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Changeset 5965 for branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles – NEMO

Ignore:
Timestamp:
2015-12-01T16:35:30+01:00 (8 years ago)
Author:
timgraham
Message:

Upgraded branch to r5518 of trunk (v3.6 stable revision)

Location:
branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles
Files:
14 edited
4 copied

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  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Biblio/Biblio.bib

    r4560 r5965  
    271271  volume = {326}, 
    272272  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} 
    273282} 
    274283 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Chapters/Chap_DIA.tex

    r4153 r5965  
    7474The 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.  
    7575 
    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. 
     76In 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. 
    7777 
    7878Even 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. 
    … …  
    466466\end{verbatim} 
    467467}}\end{alltt}  
    468 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 99) 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:\\ 
     468However 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:\\ 
    469469\\ 
    470470\begin{tabular}{|p{4cm}|p{8cm}|} 
    … …  
    543543\end{tabular} 
    544544 
     545\subsubsection{Advanced use of XIOS functionalities} 
    545546 
    546547\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 
     563in 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}  
     570in 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}  
     577Note 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}  
     590Note 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} 
     630The 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} 
     652The 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} 
     675The 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 
    547678 
    548679\subsubsection{Tag list} 
    … …  
    849980\end{longtable} 
    850981 
     982\subsection{CF metadata standard compliance} 
     983 
     984Output 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 
     986Some 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. 
    851987 
    852988 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Chapters/Chap_DOM.tex

    r4147 r5965  
    493493$z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). This option can be used with full step  
    494494bathymetry or $s$-coordinate (hybrid and partial step coordinates have not  
    495 yet been tested in NEMO v2.3).  
     495yet 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). 
    496497 
    497498Contrary to the horizontal grid, the vertical grid is computed in the code and no  

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Chapters/Chap_DYN.tex

    r4560 r5965  
    627627\eqref{Eq_dynhpg_zco_surf} - \eqref{Eq_dynhpg_zco}, and $z_T$ is the depth of  
    628628the $T$-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). 
     632This scheme need the activation of ice shelf cavities (\np{ln\_isfcav}=true). 
    630633 
    631634$\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln\_dynhpg\_prj}=true) 
    … …  
    795798%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    796799\begin{figure}[!t]    \begin{center} 
    797 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_time_split.pdf} 
     800\includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_DYN_dynspg_ts.pdf} 
    798801\caption{  \label{Fig_DYN_dynspg_ts} 
    799802Schematic of the split-explicit time stepping scheme for the external  

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Chapters/Chap_MISC.tex

    r4147 r5965  
    141141computational domain is laid out on local processor memories following a 2D  
    142142horizontal 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 
     146The extended grids for use with the under-shelf ice cavities will result in redundant rows 
     147around Antarctica if the ice cavities are not active. A simple mechanism for subsetting 
     148input files associated with the extended domains has been implemented to avoid the need to 
     149maintain different sets of input fields for use with or without active ice cavities. The 
     150existing 'zoom' options are overly complex for this task and marked for deletion anyway. 
     151This alternative subsetting operates for the j-direction only and works by optionally 
     152looking for and using a global file attribute (named: \np{open\_ocean\_jstart}) to 
     153determine the starting j-row for input. The use of this option is best explained with an 
     154example: Consider an ORCA1 configuration using the extended grid bathymetry and coordinate 
     155files: 
     156\vspace{-10pt} 
     157\begin{alltt} 
     158\tiny 
     159\begin{verbatim} 
     160eORCA1_bathymetry_v2.nc 
     161eORCA1_coordinates.nc 
     162\end{verbatim} 
     163\end{alltt} 
     164\noindent These files define a horizontal domain of 362x332. Assuming the first row with 
     165open ocean wet points in the non-isf bathymetry for this set is row 42 (Fortran indexing) 
     166then the formally correct setting for \np{open\_ocean\_jstart} is 41. Using this value as the 
     167first row to be read will result in a 362x292 domain which is the same size as the original 
     168ORCA1 domain. Thus the extended coordinates and bathymetry files can be used with all the 
     169original 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} 
     177ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc  
     178ncatted  -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 
     189bathymetry and coordinates currently. However the option can be extended to any global, 2D 
     190and 3D, netcdf, input field by adding the: 
     191\vspace{-10pt} 
     192\begin{alltt} 
     193\tiny 
     194\begin{verbatim} 
     195lrowattr=ln_use_jattr 
     196\end{verbatim} 
     197\end{alltt} 
     198optional 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. 
    143199 
    144200%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Chapters/Chap_SBC.tex

    r4230 r5965  
    11% ================================================================ 
    2 % Chapter � Surface Boundary Condition (SBC, ICB)  
    3 % ================================================================ 
    4 \chapter{Surface Boundary Condition (SBC, ICB) } 
     2% Chapter � Surface Boundary Condition (SBC, ISF, ICB)  
     3% ================================================================ 
     4\chapter{Surface Boundary Condition (SBC, ISF, ICB) } 
    55\label{SBC} 
    66\minitoc 
    … …  
    4848below ice-covered areas (using observed ice-cover or a sea-ice model)  
    4949(\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  
     50fluxes 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);  
     53the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the  
    5254transformation of the solar radiation (if provided as daily mean) into a diurnal  
    5355cycle (\np{ln\_dm2dc}~=~true); and a neutral drag coefficient can be read from an external wave  
    … …  
    6062Finally, the different options that further modify the fluxes applied to the ocean are discussed. 
    6163One of these is modification by icebergs (see \S\ref{ICB_icebergs}), which act as drifting sources of fresh water. 
     64Another example of modification is that due to the ice shelf melting/freezing (see \S\ref{SBC_isf}),  
     65which provides additional sources of fresh water. 
    6266 
    6367 
    … …  
    348352horizontal and vertical dimensions of the associated variable and should  
    349353be equal to 1 over land and 0 elsewhere. 
    350 The procedure can be recursively applied setting nn_lsm > 1 in namsbc namelist.  
    351 Note that nn_lsm=0 forces the code to not apply the procedure even if a file for land/sea mask is supplied. 
     354The procedure can be recursively applied setting nn\_lsm > 1 in namsbc namelist.  
     355Note that nn\_lsm=0 forces the code to not apply the procedure even if a file for land/sea mask is supplied. 
    352356 
    353357\subsubsection{Bilinear Interpolation} 
    … …  
    686690air temperature, sea-surface temperature, cloud cover and relative humidity. 
    687691Sensible heat and latent heat fluxes are computed by classical 
    688 bulk formulae parameterized according to \citet{Kondo1975}. 
     692bulk formulae parameterised according to \citet{Kondo1975}. 
    689693Details on the bulk formulae used can be found in \citet{Maggiore_al_PCE98} and \citet{Castellari_al_JMS1998}. 
    690694 
    … …  
    826830\Pi-g\delta = (1+k-h) \Pi_{A}(\lambda,\phi) 
    827831\end{equation} 
    828 with $k$ a number of Love estimated to 0.6 which parametrized the astronomical tidal land, 
    829 and $h$ a number of Love to 0.3 which parametrized the parametrization due to the astronomical tidal land. 
     832with $k$ a number of Love estimated to 0.6 which parameterised the astronomical tidal land, 
     833and $h$ a number of Love to 0.3 which parameterised the parameterisation due to the astronomical tidal land. 
    830834 
    831835% ================================================================ 
    … …  
    945949 
    946950%} 
    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%-------------------------------------------------------------------------------------------------------- 
     960Namelist variable in \ngn{namsbc}, \np{nn\_isf},  control the kind of ice shelf representation used.  
     961\begin{description} 
     962\item[\np{nn\_isf}~=~1] 
     963The ice shelf cavity is represented. The fwf and heat flux are computed.  
     964Full description, sensitivity and validation in preparation.  
     965 
     966\item[\np{nn\_isf}~=~2] 
     967A parameterisation of isf is used. The ice shelf cavity is not represented.  
     968The 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).  
     970Furthermore the fwf is computed using the \citet{Beckmann2003} parameterisation of isf melting.  
     971The effective melting length (\np{sn\_Leff\_isf}) is read from a file. 
     972 
     973\item[\np{nn\_isf}~=~3] 
     974A simple parameterisation of isf is used. The ice shelf cavity is not represented.  
     975The 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}). 
     977Full description, sensitivity and validation in preparation. 
     978 
     979\item[\np{nn\_isf}~=~4] 
     980The ice shelf cavity is represented. However, the fwf (\np{sn\_fwfisf}) and heat flux (\np{sn\_qisf}) are  
     981not 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  
     990coarse to have realistic melting or for sensitivity studies where you want to control your input.  
     991Full description, sensitivity and validation in preparation.  
     992 
     993There 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% 
    949999% ================================================================ 
    9501000%        Handling of icebergs 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Chapters/Chap_TRA.tex

    r4147 r5965  
    10771077correctly set  ($i.e.$ that $T_o$ and $S_o$ are provided in input files and read  
    10781078using \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}.  
     1079The 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. 
    10811080 
    10821081The two main cases in which \eqref{Eq_tra_dmp} is used are \textit{(a)}  
    … …  
    10921091diagnostic method \citep{Sarmiento1982}. It allows us to find the velocity  
    10931092field 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}.   
     1093close to a given climatological field ($T_o$, $S_o$).  
    11131094 
    11141095The robust diagnostic method is very efficient in preventing temperature  
    … …  
    11181099by stabilising the water column too much. 
    11191100 
    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.  
     1101The 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 
     1105DMP\_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 
     1113The 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 
     1115The 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}.   
    11251116 
    11261117% ================================================================ 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Chapters/Chap_ZDF.tex

    r4147 r5965  
    830830% Bottom Friction 
    831831% ================================================================ 
    832 \section  [Bottom Friction (\textit{zdfbfr})]   {Bottom Friction (\mdl{zdfbfr} module)} 
     832\section  [Bottom and top Friction (\textit{zdfbfr})]   {Bottom Friction (\mdl{zdfbfr} module)} 
    833833\label{ZDF_bfr} 
    834834 
    … …  
    837837%-------------------------------------------------------------------------------------------------------------- 
    838838 
    839 Options are defined through the  \ngn{nambfr} namelist variables. 
     839Options to define the top and bottom friction are defined through the  \ngn{nambfr} namelist variables. 
     840The top friction is activated only if the ice shelf cavities are opened (\np{ln\_isfcav}~=~true). 
     841As the friction processes at the top and bottom are the represented similarly, only the bottom friction is described in detail. 
     842 
    840843Both the surface momentum flux (wind stress) and the bottom momentum  
    841844flux (bottom friction) enter the equations as a condition on the vertical  

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Chapters/Introduction.tex

    r4147 r5965  
    1919the model design. More specific information about running the model on different  
    2020computers, or how to set up a configuration, are found on the \NEMO web site  
    21 (www.locean-ipsl.upmc.fr/NEMO).  
     21(www.nemo-ocean.eu).  
    2222 
    2323The ocean component of \NEMO has been developed from the OPA model,  

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Namelist/nambfr

    r4147 r5965  
    55                           !                              = 2 : nonlinear friction 
    66   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) 
    89   rn_bfeb2    =    2.5e-3 !  bottom turbulent kinetic energy background  (m2/s2) 
    9    rn_bfrz0    =    3.e-3  ! bottom roughness for loglayer bfr coeff  
     10   rn_bfrz0    =    3.e-3  !  bottom roughness [m] if ln_loglayer=T 
    1011   ln_bfr2d    = .false.   !  horizontal variation of the bottom friction coef (read a 2D mask file ) 
    1112   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 
    1221   ln_bfrimp   = .true.    !  implicit bottom friction (requires ln_zdfexp = .false. if true) 
     22   ln_loglayer = .false.   !  logarithmic formulation (non linear case) 
    1323/ 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Namelist/namdyn_hpg

    r4147 r5965  
    55   ln_hpg_zps  = .true.    !  z-coordinate - partial steps (interpolation) 
    66   ln_hpg_sco  = .false.   !  s-coordinate (standard jacobian formulation) 
     7   ln_hpg_isf  = .false.   !  s-coordinate (sco ) adapted to ice shelf cavity 
    78   ln_hpg_djc  = .false.   !  s-coordinate (Density Jacobian with Cubic polynomial) 
    89   ln_hpg_prj  = .false.   !  s-coordinate (Pressure Jacobian scheme) 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Namelist/namsbc

    r4230 r5965  
    1919   ln_dm2dc    = .false.   !  daily mean to diurnal cycle on short wave 
    2020   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) 
    2126   ln_ssr      = .true.    !  Sea Surface Restoring on T and/or S       (T => fill namsbc_ssr) 
    2227   nn_fwb      = 3         !  FreshWater Budget: =0 unchecked 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Namelist/namtra_dmp

    r3294 r5965  
    22&namtra_dmp    !   tracer: T & S newtonian damping 
    33!----------------------------------------------------------------------- 
    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 
    1510/ 

  • branches/2014/dev_r4650_UKMO14.5_SST_BIAS_CORRECTION/DOC/TexFiles/Namelist/namzgr

    r3294 r5965  
    55   ln_zps      = .true.    !  z-coordinate - partial steps   (T/F) 
    66   ln_sco      = .false.   !  s- or hybrid z-s-coordinate    (T/F) 
     7   ln_isfcav   = .false.   !  ice shelf cavity               (T/F) 
    78/ 
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