \begin{verbatim} 623 <file\_group id="5d" output\_freq="5d" output\_level="10" enabled=".TRUE." > <!-- 5d files --> 624 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 625 <field field\_ref="toce" operation="instant" freq\_op="5d" > @toce\_e3t / @e3t </field> 626 </file> 627 </file\_group> 628 \end{verbatim} 629 }}\end{alltt} 630 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. 631 632 (6) use of the ``@'' function: example 2, monthly SSH standard deviation 633 634 - define a new variable in field\_definition 635 \vspace{-20pt} 636 \begin{alltt} {{\scriptsize 637 \begin{verbatim} 638 <field id="ssh2" long\_name="square of sea surface temperature" unit="degC2" > ssh * ssh </field > 639 \end{verbatim} 640 }}\end{alltt} 641 - use it when defining your file. 642 \vspace{-20pt} 643 \begin{alltt} {{\scriptsize 644 \begin{verbatim} 645 <file\_group id="1m" output\_freq="1m" output\_level="10" enabled=".TRUE." > <!-- 1m files --> 646 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 647 <field field\_ref="ssh" name="sshstd" long\_name="sea\_surface\_temperature\_standard\_deviation" operation="instant" freq\_op="1m" > sqrt( @ssh2 - @ssh * @ssh ) </field> 648 </file> 649 </file\_group> 650 \end{verbatim} 651 }}\end{alltt} 652 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. 653 654 (7) use of the ``@'' function: example 3, monthly average of SST diurnal cycle 655 656 - define 2 new variables in field\_definition 657 \vspace{-20pt} 658 \begin{alltt} {{\scriptsize 659 \begin{verbatim} 660 <field id="sstmax" field\_ref="sst" long\_name="max of sea surface temperature" operation="maximum" /> 661 <field id="sstmin" field\_ref="sst" long\_name="min of sea surface temperature" operation="minimum" /> 662 \end{verbatim} 663 }}\end{alltt} 664 - use these 2 new variables when defining your file. 665 \vspace{-20pt} 666 \begin{alltt} {{\scriptsize 667 \begin{verbatim} 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="sst" name="sstdcy" long\_name="amplitude of sst diurnal cycle" operation="average" freq\_op="1d" > @sstmax - @sstmin </field> 671 </file> 672 </file\_group> 673 \end{verbatim} 674 }}\end{alltt} 675 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. 676 677 547 678 548 679 \subsubsection{Tag list} … … 849 980 \end{longtable} 850 981 982 \subsection{CF metadata standard compliance} 983 984 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. 985 986 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. 851 987 852 988 -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Chapters/Chap_DOM.tex
r4147 r5682 493 493 $z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). This option can be used with full step 494 494 bathymetry or $s$-coordinate (hybrid and partial step coordinates have not 495 yet been tested in NEMO v2.3). 495 yet been tested in NEMO v2.3). If using $z$-coordinate with partial step bathymetry 496 (\np{ln\_zps}~=~true), ocean cavity beneath ice shelves can be open (\np{ln\_isfcav}~=~true). 496 497 497 498 Contrary to the horizontal grid, the vertical grid is computed in the code and no -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Chapters/Chap_DYN.tex
r4759 r5682 627 627 \eqref{Eq_dynhpg_zco_surf} - \eqref{Eq_dynhpg_zco}, and $z_T$ is the depth of 628 628 the $T$-point evaluated from the sum of the vertical scale factors at the $w$-point 629 ($e_{3w}$). 629 ($e_{3w}$). 630 631 $\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln\_dynhpg\_isf}=true). 632 This scheme need the activation of ice shelf cavities (\np{ln\_isfcav}=true). 630 633 631 634 $\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln\_dynhpg\_prj}=true) -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Chapters/Chap_MISC.tex
r4147 r5682 141 141 computational domain is laid out on local processor memories following a 2D 142 142 horizontal splitting. % (see {\S}IV.2-c) ref to the section to be updated 143 144 \subsection{Simple subsetting of input files via netCDF attributes} 145 146 The extended grids for use with the under-shelf ice cavities will result in redundant rows 147 around Antarctica if the ice cavities are not active. A simple mechanism for subsetting 148 input files associated with the extended domains has been implemented to avoid the need to 149 maintain different sets of input fields for use with or without active ice cavities. The 150 existing 'zoom' options are overly complex for this task and marked for deletion anyway. 151 This alternative subsetting operates for the j-direction only and works by optionally 152 looking for and using a global file attribute (named: \np{open\_ocean\_jstart}) to 153 determine the starting j-row for input. The use of this option is best explained with an 154 example: Consider an ORCA1 configuration using the extended grid bathymetry and coordinate 155 files: 156 \vspace{-10pt} 157 \begin{alltt} 158 \tiny 159 \begin{verbatim} 160 eORCA1_bathymetry_v2.nc 161 eORCA1_coordinates.nc 162 \end{verbatim} 163 \end{alltt} 164 \noindent These files define a horizontal domain of 362x332. Assuming the first row with 165 open ocean wet points in the non-isf bathymetry for this set is row 42 (Fortran indexing) 166 then the formally correct setting for \np{open\_ocean\_jstart} is 41. Using this value as the 167 first row to be read will result in a 362x292 domain which is the same size as the original 168 ORCA1 domain. Thus the extended coordinates and bathymetry files can be used with all the 169 original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav = 170 .false.}). Full instructions for achieving this are: 171 172 \noindent Add the new attribute to any input files requiring a j-row offset, i.e: 173 \vspace{-10pt} 174 \begin{alltt} 175 \tiny 176 \begin{verbatim} 177 ncatted -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc 178 ncatted -a open_ocean_jstart,global,a,d,41 eORCA1_bathymetry_v2.nc 179 \end{verbatim} 180 \end{alltt} 181 182 \noindent Add the logical switch to \ngn{namcfg} in the configuration namelist and set true: 183 %--------------------------------------------namcfg-------------------------------------------------------- 184 \namdisplay{namcfg_orca1} 185 %-------------------------------------------------------------------------------------------------------------- 186 187 \noindent Note the j-size of the global domain is the (extended j-size minus 188 \np{open\_ocean\_jstart} + 1 ) and this must match the size of all datasets other than 189 bathymetry and coordinates currently. However the option can be extended to any global, 2D 190 and 3D, netcdf, input field by adding the: 191 \vspace{-10pt} 192 \begin{alltt} 193 \tiny 194 \begin{verbatim} 195 lrowattr=ln_use_jattr 196 \end{verbatim} 197 \end{alltt} 198 optional argument to the appropriate \np{iom\_get} call and the \np{open\_ocean\_jstart} attribute to the corresponding input files. It remains the users responsibility to set \np{jpjdta} and \np{jpjglo} values in the \np{namelist\_cfg} file according to their needs. 143 199 144 200 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Chapters/Chap_SBC.tex
r4661 r5682 1 1 % ================================================================ 2 % Chapter � Surface Boundary Condition (SBC, I CB)3 % ================================================================ 4 \chapter{Surface Boundary Condition (SBC, I CB) }2 % Chapter � Surface Boundary Condition (SBC, ISF, ICB) 3 % ================================================================ 4 \chapter{Surface Boundary Condition (SBC, ISF, ICB) } 5 5 \label{SBC} 6 6 \minitoc … … 48 48 below ice-covered areas (using observed ice-cover or a sea-ice model) 49 49 (\np{nn\_ice}~=~0,1, 2 or 3); the addition of river runoffs as surface freshwater 50 fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of a freshwater flux adjustment 51 in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the 50 fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of isf melting as lateral inflow (parameterisation) 51 (\np{nn\_isf}~=~2 or 3 and \np{ln\_isfcav}~=~false) or as surface flux at the land-ice ocean interface 52 (\np{nn\_isf}~=~1 or 4 and \np{ln\_isfcav}~=~true); 53 the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the 52 54 transformation of the solar radiation (if provided as daily mean) into a diurnal 53 55 cycle (\np{ln\_dm2dc}~=~true); and a neutral drag coefficient can be read from an external wave … … 60 62 Finally, the different options that further modify the fluxes applied to the ocean are discussed. 61 63 One of these is modification by icebergs (see \S\ref{ICB_icebergs}), which act as drifting sources of fresh water. 64 Another example of modification is that due to the ice shelf melting/freezing (see \S\ref{SBC_isf}), 65 which provides additional sources of fresh water. 62 66 63 67 … … 686 690 air temperature, sea-surface temperature, cloud cover and relative humidity. 687 691 Sensible heat and latent heat fluxes are computed by classical 688 bulk formulae parameteri zed according to \citet{Kondo1975}.692 bulk formulae parameterised according to \citet{Kondo1975}. 689 693 Details on the bulk formulae used can be found in \citet{Maggiore_al_PCE98} and \citet{Castellari_al_JMS1998}. 690 694 … … 826 830 \Pi-g\delta = (1+k-h) \Pi_{A}(\lambda,\phi) 827 831 \end{equation} 828 with $k$ a number of Love estimated to 0.6 which paramet rized the astronomical tidal land,829 and $h$ a number of Love to 0.3 which paramet rized the parametrization due to the astronomical tidal land.832 with $k$ a number of Love estimated to 0.6 which parameterised the astronomical tidal land, 833 and $h$ a number of Love to 0.3 which parameterised the parameterisation due to the astronomical tidal land. 830 834 831 835 % ================================================================ … … 945 949 946 950 %} 947 948 951 % ================================================================ 952 % Ice shelf melting 953 % ================================================================ 954 \section [Ice shelf melting (\textit{sbcisf})] 955 {Ice shelf melting (\mdl{sbcisf})} 956 \label{SBC_isf} 957 %------------------------------------------namsbc_isf---------------------------------------------------- 958 \namdisplay{namsbc_isf} 959 %-------------------------------------------------------------------------------------------------------- 960 Namelist variable in \ngn{namsbc}, \np{nn\_isf}, control the kind of ice shelf representation used. 961 \begin{description} 962 \item[\np{nn\_isf}~=~1] 963 The ice shelf cavity is represented. The fwf and heat flux are computed. 964 Full description, sensitivity and validation in preparation. 965 966 \item[\np{nn\_isf}~=~2] 967 A parameterisation of isf is used. The ice shelf cavity is not represented. 968 The fwf is distributed along the ice shelf edge between the depth of the average grounding line (GL) 969 (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}~=~3). 970 Furthermore the fwf is computed using the \citet{Beckmann2003} parameterisation of isf melting. 971 The effective melting length (\np{sn\_Leff\_isf}) is read from a file. 972 973 \item[\np{nn\_isf}~=~3] 974 A simple parameterisation of isf is used. The ice shelf cavity is not represented. 975 The fwf (\np{sn\_rnfisf}) is distributed along the ice shelf edge between the depth of the average grounding line (GL) 976 (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}). 977 Full description, sensitivity and validation in preparation. 978 979 \item[\np{nn\_isf}~=~4] 980 The ice shelf cavity is represented. However, the fwf (\np{sn\_fwfisf}) and heat flux (\np{sn\_qisf}) are 981 not computed but specified from file. 982 \end{description} 983 984 \np{nn\_isf}~=~1 and \np{nn\_isf}~=~2 compute a melt rate based on the water masse properties, ocean velocities and depth. 985 This flux is thus highly dependent of the model resolution (horizontal and vertical), realism of the water masse onto the shelf ... 986 987 \np{nn\_isf}~=~3 and \np{nn\_isf}~=~4 read the melt rate and heat flux from a file. You have total control of the fwf scenario. 988 989 This can be usefull if the water masses on the shelf are not realistic or the resolution (horizontal/vertical) are too 990 coarse to have realistic melting or for sensitivity studies where you want to control your input. 991 Full description, sensitivity and validation in preparation. 992 993 There is 2 ways to apply the fwf to NEMO. The first possibility (\np{ln\_divisf}~=~false) applied the fwf 994 and heat flux directly on the salinity and temperature tendancy. The second possibility (\np{ln\_divisf}~=~true) 995 apply the fwf as for the runoff fwf (see \S\ref{SBC_rnf}). The mass/volume addition due to the ice shelf melting is, 996 at each relevant depth level, added to the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div} 997 (called from \mdl{divcur}). 998 % 949 999 % ================================================================ 950 1000 % Handling of icebergs -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Chapters/Chap_TRA.tex
r4147 r5682 1077 1077 correctly set ($i.e.$ that $T_o$ and $S_o$ are provided in input files and read 1078 1078 using \mdl{fldread}, see \S\ref{SBC_fldread}). 1079 The restoring coefficient $\gamma$ is a three-dimensional array initialized by the 1080 user in routine \rou{dtacof} also located in module \mdl{tradmp}. 1079 The restoring coefficient $\gamma$ is a three-dimensional array read in during the \rou{tra\_dmp\_init} routine. The file name is specified by the namelist variable \np{cn\_resto}. The DMP\_TOOLS tool is provided to allow users to generate the netcdf file. 1081 1080 1082 1081 The two main cases in which \eqref{Eq_tra_dmp} is used are \textit{(a)} … … 1092 1091 diagnostic method \citep{Sarmiento1982}. It allows us to find the velocity 1093 1092 field consistent with the model dynamics whilst having a $T$, $S$ field 1094 close to a given climatological field ($T_o$, $S_o$). The time scale 1095 associated with $S_o$ is generally not a constant but spatially varying 1096 in order to respect other properties. For example, it is usually set to zero 1097 in the mixed layer (defined either on a density or $S_o$ criterion) 1098 \citep{Madec_al_JPO96} and in the equatorial region 1099 \citep{Reverdin1991, Fujio1991, Marti_PhD92} since these two regions 1100 have a short time scale of adjustment; while smaller $\gamma$ are used 1101 in the deep ocean where the typical time scale is long \citep{Sarmiento1982}. 1102 In addition the time scale is reduced (even to zero) along the western 1103 boundary to allow the model to reconstruct its own western boundary 1104 structure in equilibrium with its physics. 1105 The choice of the shape of the Newtonian damping is controlled by two 1106 namelist parameters \np{nn\_hdmp} and \np{nn\_zdmp}. The former allows us to specify: the 1107 width of the equatorial band in which no damping is applied; a decrease 1108 in the vicinity of the coast; and a damping everywhere in the Red and Med Seas. 1109 The latter sets whether damping should act in the mixed layer or not. 1110 The time scale associated with the damping depends on the depth as 1111 a hyperbolic tangent, with \np{rn\_surf} as surface value, \np{rn\_bot} as 1112 bottom value and a transition depth of \np{rn\_dep}. 1093 close to a given climatological field ($T_o$, $S_o$). 1113 1094 1114 1095 The robust diagnostic method is very efficient in preventing temperature … … 1118 1099 by stabilising the water column too much. 1119 1100 1120 An example of the computation of $\gamma$ for a robust diagnostic experiment 1121 with the ORCA2 model is provided in the \mdl{tradmp} module 1122 (subroutines \rou{dtacof} and \rou{cofdis} which compute the coefficient 1123 and the distance to the bathymetry, respectively). These routines are 1124 provided as examples and can be customised by the user. 1101 The namelist parameter \np{nn\_zdmp} sets whether the damping should be applied in the whole water column or only below the mixed layer (defined either on a density or $S_o$ criterion). It is common to set the damping to zero in the mixed layer as the adjustment time scale is short here \citep{Madec_al_JPO96}. 1102 1103 \subsection[DMP\_TOOLS]{Generating resto.nc using DMP\_TOOLS} 1104 1105 DMP\_TOOLS can be used to generate a netcdf file containing the restoration coefficient $\gamma$. Note that in order to maintain bit comparison with previous NEMO versions DMP\_TOOLS must be compiled and run on the same machine as the NEMO model. A mesh\_mask.nc file for the model configuration is required as an input. This can be generated by carrying out a short model run with the namelist parameter \np{nn\_msh} set to 1. The namelist parameter \np{ln\_tradmp} will also need to be set to .false. for this to work. The \nl{nam\_dmp\_create} namelist in the DMP\_TOOLS directory is used to specify options for the restoration coefficient. 1106 1107 %--------------------------------------------nam_dmp_create------------------------------------------------- 1108 \namdisplay{nam_dmp_create} 1109 %------------------------------------------------------------------------------------------------------- 1110 1111 \np{cp\_cfg}, \np{cp\_cpz}, \np{jp\_cfg} and \np{jperio} specify the model configuration being used and should be the same as specified in \nl{namcfg}. The variable \nl{lzoom} is used to specify that the damping is being used as in case \textit{a} above to provide boundary conditions to a zoom configuration. In the case of the arctic or antarctic zoom configurations this includes some specific treatment. Otherwise damping is applied to the 6 grid points along the ocean boundaries. The open boundaries are specified by the variables \np{lzoom\_n}, \np{lzoom\_e}, \np{lzoom\_s}, \np{lzoom\_w} in the \nl{nam\_zoom\_dmp} name list. 1112 1113 The remaining switch namelist variables determine the spatial variation of the restoration coefficient in non-zoom configurations. \np{ln\_full\_field} specifies that newtonian damping should be applied to the whole model domain. \np{ln\_med\_red\_seas} specifies grid specific restoration coefficients in the Mediterranean Sea for the ORCA4, ORCA2 and ORCA05 configurations. If \np{ln\_old\_31\_lev\_code} is set then the depth variation of the coeffients will be specified as a function of the model number. This option is included to allow backwards compatability of the ORCA2 reference configurations with previous model versions. \np{ln\_coast} specifies that the restoration coefficient should be reduced near to coastlines. This option only has an effect if \np{ln\_full\_field} is true. \np{ln\_zero\_top\_layer} specifies that the restoration coefficient should be zero in the surface layer. Finally \np{ln\_custom} specifies that the custom module will be called. This module is contained in the file custom.F90 and can be edited by users. For example damping could be applied in a specific region. 1114 1115 The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}. Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to the full values of a 10$^{\circ}$ latitud band. This is often used because of the short adjustment time scale in the equatorial region \citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a hyperbolic tangent, with \np{rn\_surf} as surface value, \np{rn\_bot} as bottom value and a transition depth of \np{rn\_dep}. 1125 1116 1126 1117 % ================================================================ -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Chapters/Chap_ZDF.tex
r4147 r5682 830 830 % Bottom Friction 831 831 % ================================================================ 832 \section [Bottom Friction (\textit{zdfbfr})] {Bottom Friction (\mdl{zdfbfr} module)}832 \section [Bottom and top Friction (\textit{zdfbfr})] {Bottom Friction (\mdl{zdfbfr} module)} 833 833 \label{ZDF_bfr} 834 834 … … 837 837 %-------------------------------------------------------------------------------------------------------------- 838 838 839 Options are defined through the \ngn{nambfr} namelist variables. 839 Options to define the top and bottom friction are defined through the \ngn{nambfr} namelist variables. 840 The top friction is activated only if the ice shelf cavities are opened (\np{ln\_isfcav}~=~true). 841 As the friction processes at the top and bottom are the represented similarly, only the bottom friction is described in detail. 842 840 843 Both the surface momentum flux (wind stress) and the bottom momentum 841 844 flux (bottom friction) enter the equations as a condition on the vertical -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Namelist/nambfr
r4147 r5682 5 5 ! = 2 : nonlinear friction 6 6 rn_bfri1 = 4.e-4 ! bottom drag coefficient (linear case) 7 rn_bfri2 = 1.e-3 ! bottom drag coefficient (non linear case) 7 rn_bfri2 = 1.e-3 ! bottom drag coefficient (non linear case). Minimum coeft if ln_loglayer=T 8 rn_bfri2_max = 1.e-1 ! max. bottom drag coefficient (non linear case and ln_loglayer=T) 8 9 rn_bfeb2 = 2.5e-3 ! bottom turbulent kinetic energy background (m2/s2) 9 rn_bfrz0 = 3.e-3 ! bottom roughness for loglayer bfr coeff10 rn_bfrz0 = 3.e-3 ! bottom roughness [m] if ln_loglayer=T 10 11 ln_bfr2d = .false. ! horizontal variation of the bottom friction coef (read a 2D mask file ) 11 12 rn_bfrien = 50. ! local multiplying factor of bfr (ln_bfr2d=T) 13 rn_tfri1 = 4.e-4 ! top drag coefficient (linear case) 14 rn_tfri2 = 2.5e-3 ! top drag coefficient (non linear case). Minimum coeft if ln_loglayer=T 15 rn_tfri2_max = 1.e-1 ! max. top drag coefficient (non linear case and ln_loglayer=T) 16 rn_tfeb2 = 0.0 ! top turbulent kinetic energy background (m2/s2) 17 rn_tfrz0 = 3.e-3 ! top roughness [m] if ln_loglayer=T 18 ln_tfr2d = .false. ! horizontal variation of the top friction coef (read a 2D mask file ) 19 rn_tfrien = 50. ! local multiplying factor of tfr (ln_tfr2d=T) 20 12 21 ln_bfrimp = .true. ! implicit bottom friction (requires ln_zdfexp = .false. if true) 22 ln_loglayer = .false. ! logarithmic formulation (non linear case) 13 23 / -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Namelist/namdyn_hpg
r4147 r5682 5 5 ln_hpg_zps = .true. ! z-coordinate - partial steps (interpolation) 6 6 ln_hpg_sco = .false. ! s-coordinate (standard jacobian formulation) 7 ln_hpg_isf = .false. ! s-coordinate (sco ) adapted to ice shelf cavity 7 8 ln_hpg_djc = .false. ! s-coordinate (Density Jacobian with Cubic polynomial) 8 9 ln_hpg_prj = .false. ! s-coordinate (Pressure Jacobian scheme) -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Namelist/namsbc
r4230 r5682 19 19 ln_dm2dc = .false. ! daily mean to diurnal cycle on short wave 20 20 ln_rnf = .true. ! runoffs (T => fill namsbc_rnf) 21 nn_isf = 0 ! ice shelf melting/freezing (/=0 => fill namsbc_isf) 22 ! 0 =no isf 1 = presence of ISF 23 ! 2 = bg03 parametrisation 3 = rnf file for isf 24 ! 4 = ISF fwf specified 25 ! option 1 and 4 need ln_isfcav = .true. (domzgr) 21 26 ln_ssr = .true. ! Sea Surface Restoring on T and/or S (T => fill namsbc_ssr) 22 27 nn_fwb = 3 ! FreshWater Budget: =0 unchecked -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Namelist/namtra_dmp
r3294 r5682 2 2 &namtra_dmp ! tracer: T & S newtonian damping 3 3 !----------------------------------------------------------------------- 4 ln_tradmp = .true. ! add a damping termn (T) or not (F) 5 nn_hdmp = -1 ! horizontal shape =-1, damping in Med and Red Seas only 6 ! =XX, damping poleward of XX degrees (XX>0) 7 ! + F(distance-to-coast) + Red and Med Seas 8 nn_zdmp = 0 ! vertical shape =0 damping throughout the water column 9 ! =1 no damping in the mixing layer (kz criteria) 10 ! =2 no damping in the mixed layer (rho crieria) 11 rn_surf = 50. ! surface time scale of damping [days] 12 rn_bot = 360. ! bottom time scale of damping [days] 13 rn_dep = 800. ! depth of transition between rn_surf and rn_bot [meters] 14 nn_file = 0 ! create a damping.coeff NetCDF file (=1) or not (=0) 4 ln_tradmp = .true. ! add a damping termn (T) or not (F) 5 nn_zdmp = 0 ! vertical shape =0 damping throughout the water column 6 ! =1 no damping in the mixing layer (kz criteria) 7 ! =2 no damping in the mixed layer (rho crieria) 8 cn_resto = 'resto.nc' ! Name of file containing restoration coefficient field (use dmp_tools to create this) 9 15 10 / -
branches/2015/dev_r5072_UKMO2_OBS_simplification/DOC/TexFiles/Namelist/namzgr
r3294 r5682 5 5 ln_zps = .true. ! z-coordinate - partial steps (T/F) 6 6 ln_sco = .false. ! s- or hybrid z-s-coordinate (T/F) 7 ln_isfcav = .false. ! ice shelf cavity (T/F) 7 8 /
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