# Changeset 9394

Ignore:
Timestamp:
2018-03-13T21:21:44+01:00 (2 years ago)
Message:

Fix several typos, reverse (biblio then index) and shrink the manual backmatter (columns, font size, separator height) #1793

Location:
branches/2017/dev_merge_2017/DOC
Files:
13 edited

Unmodified
Removed

• ## branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.sty

• ## branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.tex

 r9393 %% Bibliography \cleardoublepage \phantomsection \addcontentsline{toc}{chapter}{Bibliography} \bibliography{../tex_main/NEMO_manual} %% Index \cleardoublepage \phantomsection \addcontentsline{toc}{chapter}{Index} \printindex %% Bibliography \addcontentsline{toc}{chapter}{Bibliography} \bibliography{../tex_main/NEMO_manual} \end{document}
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_CONFIG.tex

 r9393 $z$-coordinates and is forced with tidal lateral boundary conditions using a flather boundary condition from the BDY module. The AMM configuration  uses the GLS (key\_zdfgls) turbulence scheme, the VVL non-linear free surface(key\_vvl) and time-splitting (key\_dynspg\_ts). The AMM configuration  uses the GLS (\key{zdfgls}) turbulence scheme, the VVL non-linear free surface(\key{vvl}) and time-splitting (\key{dynspg\_ts}). In addition to the tidal boundary condition the model may also take
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex

 r9393 with the size of the array passed to iomput. The grid\_ref attribute refers to definitions set in iodef.xml which, in turn, reference grids and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in iom.F90) and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file. $e.g.$: \begin{xmllines} Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step, add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$ which has been defined with the correct frequency of operations (iom\_set\_field\_attr in iom.F90) which has been defined with the correct frequency of operations (iom\_set\_field\_attr in \mdl{iom}) \item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules) \subsubsection{Other controls of the XML attributes from NEMO} The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in iom.F90). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary). The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in \mdl{iom}). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary). Here is the list of these attributes:\\
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIU.tex

 r9393 \end{itemize} Models are provided for both the warm layer, diurnal\_bulk.F90, and the cool skin, cool\_skin.F90.  Foundation SST is not considered as it can be obtained Models are provided for both the warm layer, \mdfl{diurnal_bulk}, and the cool skin, \mdl{cool_skin}.  Foundation SST is not considered as it can be obtained either from the main NEMO model ($i.e.$ from the temperature of the top few model levels) or from some other source.
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_DYN.tex

 r9393 For term \textit{ttt} in the momentum equations, the logical namelist variables are \textit{ln\_dynttt\_xxx}, where \textit{xxx} is a 3 or 4 letter acronym corresponding to each optional scheme. If a CPP key is used for this term its name is \textbf{key\_ttt}. The corresponding If a CPP key is used for this term its name is \key{ttt}. The corresponding code can be found in the \textit{dynttt\_xxx} module in the DYN directory, and it is usually computed in the \textit{dyn\_ttt\_xxx} subroutine.
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_LDF.tex

 r9393 The specification of the space variation of the coefficient is made in \mdl{ldftra} and \mdl{ldfdyn}, or more precisely in include files \textit{traldf\_cNd.h90} and \textit{dynldf\_cNd.h90}, with N=1, 2 or 3. \hf{traldf\_cNd} and \hf{dynldf\_cNd}, with N=1, 2 or 3. The user can modify these include files as he/she wishes. The way the mixing coefficient are set in the reference version can be briefly described \subsubsection{Constant mixing coefficients (default option)} When none of the \textbf{key\_dynldf\_...} and \textbf{key\_traldf\_...} keys are When none of the \key{dynldf\_...} and \key{traldf\_...} keys are defined, a constant value is used over the whole ocean for momentum and tracers, which is specified through the \np{rn\_ahm0} and \np{rn\_aht0} namelist the eddy induced coefficient has to be defined. Its space variations are controlled by the same CPP variable as for the eddy diffusivity coefficient ($i.e.$ \textbf{key\_traldf\_cNd}). \key{traldf\_cNd}). (5) the eddy coefficient associated with a biharmonic operator must be set to a \emph{negative} value.
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_OBS.tex

 r9393 In addition to \emph{OPA\_SRC} the offline obs oper requires the inclusion of the \emph{OOO\_SRC} directory. \emph{OOO\_SRC} contains a replacement \textbf{nemo.f90} and \textbf{nemogcm.F90} which overwrites the resultant \textbf{nemo.exe}. This is the approach taken of the \emph{OOO\_SRC} directory. \emph{OOO\_SRC} contains a replacement \mdl{nemo} and \mdl{nemogcm} which overwrites the resultant \textbf{nemo.exe}. This is the approach taken by \emph{SAS\_SRC} and \emph{OFF\_SRC}.
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex

 r9393 A generic interface has been introduced to manage the way input data (2D or 3D fields, like surface forcing or ocean T and S) are specify in \NEMO. This task is archieved by fldread.F90. like surface forcing or ocean T and S) are specify in \NEMO. This task is archieved by \mdl{fldread}. The module was design with four main objectives in mind: \begin{enumerate} \begin{itemize} \item \mdl{nemogcm} : This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (step.F90) \item \mdl{nemogcm} : This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (\mdl{step}) Since the ocean state is not calculated all associated initialisations have been removed. \item  \mdl{step} : The main time stepping routine now only needs to call the sbc routine (and a few utility functions). and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used (seek advice from UKMO if necessary).  Currently the code is only designed to work when using the CORE forcing option for NEMO (with \textit{calc\_strair~=~true} and \textit{calc\_Tsfc~=~true} in the CICE name-list), or alternatively when NEMO is coupled to the HadGAM3 atmosphere model (with \textit{calc\_strair~=~false} and \textit{calc\_Tsfc~=~false}). \textit{calc\_strair}\forcode{ = .true.} and \textit{calc\_Tsfc}\forcode{ = .true.} in the CICE name-list), or alternatively when NEMO is coupled to the HadGAM3 atmosphere model (with \textit{calc\_strair}\forcode{ = .false.} and \textit{calc\_Tsfc}\forcode{ = false}). The code is intended to be used with \np{nn\_fsbc} set to 1 (although coupling ocean and ice less frequently should work, it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly - the
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_TRA.tex

 r9393 For each equation term  \textit{TTT}, the namelist logicals are \textit{ln\_traTTT\_xxx}, where \textit{xxx} is a 3 or 4 letter acronym corresponding to each optional scheme. The CPP key (when it exists) is \textbf{key\_traTTT}. The equivalent code can be The CPP key (when it exists) is \key{traTTT}. The equivalent code can be found in the \textit{traTTT} or \textit{traTTT\_xxx} module, in the NEMO/OPA/TRA directory. The choice is made in the \textit{\ngn{namtra\_adv}} namelist, by setting to \forcode{.true.} one of the logicals \textit{ln\_traadv\_xxx}. The corresponding code can be found in the \textit{traadv\_xxx.F90} module, The corresponding code can be found in the \mdl{traadv\_xxx} module, where \textit{xxx} is a 3 or 4 letter acronym corresponding to each scheme. By default ($i.e.$ in the reference namelist, \ngn{namelist\_ref}), all the logicals \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. This module is contained in the file \mdl{custom} and can be edited by users. For example damping could be applied in a specific region. The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}.
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_misc.tex

 r9393 duplicated rows and columns due to cyclic or north fold boundary condition as well as overlap MPP areas). The self-compensated summation method should be used in all summation in i- and/or j-direction. See closea.F90 module for an example. in i- and/or j-direction. See \mdl{closea} module for an example. Note also that this implementation may be sensitive to the optimization level.
• ## branches/2017/dev_merge_2017/DOC/tex_sub/chap_time_domain.tex

 r9393 where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient. $\gamma$ is initialized as \np{rn\_atfp} (namelist parameter). Its default value is \np{rn_atfp}\forcode{ = 10.e-3} (see \S~\ref{STP_mLF}), Its default value is \np{rn\_atfp}\forcode{ = 10.e-3} (see \S~\ref{STP_mLF}), causing only a weak dissipation of high frequency motions (\citep{Farge1987}). The addition of a time filter degrades the accuracy of the
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