New URL for NEMO forge!   http://forge.nemo-ocean.eu

Since March 2022 along with NEMO 4.2 release, the code development moved to a self-hosted GitLab.
This present forge is now archived and remained online for history.
Changeset 4153 for branches/2013/dev_LOCEAN_2013 – NEMO

Ignore:
Timestamp:
2013-11-05T13:25:45+01:00 (10 years ago)
Author:
cetlod
Message:

dev_LOCEAN_2013: merge in trunk changes between r3940 and r4028, see ticket #1169

Location:
branches/2013/dev_LOCEAN_2013
Files:
39 edited
1 copied

Legend:

Unmodified
Added
Removed

  • branches/2013/dev_LOCEAN_2013/DOC/NEMO_book.tex

    r4147 r4153  
    2323\usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption} % Gives small font for captions 
    2424\usepackage{enumitem}                          % allows non-bold description items 
     25\usepackage{longtable}                         % allows multipage tables 
    2526%\usepackage{colortbl}                           % gives coloured panels behind table columns 
    2627 

  • branches/2013/dev_LOCEAN_2013/DOC/TexFiles/Chapters/Chap_DIA.tex

    r4148 r4153  
    11% ================================================================ 
    2 % Chapter � I/O & Diagnostics 
     2% Chapter I/O & Diagnostics 
    33% ================================================================ 
    44\chapter{Ouput and Diagnostics (IOM, DIA, TRD, FLO)} 
    … …  
    1616 
    1717The model outputs are of three types: the restart file, the output listing,  
    18 and the output file(s). The restart file is used internally by the code when  
     18and the diagnostic output file(s). The restart file is used internally by the code when  
    1919the user wants to start the model with initial conditions defined by a  
    2020previous simulation. It contains all the information that is necessary in  
    … …  
    2525that it is saved in the same binary format as the one used by the computer  
    2626that is to read it (in particular, 32 bits binary IEEE format must not be used for  
    27 this file). The output listing and file(s) are predefined but should be checked  
     27this file).  
     28 
     29The output listing and file(s) are predefined but should be checked  
    2830and eventually adapted to the user's needs. The output listing is stored in  
    2931the $ocean.output$ file. The information is printed from within the code on the  
    … …  
    3133"\textit{grep -i numout}" in the source code directory. 
    3234 
    33 By default, outpout files are written in NetCDF format but an IEEE output format, called DIMG, can be choosen when defining \key{dimgout}. Since version 3.2, when defining \key{iomput}, an I/O server has been added which provides more flexibility in the choice of the fields to be outputted as well as how the writing work is distributed over the processors in massively parallel computing. The complete description of the use of this I/O server is presented in next section. If neither \key{iomput} nor \key{dimgout} are defined, NEMO is producing NetCDF with the old IOIPSL library which has been kept for compatibility and its easy installation, but it is quite inefficient on parrallel machines. If \key{iomput} is not defined, output files are defined in the \mdl{diawri} module and containing mean (or instantaneous if \key{diainstant} is defined) values over a period of nn\_write time-step (namelist parameter).  
     35By default, diagnostic output files are written in NetCDF format but an IEEE binary output format, called DIMG, can be choosen by defining \key{dimgout}.  
     36 
     37Since version 3.2, when defining \key{iomput}, an I/O server has been added which provides more flexibility in the choice of the fields to be written as well as how the writing work is distributed over the processors in massively parallel computing. The complete description of the use of this I/O server is presented in the next section.  
     38 
     39By default, if neither \key{iomput} nor \key{dimgout} are defined, NEMO produces NetCDF with the old IOIPSL library which has been kept for compatibility and its easy installation. However, the IOIPSL library is quite inefficient on parallel machines and, since version 3.2, many diagnostic options have been added presuming the use of \key{iomput}. The usefulness of the default IOIPSL-based option is expected to reduce with each new release. If \key{iomput} is not defined, output files and content are defined in the \mdl{diawri} module and contain mean (or instantaneous if \key{diainstant} is defined) values over a regular period of nn\_write time-steps (namelist parameter).  
    3440 
    3541%\gmcomment{                    % start of gmcomment 
    … …  
    4248 
    4349 
    44 Since version 3.2, iomput is the NEMO output interface. It was designed to be simple to use, flexible and efficient. The two main purposes of iomput are: \\ 
    45 (1) the complete and flexible control of the output files through an external xml file defined by the user \\ 
    46 (2) to achieve high performance outputs through the distribution (or not) of all tasks related to output files on dedicated processes. \\ 
    47 The first functionality allows the user to specify, without touching anything into the code, the way he want to output data: \\ 
    48 - choice of output frequencies that can be different for each file (including real months and years) \\ 
    49 - choice of file contents: decide which data will be written in which file (the same data can be outputted in different files)  \\ 
    50 - possibility to split output files at a choosen frequency \\ 
    51 - possibility to extract a vertical or an horizontal subdomain  \\ 
    52 - choice of the temporal operation to perform: average, accumulate, instantaneous, min, max and once  \\ 
    53 - extremely large choice of data available   \\ 
    54 - redefine variables name and long\_name  \\ 
    55 In addition, iomput allows the user to output any variable (scalar, 2D or 3D) in the code in a very easy way. All details of iomput functionalities are listed in the following subsections. Example of the iodef.xml files that control the outputs can be found here: NEMOGCM/CONFIG/ORCA2\_LIM/EXP00/iodef*.xml 
    56  
    57 The second functionality targets outputs performances when running on a very large number of processes. First, iomput provides the possibility to dedicate N specific processes (in addition to NEMO processes) to write the outputs, where N is big enough (and defined by the user) to suppress the bottle neck associated with the the writing of the output files. Since version 3.5, this interface depends on an external code called \href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}. This new IO server takes advantage of the new functionalitiy of NetCDF4 that allows the user to write files in parallel and therefore to bypass the rebuilding phase. Note that writting 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 trough xios are incompatible with NetCDF3. All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3. 
    58  
    59 \subsection{Basic knowledge} 
    60  
     50Since version 3.2, iomput is the NEMO output interface of choice. It has been designed to be simple to use, flexible and efficient. The two main purposes of iomput are:  
     51\begin{enumerate} 
     52\item The complete and flexible control of the output files through external XML files adapted by the user from standard templates.  
     53\item To achieve high performance and scalable output through the optional distribution of all diagnostic output related tasks to dedicated processes.  
     54\end{enumerate} 
     55The first functionality allows the user to specify, without code changes or recompilation, aspects of the diagnostic output stream, such as: 
     56\begin{itemize} 
     57\item The choice of output frequencies that can be different for each file (including real months and years). 
     58\item The choice of file contents; includes complete flexibility over which data are written in which files (the same data can be written in different files).  
     59\item The possibility to split output files at a choosen frequency. 
     60\item The possibility to extract a vertical or an horizontal subdomain. 
     61\item The choice of the temporal operation to perform, e.g.: average, accumulate, instantaneous, min, max and once. 
     62\item Control over metadata via a large XML "database" of possible output fields. 
     63\end{itemize} 
     64In addition, iomput allows the user to add the output of any new variable (scalar, 2D or 3D) in the code in a very easy way. All details of iomput functionalities are listed in the following subsections. Examples of the XML files that control the outputs can be found in: 
     65\begin{alltt} 
     66\begin{verbatim} 
     67  NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml 
     68  NEMOGCM/CONFIG/SHARED/field_def.xml 
     69  and 
     70  NEMOGCM/CONFIG/SHARED/domain_def.xml. 
     71\end{verbatim} 
     72\end{alltt} 
     73 
     74The 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 
     76Since 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. 
     77 
     78Even 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. 
     79 
     80\subsection{XIOS: the IO\_SERVER} 
     81 
     82\subsubsection{Attached or detached mode?} 
     83 
     84Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS}, the io\_server developed by Yann Meurdesoif from IPSL. The behaviour of the io subsystem is controlled by settings in the external XML files listed above. Key settings in the iodef.xml file are {\tt using\_server} and the {\tt type} tag associated with each defined file. The {\tt using\_server} setting determines whether or not the server will be used in ''attached mode'' (as a library) [{\tt false}] or in ''detached mode'' (as an external executable on N additional, dedicated cpus) [{\tt true}]. The ''attached mode'' is simpler to use but much less efficient for massively parallel applications. The type of each file can be either ''multiple\_file'' or ''one\_file''. 
     85 
     86In attached mode and if the type of file is ''multiple\_file'', then each NEMO process will also act as an IO server and produce its own set of output files. Superficially, this emulates the standard behaviour in previous versions, However, the subdomain written out by each process does not correspond to the {\tt jpi x jpj x jpk} domain actually computed by the process (although it may if {\tt jpni=1}). Instead each process will have collected and written out a number of complete longitudinal strips. If the ''one\_file'' option is chosen then all processes will collect their longitudinal strips and write (in parallel) to a single output file.  
     87 
     88In detached mode and if the type of file is ''multiple\_file'', then each stand-alone XIOS process will collect data for a range of complete longitudinal strips and write to its own set of output files. If the ''one\_file'' option is chosen then all XIOS processes will collect their longitudinal strips and write (in parallel) to a single output file. Note running in detached mode requires launching a Multiple Process Multiple Data (MPMD) parallel job. The following subsection provides a typical example but the syntax will vary in different MPP environments. 
     89 
     90\subsubsection{Number of cpu used by XIOS in detached mode} 
     91 
     92The number of cores used by the XIOS is specified when launching the model. The number of cores dedicated to XIOS should be from ~1/10 to ~1/50 of the number or cores dedicated to NEMO. Some manufacturers suggest using O($\sqrt{N}$) dedicated IO processors for N processors but this is a general recommendation and not specific to NEMO. It is difficult to provide precise recommendations because the optimal choice will depend on the particular hardware properties of the target system (parallel filesystem performance, available memory, memory bandwidth etc.) and the volume and frequency of data to be created. Here is an example of 2 cpus for the io\_server and 62 cpu for nemo using mpirun: 
     93 
     94\texttt{ mpirun -np 62 ./nemo.exe : -np 2 ./xios\_server.exe } 
     95 
     96\subsubsection{Control of XIOS: the XIOS context in iodef.xml} 
     97 
     98As well as the {\tt using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml. See the XML basics section below for more details on XML syntax and rules. 
     99 
     100\begin{tabular}{|p{4cm}|p{6.0cm}|p{2.0cm}|} 
     101   \hline 
     102   variable name &  
     103   description &  
     104   example \\  
     105   \hline    
     106   \hline 
     107   buffer\_size &  
     108   buffer size used by XIOS to send data from NEMO to XIOS. Larger is more efficient. Note that needed/used buffer sizes are summarized at the end of the job &  
     109   25000000 \\  
     110   \hline    
     111   buffer\_server\_factor\_size &  
     112   ratio between NEMO and XIOS buffer size. Should be 2. &  
     113   2 \\  
     114   \hline 
     115   info\_level &  
     116   verbosity level (0 to 100) &  
     117   0 \\  
     118   \hline 
     119   using\_server &  
     120   activate attached(false) or detached(true) mode &  
     121   true \\  
     122   \hline 
     123   using\_oasis &  
     124   XIOS is used with OASIS(true) or not (false) &  
     125   false \\  
     126   \hline 
     127   oasis\_codes\_id &  
     128   when using oasis, define the identifier of NEMO in the namcouple. Note that the identifier of XIOS is xios.x &  
     129   oceanx \\  
     130   \hline    
     131\end{tabular} 
     132 
     133 
     134\subsection{Practical issues} 
     135 
     136\subsubsection{Installation} 
     137 
     138As mentioned, XIOS is supported separately and must be downloaded and compiled before it can be used with NEMO. See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance. NEMO will need to link to the compiled XIOS library. The  
     139\href{http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/XIOS-IO-server-installation-and-use}{XIOS with NEMO} guide provides an example illustration of how this can be achieved. 
     140 
     141\subsubsection{Add your own outputs} 
     142 
     143It is very easy to add your own outputs with iomput. Many standard fields and diagnostics are already prepared (i.e., steps 1 to 3 below have been done) and simply need to be activated by including the required output in a file definition in iodef.xml (step 4). To add new output variables, all 4 of the following steps must be taken. 
     144\begin{description} 
     145\item[1.] in NEMO code, add a \\ 
     146\texttt{      CALL iom\_put( 'identifier', array ) } \\ 
     147where you want to output a 2D or 3D array. 
     148 
     149\item[2.] If necessary, add \\ 
     150\texttt{   USE iom\ \ \ \ \ \ \ \ \ \ \ \ ! I/O manager library }  \\ 
     151to the list of used modules in the upper part of your module.  
     152 
     153\item[3.] in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code (see subsequent sections for a details of the XML syntax and rules). For example: 
     154\vspace{-20pt} 
     155\begin{alltt}  {{\scriptsize 
     156\begin{verbatim} 
     157   <field_definition> 
     158      <!-- T grid --> 
     159 
     160     <field_group id="grid_T" grid_ref="grid_T_3D"> 
     161      ... 
     162      <field id="identifier" long_name="blabla" ... />    
     163      ... 
     164   </field_definition>  
     165\end{verbatim} 
     166}}\end{alltt}  
     167Note your definition must be added to the field\_group whose reference grid is consistent 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) or defined in the domain\_def.xml file. E.g.: 
     168\vspace{-20pt} 
     169\begin{alltt}  {{\scriptsize 
     170\begin{verbatim} 
     171     <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> 
     172\end{verbatim} 
     173}}\end{alltt}  
     174Note, if your array is computed within the surface module each nn\_fsbc time\_step,  
     175add 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) 
     176 
     177\item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules)   \\ 
     178\vspace{-20pt} 
     179\begin{alltt}  {{\scriptsize 
     180\begin{verbatim} 
     181   <file id="file1" .../>    
     182      ... 
     183      <field field_ref="identifier" />    
     184      ... 
     185   </file>    
     186\end{verbatim} 
     187}}\end{alltt}  
     188 
     189\end{description} 
     190\subsection{XML fundamentals} 
    61191 
    62192\subsubsection{ XML basic rules} 
    … …  
    72202 
    73203The XML file used in XIOS is structured by 7 families of tags: context, axis, domain, grid, field, file and variable. Each tag family has hierarchy of three flavors (except for context): 
    74 \begin{description} 
    75 \item[root]: declaration of the root element that can contain element groups or elements, for example : $<$file\_definition ...$/>$ \\ 
    76 \item[group]: declaration of a group element that can contain element groups or elements, for example : $<$file\_group ...$/>$ \\ 
    77 \item[element]: declaration of an element that can contain elements, for example : $<$file ...$/>$  \\ 
    78 \end{description} 
     204\\ 
     205\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|} 
     206   \hline 
     207   flavor & 
     208   description & 
     209   example \\ 
     210   \hline 
     211   \hline 
     212   root & 
     213   declaration of the root element that can contain element groups or elements & 
     214   {\scriptsize \verb? < file_definition ... >?} \\ 
     215   \hline 
     216   group & 
     217   declaration of a group element that can contain element groups or elements & 
     218   {\scriptsize \verb? < file_group ... >?} \\ 
     219   \hline 
     220   element & 
     221   declaration of an element that can contain elements & 
     222   {\scriptsize \verb? < file ... >?} \\ 
     223   \hline 
     224\end{tabular} 
     225\\ 
    79226 
    80227Each element may have several attributes. Some attributes are mandatory, other are optional but have a default value and other are are completely optional. Id is a special attribute used to identify an element or a group of elements. It must be unique for a kind of element. It is optional, but no reference to the corresponding element can be done if it is not defined. 
    81228 
    82 The XML file is split into context tags that are used to isolate IO definition from different codes or different parts of a code. No interference is possible between 2 different contexts. Each context has its own calendar and an associated timestep. In NEMO, we used the following contexts (that can be defined in any order): 
    83 \begin{description} 
    84 \item[contex xios]: context containing informations for XIOS \\ 
    85 \verb?   <context id="xios" ... ?  
    86 \item[context nemo]: contex containing IO informations for NEMO (mother grid when using AGRIF) \\ 
    87 \verb?   <context id="nemo" ... ?  
    88 \item[context 1\_nemo]: contex containing IO informations for NEMO child grid 1 (when using AGRIF) \\ 
    89 \verb?   <context id="1_nemo" ... ?   
    90 \item[context n\_nemo]: contex containing IO informations for NEMO child grid n (when using AGRIF) \\ 
    91 \verb?   <context id="n_nemo" ... ? 
    92 \end{description} 
    93  
    94 Each context tag related to NEMO (mother or child grids) is divided into 5 parts (that can be defined in any order): 
    95 \begin{description} 
    96 \item[field definition]: define all variables that can potentially be outputted \\ 
    97 \verb?   <field_definition ... ? 
    98 \item[file definition]: define the netcdf files to be created and the variables they will contain \\ 
    99 \verb?   <file_definition ... ?  
    100 \item[axis definitions]: define vertical axis \\ 
    101 \verb?   <axis_definition ... ? 
    102 \item[domain definitions]: define the horizontal grids \\ 
    103 \verb?   <domain_definition ... ? 
    104 \item[grid definitions]: define the 2D and 3D grids (association of an axis and a domain) \\ 
    105 \verb?   <grid_definition ... ?  
    106 \end{description} 
    107  
    108 the xios context contains only 1 tag: 
    109 \begin{description} 
    110 \item[variable definition]: define variables needed by xios. This can be seen as a kind of namelist for xios. \\ 
    111 \verb?   <variable_definition ... ?  
    112 \end{description} 
    113  
    114 The XML file can be split in different parts to improve its readability and facilitate its use. The inclusing of XML files into the main XML file can be done through the attribute src: \\ 
    115 \verb?   <context src="./nemo_def.xml" /> ?  
    116 In NEMO, by default, the field and domain définition is done in 2 séparate files: \\ 
    117 NEMOGCM/CONFIG/SHARED/field\_def.xml and \\ 
    118 NEMOGCM/CONFIG/SHARED/domain\_def.xml that are included in the main iodef.xml file through the following commands: \\ 
    119 \verb?   <field_definition src="./field_def.xml" /> ? \\ 
    120 \verb?   <domain_definition src="./domain_def.xml" /> ?  
     229The XML file is split into context tags that are used to isolate IO definition from different codes or different parts of a code. No interference is possible between 2 different contexts. Each context has its own calendar and an associated timestep. In NEMO, we used the following contexts (that can be defined in any order):\\ 
     230\\ 
     231\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|} 
     232   \hline 
     233   context & 
     234   description & 
     235   example \\ 
     236   \hline 
     237   \hline 
     238   context xios & 
     239   context containing information for XIOS & 
     240   {\scriptsize \verb? <context id="xios" ...  ?} \\ 
     241   \hline 
     242   context nemo & 
     243   context containing IO information for NEMO (mother grid when using AGRIF) & 
     244   {\scriptsize \verb? <context id="nemo" ... ?} \\ 
     245   \hline 
     246   context 1\_nemo & 
     247   context containing IO information for NEMO child grid 1 (when using AGRIF) & 
     248   {\scriptsize \verb? <context id="1_nemo" ...  ?} \\ 
     249   \hline 
     250   context n\_nemo & 
     251   context containing IO information for NEMO child grid n (when using AGRIF) & 
     252   {\scriptsize \verb? <context id="n_nemo" ...  ?} \\ 
     253   \hline 
     254\end{tabular} 
     255\\ 
     256 
     257\noindent The xios context contains only 1 tag: 
     258\\ 
     259\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|} 
     260   \hline 
     261   context tag & 
     262   description & 
     263   example \\ 
     264   \hline 
     265   \hline 
     266   variable\_definition & 
     267   define variables needed by XIOS. This can be seen as a kind of namelist for XIOS. & 
     268   {\scriptsize \verb? <variable_definition ... ?} \\ 
     269   \hline 
     270\end{tabular} 
     271\\ 
     272 
     273\noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts (that can be defined in any order):\\ 
     274\\ 
     275\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|} 
     276   \hline 
     277   context tag & 
     278   description & 
     279   example \\ 
     280   \hline 
     281   \hline 
     282   field\_definition & 
     283   define all variables that can potentially be outputted & 
     284   {\scriptsize \verb? <field_definition ... ?} \\ 
     285   \hline 
     286   file\_definition & 
     287   define the netcdf files to be created and the variables they will contain & 
     288   {\scriptsize \verb? <file_definition ... ?} \\ 
     289   \hline 
     290   axis\_definition & 
     291   define vertical axis & 
     292   {\scriptsize \verb? <axis_definition ... ?} \\ 
     293   \hline 
     294   domain\_definition & 
     295   define the horizontal grids & 
     296   {\scriptsize \verb? <domain_definition ... ?} \\ 
     297   \hline 
     298   grid\_definition & 
     299   define the 2D and 3D grids (association of an axis and a domain) & 
     300   {\scriptsize \verb? <grid_definition ... ?} \\ 
     301   \hline 
     302\end{tabular} 
     303\\ 
     304 
     305\subsubsection{Nesting XML files} 
     306 
     307The XML file can be split in different parts to improve its readability and facilitate its use. The inclusion of XML files into the main XML file can be done through the attribute src: \\ 
     308{\scriptsize \verb? <context src="./nemo_def.xml" /> ?}\\ 
     309  
     310\noindent In NEMO, by default, the field and domain definition is done in 2 separate files: 
     311{\scriptsize \tt 
     312\begin{verbatim} 
     313NEMOGCM/CONFIG/SHARED/field_def.xml 
     314and 
     315NEMOGCM/CONFIG/SHARED/domain_def.xml  
     316\end{verbatim} 
     317} 
     318\noindent that are included in the main iodef.xml file through the following commands: \\ 
     319{\scriptsize \verb? <field_definition src="./field_def.xml" /> ? \\ 
     320\verb? <domain_definition src="./domain_def.xml" /> ? } 
    121321 
    122322 
    123323\subsubsection{Use of inheritance} 
    124324 
    125 XML extensively uses the concept of inheritance. XML has a based tree structure with a parent-child oriented relation: all children inherit attributes from parent, but an attribute defined in a child replace the inherited attribute value. Note that the special attribute ''id'' is never inherited.  \\ 
     325XML extensively uses the concept of inheritance. XML has a tree based structure with a parent-child oriented relation: all children inherit attributes from parent, but an attribute defined in a child replace the inherited attribute value. Note that the special attribute ''id'' is never inherited.  \\ 
    126326\\ 
    127 example 1: Direct inheritance. \\ 
     327example 1: Direct inheritance. 
     328\vspace{-20pt} 
    128329\begin{alltt}  {{\scriptsize     
    129330\begin{verbatim} 
    130331   <field_definition operation="average" > 
    131       <field id="sst"                    />   <!-- averaged      sst -->  
    132       <field id="sss" operation="instant"/>   <!-- instantaneous sss -->  
     332     <field id="sst"                    />   <!-- averaged      sst -->  
     333     <field id="sss" operation="instant"/>   <!-- instantaneous sss -->  
    133334   </field_definition>  
    134335\end{verbatim} 
    … …  
    140341for example output instantaneous values instead of average values. \\ 
    141342\\ 
    142 example 2: Inheritance by reference. \\ 
     343example 2: Inheritance by reference. 
     344\vspace{-20pt} 
    143345\begin{alltt}  {{\scriptsize 
    144346\begin{verbatim} 
    145347   <field_definition> 
    146       <field id="sst" long_name="sea surface temperature" />    
    147       <field id="sss" long_name="sea surface salinity"    />   
     348     <field id="sst" long_name="sea surface temperature" />    
     349     <field id="sss" long_name="sea surface salinity"    />   
    148350   </field_definition>       
    149351 
    150352   <file_definition> 
    151       <file id="myfile" output_freq="1d" />    
    152             <field field_ref="sst"                            />  <!-- default def --> 
    153             <field field_ref="sss" long_name="my description" />  <!-- overwrite   --> 
    154       </file>    
     353     <file id="myfile" output_freq="1d" />    
     354       <field field_ref="sst"                            />  <!-- default def --> 
     355       <field field_ref="sss" long_name="my description" />  <!-- overwrite   --> 
     356     </file>    
    155357   </file_definition>  
    156358\end{verbatim} 
    157359}}\end{alltt}  
    158 Inherite (and overwrite, if needed) the attributes of a tag you are refering to. 
    159  
    160 \subsubsection{Use of Group} 
    161  
    162 Groups can be used fort 2 purposes. \\ 
    163  
    164 First, the group can be used to define common attributes to be shared by the elements of the group through the inheritance. In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''. Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''. 
     360Inherit (and overwrite, if needed) the attributes of a tag you are refering to. 
     361 
     362\subsubsection{Use of Groups} 
     363 
     364Groups can be used for 2 purposes. Firstly, the group can be used to define common attributes to be shared by the elements of the group through inheritance. In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''. Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''. 
     365\vspace{-20pt} 
    165366\begin{alltt}  {{\scriptsize 
    166367\begin{verbatim} 
    167368   <field_group id="grid_T" grid_ref="grid_T_2D"> 
    168       <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/> 
    169       <field id="sst"  long_name="sea surface temperature" unit="degC"                     /> 
    170       <field id="sss"  long_name="sea surface salinity"    unit="psu"                      /> 
    171       <field id="ssh"  long_name="sea surface height"      unit="m"                        /> 
     369    <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/> 
     370    <field id="sst"  long_name="sea surface temperature" unit="degC"                     /> 
     371    <field id="sss"  long_name="sea surface salinity"    unit="psu"                      /> 
     372    <field id="ssh"  long_name="sea surface height"      unit="m"                        /> 
    172373         ... 
    173374\end{verbatim} 
    174375}}\end{alltt}  
    175376 
    176 Second, the group can be used to replace a list of elements. Several examples of groups of fields are proposed at the end of the file \\ 
    177 NEMOGCM/CONFIG/SHARED/field\_def.xml. For example, a short list of usual variables related to the U grid: 
     377Secondly, the group can be used to replace a list of elements. Several examples of groups of fields are proposed at the end of the file {\tt CONFIG/SHARED/field\_def.xml}. For example, a short list of the usual variables related to the U grid: 
     378\vspace{-20pt} 
    178379\begin{alltt}  {{\scriptsize 
    179380\begin{verbatim} 
    180381   <field_group id="groupU" > 
    181       <field field_ref="uoce"  /> 
    182       <field field_ref="suoce" /> 
    183       <field field_ref="utau"  /> 
     382    <field field_ref="uoce"  /> 
     383    <field field_ref="suoce" /> 
     384    <field field_ref="utau"  /> 
    184385   </field_group> 
    185386\end{verbatim} 
    186387}}\end{alltt}  
    187 that can be directly include in a file through the following syntaxe: 
     388that can be directly included in a file through the following syntax: 
     389\vspace{-20pt} 
    188390\begin{alltt}  {{\scriptsize 
    189391\begin{verbatim} 
    190392   <file id="myfile_U" output_freq="1d" />    
    191       <field_group group_ref="groupU"/>   
    192       <field field_ref="uocetr_eff"  />  <!-- add another field --> 
     393    <field_group group_ref="groupU"/>   
     394    <field field_ref="uocetr_eff"  />  <!-- add another field --> 
    193395   </file>    
    194396\end{verbatim} 
    … …  
    197399\subsection{Detailed functionalities } 
    198400 
    199 The file NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml provides several examples of the use of the new functionalities offered by the XML interface of XIOS.  
     401The file {\tt NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml} provides several examples of the use of the new functionalities offered by the XML interface of XIOS.  
    200402 
    201403\subsubsection{Define horizontal subdomains} 
    202 Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of the tag family domain. It must therefore be done in the domain part of the XML file. For example, in NEMOGCM/CONFIG/SHARED/domain\_def.xml, we provide the following example of a definition of a 5 by 5 box with the bottom left corner at point (10,10). 
     404Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of the tag family domain. It must therefore be done in the domain part of the XML file. For example, in {\tt CONFIG/SHARED/domain\_def.xml}, we provide the following example of a definition of a 5 by 5 box with the bottom left corner at point (10,10). 
     405\vspace{-20pt} 
    203406\begin{alltt}  {{\scriptsize 
    204407\begin{verbatim} 
    205408   <domain_group id="grid_T"> 
    206       <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" /> 
     409    <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" /> 
    207410\end{verbatim} 
    208411}}\end{alltt}  
    209412The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. For example: 
     413\vspace{-20pt} 
    210414\begin{alltt}  {{\scriptsize 
    211415\begin{verbatim} 
    … …  
    216420}}\end{alltt}  
    217421Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain. The Equatorial section, the TAO, RAMA and PIRATA moorings are alredy registered in the code and can therefore be outputted without taking care of their (i,j) position in the grid. These predefined domains can be activated by the use of specific domain\_ref: ''EqT'', ''EqU'' or ''EqW'' for the equatorial sections and the mooring position for TAO, RAMA and PIRATA followed by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...) 
     422\vspace{-20pt} 
    218423\begin{alltt}  {{\scriptsize 
    219424\begin{verbatim} 
    … …  
    227432\subsubsection{Define vertical zooms} 
    228433Vertical 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: 
     434\vspace{-20pt} 
    229435\begin{alltt}  {{\scriptsize 
    230436\begin{verbatim} 
    … …  
    235441}}\end{alltt}  
    236442The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. For example: 
     443\vspace{-20pt} 
    237444\begin{alltt}  {{\scriptsize 
    238445\begin{verbatim} 
    … …  
    246453 
    247454The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. for example: 
     455\vspace{-20pt} 
    248456\begin{alltt}  {{\scriptsize 
    249457\begin{verbatim} 
    … …  
    258466\end{verbatim} 
    259467}}\end{alltt}  
    260 However it is also often very convienent to define the file name with the name of the experience, 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 section or mooring (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 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:\\ 
    261469\\ 
    262470\begin{tabular}{|p{4cm}|p{8cm}|} 
    263471   \hline 
    264    \centering part of the name automatically to be replaced & 
    265    by \\ 
     472   \centering placeholder string & automatically  replaced by \\ 
    266473   \hline 
    267474   \hline 
    268475   \centering @expname@ & 
    269    the experience name (from cn\_exp in the namelist) \\ 
     476   the experiment name (from cn\_exp in the namelist) \\ 
    270477   \hline 
    271478   \centering @freq@ & 
    … …  
    284491   ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \verb?yyyymmdd_hh:mm:ss? format \\ 
    285492   \hline 
    286 \end{tabular} 
     493\end{tabular}\\ 
    287494\\ 
    288495 
    289 For example,  
    290  
    291 \begin{alltt}  {{\scriptsize 
     496\noindent For example,  
     497{{\scriptsize 
    292498\begin{verbatim} 
    293499   <file id="myfile_hzoom" name="myfile_@expname@_@startdate@_freq@freq@" output_freq="1d" > 
    294500\end{verbatim} 
    295 }}\end{alltt}  
    296  
    297 With, in the namelist: 
    298  
    299 \begin{alltt}  {{\scriptsize 
     501}} 
     502\noindent with the namelist: 
     503{{\scriptsize 
    300504\begin{verbatim} 
    301505   cn_exp      =  "ORCA2" 
    … …  
    303507   ln_rstart   = .false. 
    304508\end{verbatim} 
    305 }}\end{alltt}  
    306  
    307 will give the following file name radical: 
    308  
    309 \begin{alltt}  {{\scriptsize 
     509}} 
     510\noindent will give the following file name radical: 
     511{{\scriptsize 
    310512\begin{verbatim} 
    311513   myfile_ORCA2_19891231_freq1d  
    312514\end{verbatim} 
    313 }}\end{alltt}  
    314  
     515}} 
    315516 
    316517\subsubsection{Other controls of the xml attributes from NEMO} 
    317518 
    318 The values of some attributes are automatically defined by NEMO (and any definition given in the xml file is overwritten). By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary).  
    319  
    320 Here is the list of these attributes: \\ 
     519The 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).  
     520 
     521Here is the list of these attributes:\\ 
    321522\\ 
    322523\begin{tabular}{|l|c|c|c|} 
    … …  
    343544 
    344545 
     546\subsection{XML reference tables} 
     547 
    345548\subsubsection{Tag list} 
    346549 
    347  
    348 \begin{tabular}{|p{2cm}|p{2.5cm}|p{3.5cm}|p{2cm}|p{2cm}|} 
     550\begin{longtable}{|p{2.2cm}|p{2.5cm}|p{3.5cm}|p{2.2cm}|p{1.6cm}|} 
    349551   \hline 
    350552   tag name &  
    … …  
    352554   accepted attribute &  
    353555   child of & 
    354    parent of \\ 
    355    \hline    
     556   parent of \endhead 
    356557   \hline    
    357558   simulation &  
    … …  
    362563   \hline    
    363564   context & 
    364    encapsulates parts of the xml file dédicated to different codes or different parts of a code & 
     565   encapsulates parts of the xml file dedicated to different codes or different parts of a code & 
    365566   id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin & 
    366567   simulation & 
    367    all root tags: ...\_definition \\ 
     568   all root tags: ... \_definition \\ 
    368569   \hline    
    369570   \hline    
    … …  
    389590   file\_definition &  
    390591   encapsulates the definition of all the files that will be outputted & 
    391    enabled, min\_digits, name, name\_suffix, output\_level, split\_format, split\_freq, sync\_freq, type, src & 
     592   enabled, min\_digits, name, name\_suffix, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src & 
    392593   context &  
    393594   file or file\_group \\ 
    … …  
    395596   file\_group &  
    396597   encapsulates a group of files that will be outputted & 
    397    enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_format, split\_freq, sync\_freq, type, src & 
     598   enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src & 
    398599   file\_definition, file\_group &  
    399600   file or file\_group \\ 
    400601   \hline    
    401602   file &  
    402    defile the contentof a file to be outputted & 
    403    enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_format, split\_freq, sync\_freq, type, src & 
     603   define the contents of a file to be outputted & 
     604   enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src & 
    404605   file\_definition, file\_group &  
    405606   field \\ 
    406    \hline    
    407 \end{tabular} 
    408 \begin{tabular}{|p{2cm}|p{2.5cm}|p{3.5cm}|p{2cm}|p{2cm}|} 
    409    \hline 
    410    tag name &  
    411    description &  
    412    accepted attribute &  
    413    child of & 
    414    parent of \\ 
    415    \hline    
    416607   \hline    
    417608   axis\_definition &  
    … …  
    434625   \hline    
    435626   \hline    
    436    domain\_definition &  
     627   domain\_\-definition &  
    437628   define all the horizontal domains potentially used by the variables & 
    438629   src & 
    439630   context &  
    440    domain\_group, domain \\ 
     631   domain\_\-group, domain \\ 
    441632   \hline    
    442633   domain\_group &  
    443634   encapsulates a group of horizontal domains & 
    444635   id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & 
    445    domain\_definition, domain\_group &  
    446    domain\_group, domain \\ 
     636   domain\_\-definition, domain\_group &  
     637   domain\_\-group, domain \\ 
    447638   \hline    
    448639   domain &  
    449640   define an horizontal domain & 
    450641   id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & 
    451    domain\_definition, domain\_group &  
     642   domain\_\-definition, domain\_group &  
    452643   none \\ 
    453644   \hline    
    … …  
    471662   none \\ 
    472663   \hline    
    473 \end{tabular} 
     664\end{longtable} 
    474665 
    475666 
    476667\subsubsection{Attributes list} 
    477668 
    478 \begin{tabular}{|p{2cm}|p{4cm}|p{4cm}|p{2cm}|} 
    479    \hline 
     669\begin{longtable}{|p{2.2cm}|p{4cm}|p{3.8cm}|p{2cm}|} 
     670   \hline 
     671   attribute name &  
     672   description &  
     673   example &  
     674   accepted by \endhead 
     675   \hline    
     676   axis\_ref &  
     677   refers to the id of a vertical axis &  
     678   axis\_ref="deptht" &  
     679   field, grid families \\  
     680   \hline    
     681   enabled &  
     682   switch on/off the output of a field or a file &  
     683   enabled=".TRUE." &  
     684   field, file families \\  
     685   \hline    
     686   default\_value &  
     687   missing\_value definition &  
     688   default\_value="1.e20" &  
     689   field family \\  
     690   \hline    
     691   description &  
     692   just for information, not used &  
     693   description="ocean T grid variables" &  
     694   all tags \\  
     695   \hline    
     696   domain\_ref &  
     697   refers to the id of a domain &  
     698   domain\_ref="grid\_T" &  
     699   field or grid families \\  
     700   \hline    
     701   field\_ref &  
     702   id of the field we want to add in a file &  
     703   field\_ref="toce" &  
     704   field \\  
     705   \hline    
     706   grid\_ref &  
     707   refers to the id of a grid &  
     708   grid\_ref="grid\_T\_2D" &  
     709   field family \\  
     710   \hline    
     711   group\_ref &  
     712   refer to a group of variables &  
     713   group\_ref="mooring" &  
     714   field\_group \\  
     715   \hline    
     716   id &  
     717   allow to identify a tag &  
     718   id="nemo" & 
     719   accepted by all tags except simulation \\  
     720   \hline    
     721   level &  
     722   output priority of a field: 0 (high) to 10 (low)&  
     723   level="1" &  
     724   field family \\  
     725   \hline    
     726   long\_name &  
     727   define the long\_name attribute in the NetCDF file &  
     728   long\_name="Vertical T levels" &  
     729   field \\  
     730   \hline    
     731   min\_digits &  
     732   specify the minimum of digits used in the core number in the name of the NetCDF file &  
     733   min\_digits="4" &  
     734   file family \\  
     735   \hline    
     736   name &  
     737   name of a variable or a file. If the name of a file is undefined, its id is used as a name &  
     738   name="tos" &  
     739   field or file families \\  
     740   \hline    
     741   name\_suffix &  
     742   suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file &  
     743   name\_suffix="\_myzoom" &  
     744   file family \\  
     745   \hline    
    480746   attribute name &  
    481747   description &  
    … …  
    484750   \hline    
    485751   \hline    
    486    axis\_ref &  
    487    refers to the id of a vertical axis &  
    488    axis\_ref="deptht" &  
    489    field, grid families \\  
    490    \hline    
    491    enabled &  
    492    switch on/off the output of a field or a file &  
    493    enabled=".TRUE." &  
    494    field, file families \\  
    495    \hline    
    496    default\_value &  
    497    missing\_value definition &  
    498    default\_value="1.e20" &  
     752   operation &  
     753   type of temporal operation: average, accumulate, instantaneous, min, max and once &  
     754   operation="average" &  
    499755   field family \\  
    500756   \hline    
    501    description &  
    502    just for information, not used &  
    503    description="ocean T grid variables" &  
    504    all tags \\  
    505    \hline    
    506    domain\_ref &  
    507    refers to the id of a domain &  
    508    domain\_ref="grid\_T" &  
    509    field or grid families \\  
    510    \hline    
    511    field\_ref= &  
    512    id of the field we want to add in a file &  
    513    field\_ref="toce" &  
     757   output\_freq &  
     758   operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. &  
     759   output\_freq="1d12h" &  
     760   field family \\  
     761   \hline    
     762   output\_level &  
     763   output priority of variables in a file: 0 (high) to 10 (low). All variables listed in the file with a level smaller or equal to output\_level will be output. Other variables won't be output even if they are listed in the file. &   
     764   output\_level="10"&  
     765   file family \\  
     766   \hline    
     767   positive &  
     768   convention used for the orientation of vertival axis (positive downward in \NEMO). &  
     769   positive="down" &  
     770   axis family \\  
     771   \hline    
     772   prec &  
     773   output precision: real 4 or real 8 &  
     774   prec="4" &  
     775   field family \\  
     776   \hline    
     777   split\_freq &  
     778   frequency at which to temporally split output files. Units can be ts (timestep), y, mo, d, h, mi, s. Useful for long runs to prevent over-sized output files.&  
     779   split\_freq="1mo" &  
     780   file family \\  
     781   \hline    
     782   split\_freq\-\_format &  
     783   date format used in the name of temporally split output files. Can be specified  
     784   using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s &  
     785   split\_freq\_format= "\%y\%mo\%d" &  
     786   file family \\  
     787   \hline    
     788   src &  
     789   allow to include a file &  
     790   src="./field\_def.xml" &  
     791   accepted by all tags except simulation \\  
     792   \hline    
     793   standard\_name &  
     794   define the standard\_name attribute in the NetCDF file &  
     795   standard\_name= "Eastward\_Sea\_Ice\_Transport" &  
    514796   field \\  
    515797   \hline    
    516    grid\_ref &  
    517    refers to the id of a grid &  
    518    grid\_ref="grid\_T\_2D" &  
    519    field family \\  
    520    \hline    
    521    group\_ref &  
    522    refer to a group of variables &  
    523    group\_ref="mooring" &  
    524    field\_group \\  
    525    \hline    
    526    id &  
    527    allow to identify a tag &  
    528    id="nemo" & 
    529    accepted by all tags except simulation \\  
    530    \hline    
    531    level &  
    532    output priority of a field: 0 (high) to 10 (low)&  
    533    level="1" &  
    534    field family \\  
    535    \hline    
    536    long\_name &  
    537    define the long\_name attribute in the NetCDF file &  
    538    long\_name="Vertical T levels" &  
    539    field \\  
    540    \hline    
    541    min\_digits &  
    542    specify the minimum of digits used in the core number in the name of the NetCDF file &  
    543    min\_digits="4" &  
     798   sync\_freq &  
     799   NetCDF file synchronization frequency (update of the time\_counter). units can be ts (timestep), y, mo, d, h, mi, s. &  
     800   sync\_freq="10d" &  
    544801   file family \\  
    545802   \hline    
    546    name &  
    547    name of a variable or a file. If the name of a file is undefined, its id is used as a name &  
    548    name="tos" &  
    549    field or file families \\  
    550    \hline    
    551    name\_suffix &  
    552    suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file &  
    553    name\_suffix="\_myzoom" &  
    554    file family \\  
    555    \hline    
    556 \end{tabular} 
    557 \begin{tabular}{|p{2cm}|p{4cm}|p{4cm}|p{2cm}|} 
    558    \hline 
    559803   attribute name &  
    560804   description &  
    … …  
    563807   \hline    
    564808   \hline    
    565    operation &  
    566    type of temporal operation: average, accumulate, instantaneous, min, max and once &  
    567    operation="average" &  
    568    field family \\  
    569    \hline    
    570    output\_freq &  
    571    operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. &  
    572    output\_freq="1d12h" &  
    573    field family \\  
    574    \hline    
    575    output\_level &  
    576    output priority of variables in a file: 0 (high) to 10 (low). All variables listed in the file with a level smaller or equal to output\_level will be output. Other variables won't be output even if they are listed in the file. &   
    577    output\_level="10"&  
    578    file family \\  
    579    \hline    
    580    positive &  
    581    convention used for the orientation of vertival axis (positive downward in \NEMO). &  
    582    positive="down" &  
    583    axis family \\  
    584    \hline    
    585    prec &  
    586    output precision: real 4 or real 8 &  
    587    prec="4" &  
    588    field family \\  
    589    \hline    
    590    split\_format &  
    591    date format used in the name of splitted output files. can be spécified using the following syntaxe: \%y, \%mo, \%d, \%h \%mi and \%s &  
    592    split\_format="\%yy\%mom\%dd" &  
    593    file family \\  
    594    \hline    
    595    split\_freq &  
    596    split output files frequency. units can be ts (timestep), y, mo, d, h, mi, s. &  
    597    split\_freq="1mo" &  
    598    file family \\  
    599    \hline    
    600    src &  
    601    allow to include a file &  
    602    src="./field\_def.xml" &  
    603    accepted by all tags except simulation \\  
    604    \hline    
    605    standard\_name &  
    606    define the standard\_name attribute in the NetCDF file &  
    607    standard\_name="Eastward\_Sea\_Ice\_Transport" &  
    608    field \\  
    609    \hline    
    610    sync\_freq &  
    611    NetCDF file synchronization frequency (update of the time\_counter). units can be ts (timestep), y, mo, d, h, mi, s. &  
    612    sync\_freq="10d" &  
    613    file family \\  
    614    \hline    
    615 \end{tabular} 
    616 \begin{tabular}{|p{2cm}|p{4cm}|p{4cm}|p{2cm}|} 
    617    \hline 
    618    attribute name &  
    619    description &  
    620    example &  
    621    accepted by \\  
    622    \hline    
    623    \hline    
    624809   time\_origin &  
    625810   specify the origin of the time counter &  
    … …  
    628813   \hline    
    629814   type (1)&  
    630    specify if the output files must be splitted (multiple\_file) or not (one\_file) &  
     815   specify if the output files are to be split spatially (multiple\_file) or not (one\_file) &  
    631816   type="multiple\_file" &  
    632817   file familly \\  
    … …  
    662847   domain family \\  
    663848   \hline    
    664 \end{tabular} 
    665  
    666 \subsection{XIOS: the IO\_SERVER} 
    667  
    668 \subsubsection{Attached or detached mode?} 
    669  
    670 Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS}, the io\_server developed by Yann Meurdesoif from IPSL. This server can be used in ''attached mode'' (as a library) or in ''detached mode'' (as an external executable on n cpus). The ''attached mode'' is simpler to use but much less efficient. If the type of file is ''multiple\_file'', then in attached(detached) mode, each NEMO(XIOS) process will output its own subdomain: if NEMO(XIOS) is runnning on N cores, the ouput files will be splitted into N files. If the type of file is ''one\_file'', the output files will be directly recombined into one unique file either in ''detached mode'' or ''attached mode''.   
    671  
    672 \subsubsection{Control of xios: the xios context in iodef.xml} 
    673  
    674 The control of the use of xios is done through the xios context in iodef.xml. 
    675  
    676 \begin{tabular}{|p{3cm}|p{6.5cm}|p{2.5cm}|} 
    677    \hline 
    678    variable name &  
    679    description &  
    680    example \\  
    681    \hline    
    682    \hline 
    683    buffer\_size &  
    684    buffer size used by XIOS to send data from NEMO to XIOS. Larger is more efficient. Note that needed/used buffer sizes are summarized at the end of the job &  
    685    25000000 \\  
    686    \hline    
    687    buffer\_server\_factor\_size &  
    688    ratio between NEMO and XIOS buffer size. Should be 2. &  
    689    2 \\  
    690    \hline 
    691    info\_level &  
    692    verbosity level (0 to 100) &  
    693    0 \\  
    694    \hline 
    695    using\_server &  
    696    activate attached(false) or detached(true) mode &  
    697    true \\  
    698    \hline 
    699    using\_oasis &  
    700    xios is used with OASIS(true) or not (false) &  
    701    false \\  
    702    \hline 
    703    oasis\_codes\_id &  
    704    when using oasis, define the identifier of NEMO in the namcouple. Not that the identifier of XIOS is xios.x &  
    705    oceanx \\  
    706    \hline    
    707 \end{tabular} 
    708  
    709 \subsubsection{Number of cpu used by XIOS in detached mode} 
    710  
    711 The number of cores used by the xios is specified only when launching the model. The number or cores dedicated to XIOS should be from ~1/10 to ~1/50 of the number or cores dedicated to NEMO (according of the amount of data to be created). Here is an example of 2 cpus for the io\_server and 62 cpu for opa using mpirun: 
    712  
    713 \texttt{ mpirun -np 2 ./nemo.exe : -np 62 ./xios\_server.exe } 
    714  
    715 \subsection{Practical issues} 
    716  
    717 \subsubsection{Add your own outputs} 
    718  
    719 It is very easy to add you own outputs with iomput. 4 points must be followed. 
    720 \begin{description} 
    721 \item[1-] in NEMO code, add a \\ 
    722 \texttt{      CALL iom\_put( 'identifier', array ) } \\ 
    723 where you want to output a 2D or 3D array. 
    724  
    725 \item[2-] don't forget to add \\ 
    726 \texttt{   USE iom            ! I/O manager library }  \\ 
    727 in the list of used modules in the upper part of your module.  
    728  
    729 \item[3-] in the file\_definition part of the xml file, add the definition of your variable using the same identifier you used in the f90 code. 
    730 \vspace{-20pt} 
    731 \begin{alltt}  {{\scriptsize 
    732 \begin{verbatim} 
    733    <field_definition> 
    734       ... 
    735       <field id="identifier" long_name="blabla" ... />    
    736       ... 
    737    </field_definition>  
    738 \end{verbatim} 
    739 }}\end{alltt}  
    740 attributes axis\_ref and grid\_ref must be consistent with the size of the array to pass to iomput. 
    741 if your array is computed within the surface module each nn\_fsbc time\_step,  
    742 add the field definition within the group defined with the id ''SBC'': $<$group id=''SBC''...$>$ 
    743  
    744 \item[4-] add your field in one of the output files   \\ 
    745 \vspace{-20pt} 
    746 \begin{alltt}  {{\scriptsize 
    747 \begin{verbatim} 
    748    <file id="file1" .../>    
    749       ... 
    750       <field ref="identifier" />    
    751       ... 
    752    </file>    
    753 \end{verbatim} 
    754 }}\end{alltt}  
    755  
    756 \end{description} 
     849\end{longtable} 
     850 
    757851 
    758852 
    … …  
    809903domain size in any dimension. The algorithm used is: 
    810904 
     905\vspace{-20pt} 
    811906\begin{alltt}  {{\scriptsize  
    812907\begin{verbatim} 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/ARCH/arch-X64_CURIE.fcm

    r4148 r4153  
    2929#  - fcm variables are starting with a % (and not a $) 
    3030# 
    31 %NCDF_HOME           /usr/local/netcdf-4.2_hdf5 
    32 %HDF5_HOME           /usr/local/hdf5-1.8.8 
     31%NCDF_HOME           /usr/local/netcdf-4.2_hdf5_parallel 
     32%HDF5_HOME           /usr/local/hdf5-1.8.9_parallel 
    3333%XIOS_HOME           $WORKDIR/now/models/xios 
    3434%OASIS_HOME          $WORKDIR/now/models/oa3mct 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/AMM12/EXP00/iodef.xml

    r4148 r4153  
    128128      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    129129      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     130      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    130131   </axis_definition>  
    131132     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/GYRE/EXP00/iodef.xml

    r4148 r4153  
    9191      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    9292      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     93      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    9394   </axis_definition>  
    9495     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/GYRE_BFM/EXP00/iodef.xml

    r4148 r4153  
    6262      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    6363      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     64      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    6465   </axis_definition>  
    6566     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/iodef.xml

    r4148 r4153  
    128128      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    129129      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     130      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    130131   </axis_definition>  
    131132     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef_ar5.xml

    r4148 r4153  
    248248      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    249249      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     250      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    250251   </axis_definition>  
    251252     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef_default.xml

    • Property svn:mime-type deleted
    • Property svn:keywords set to Id
    r4148 r4153  
    129129      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    130130      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     131      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    131132   </axis_definition>  
    132133     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef_demo.xml

    • Property svn:mime-type deleted
    • Property svn:keywords set to Id
    r4148 r4153  
    4444   <!-- mooring: automatic definition of the file name suffix based on id="0n180wT"  --> 
    4545   <!-- include a group of variables. see field_def.xml for mooring variables definition  --> 
    46    <file id="0n180wT" > 
    47      <field_group group_ref="mooring"/>   
     46   <file id="0n180wT"> 
     47     <field_group group_ref="mooring" domain_ref="0n180wT" />   
    4848   </file> 
    4949    
    … …  
    5353     <field_group id="EqT" domain_ref="EqT" > 
    5454       <field field_ref="toce" name="votemper" axis_ref="deptht_myzoom"  /> 
     55       <field field_ref="sss" /> 
    5556     </field_group> 
    5657   </file> 
    … …  
    8586      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    8687      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     88      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    8789   </axis_definition>  
    8890     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef_oldstyle.xml

    • Property svn:mime-type deleted
    • Property svn:keywords set to Id
    r4148 r4153  
    116116      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    117117      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     118      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    118119   </axis_definition>  
    119120     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/ORCA2_LIM_CFC_C14b/EXP00/iodef.xml

    r4152 r4153  
    125125      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    126126      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     127      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    127128   </axis_definition>  
    128129     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/ORCA2_LIM_PISCES/EXP00/iodef.xml

    r4152 r4153  
    230230      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    231231      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     232      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    232233   </axis_definition>  
    233234     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/iodef.xml

    r4152 r4153  
    8888   </file> 
    8989 
    90    <file id="file4" name_suffix="_ptrc_T" description="additional pisces diagnostics" > 
     90   <file id="file4" name_suffix="_diad_T" description="additional pisces diagnostics" > 
    9191          <field field_ref="PH"       /> 
    9292          <field field_ref="CO3"      /> 
    … …  
    158158      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    159159      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     160      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    160161   </axis_definition>  
    161162     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/ORCA2_SAS_LIM/EXP00/iodef.xml

    r4147 r4153  
    2121    --> 
    2222     
    23     <file_definition type="multiple_file" sync_freq="1d" min_digits="4"> 
     23    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4"> 
    2424     
    2525      <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files --> 
    … …  
    114114      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    115115      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     116      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    116117   </axis_definition>  
    117118     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/SHARED/1_namelist_ref

    r4147 r4153  
    124124   rn_rdtmax   = 28800.          !  maximum time step on tracers (used if nn_acc=1) 
    125125   rn_rdth     =  800.           !  depth variation of tracer time step  (used if nn_acc=1) 
     126   ln_crs      = .false.      !  Logical switch for coarsening module 
    126127   jphgr_msh   =       0               !  type of horizontal mesh 
    127128                                       !  = 0 curvilinear coordinate on the sphere read in coordinate.nc 
    … …  
    147148   ppkth2      =       48.029893720000 ! 
    148149   ppacr2      =       13.000000000000 ! 
     150/ 
     151!----------------------------------------------------------------------- 
     152&namcrs        !   Grid coarsening for dynamics output and/or 
     153               !   passive tracer coarsened online simulations 
     154!----------------------------------------------------------------------- 
     155   nn_factx    = 3         !  Reduction factor of x-direction 
     156   nn_facty    = 3         !  Reduction factor of y-direction 
     157   nn_binref   = 0         !  Bin centering preference: NORTH or EQUAT 
     158                           !  0, coarse grid is binned with preferential treatment of the north fold 
     159                           !  1, coarse grid is binned with centering at the equator 
     160                           !    Symmetry with nn_facty being odd-numbered. Asymmetry with even-numbered nn_facty. 
     161   nn_msh_crs  = 1         !  create (=1) a mesh file or not (=0) 
     162   nn_crs_kz   = 0         ! 0, MEAN of volume boxes 
     163                           ! 1, MAX of boxes 
     164                           ! 2, MIN of boxes 
     165   ln_crs_wn   = .true.    ! wn coarsened (T) or computed using horizontal divergence ( F ) 
    149166/ 
    150167!----------------------------------------------------------------------- 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/CONFIG/SHARED/field_def.xml

    r4152 r4153  
    227227      </field_group> 
    228228 
     229      <!-- variables available with iceberg trajectories --> 
     230      <field_group id="icbvar" domain_ref="grid_T"  >  
     231        <field id="berg_melt"          long_name="icb melt rate of icebergs"                     unit="kg/m2/s"   /> 
     232        <field id="berg_buoy_melt"     long_name="icb buoyancy component of iceberg melt rate"   unit="kg/m2/s"   /> 
     233        <field id="berg_eros_melt"     long_name="icb erosion component of iceberg melt rate"    unit="kg/m2/s"   /> 
     234        <field id="berg_conv_melt"     long_name="icb convective component of iceberg melt rate" unit="kg/m2/s"   /> 
     235        <field id="berg_virtual_area"  long_name="icb virtual coverage by icebergs"              unit="m2"        /> 
     236        <field id="bits_src"           long_name="icb mass source of bergy bits"                 unit="kg/m2/s"   /> 
     237        <field id="bits_melt"          long_name="icb melt rate of bergy bits"                   unit="kg/m2/s"   /> 
     238        <field id="bits_mass"          long_name="icb bergy bit density field"                   unit="kg/m2"     /> 
     239        <field id="berg_mass"          long_name="icb iceberg density field"                     unit="kg/m2"     /> 
     240        <field id="calving"            long_name="icb calving mass input"                        unit="kg/s"      /> 
     241        <field id="berg_floating_melt" long_name="icb melt rate of icebergs + bits"              unit="kg/m2/s"   /> 
     242        <field id="berg_real_calving"  long_name="icb calving into iceberg class"                unit="kg/s"     axis_ref="icbcla" /> 
     243        <field id="berg_stored_ice"    long_name="icb accumulated ice mass by class"             unit="kg"       axis_ref="icbcla" /> 
     244      </field_group> 
     245 
    229246      <!-- ptrc on T grid --> 
    230247 
    … …  
    255272       <field id="NH4"      long_name="Ammonium Concentration"                   unit="mmol/m3" /> 
    256273 
     274       <!-- PISCES with Kriest parametisation : variables available with key_kriest --> 
     275       <field id="Num"      long_name="Number of organic particles"              unit="nbr" /> 
     276 
     277       <!-- PISCES light : variables available with key_pisces_reduced --> 
    257278       <field id="DET"      long_name="Detritus"                                 unit="mmol-N/m3" /> 
    258279       <field id="DOM"      long_name="Dissolved Organic Matter"                 unit="mmol-N/m3" /> 
    259280 
     281       <!-- CFC11 : variables available with key_cfc --> 
    260282       <field id="CFC11"    long_name="CFC-11 Concentration"                     unit="umol/L" /> 
     283       <!-- Bomb C14 : variables available with key_c14b --> 
    261284       <field id="C14B"     long_name="Bomb C14 Concentration"                   unit="ration" /> 
    262285     </field_group> 
    263286 
    264       <!-- diad on T grid : variables available with key_diatrc --> 
    265  
     287      <!-- PISCES additional diagnostics on T grid  --> 
    266288     <field_group id="diad_T" grid_ref="grid_T_2D"> 
    267289       <field id="PH"          long_name="PH"                                      unit="-"          grid_ref="grid_T_3D" /> 
    … …  
    317339       <field id="Heup"        long_name="Euphotic layer depth"                    unit="m"                            /> 
    318340       <field id="Irondep"     long_name="Iron deposition from dust"               unit="mol/m2/s"                     /> 
    319        <field id="Ironsed"     long_name="Iron deposition from sediment"           unit="mol/m2/s"  grid_ref="grid_T_3D"  /> 
    320  
    321        <field id="FNO3PHY"  long_name="FNO3PHY"                             unit="-"  grid_ref="grid_T_3D" />  
    322        <field id="FNH4PHY"  long_name="FNH4PHY"                             unit="-"  grid_ref="grid_T_3D" />  
    323        <field id="FNH4NO3"  long_name="FNH4NO3"                             unit="-"  grid_ref="grid_T_3D" />  
    324        <field id="TNO3PHY"  long_name="TNO3PHY"                             unit="-"  />  
    325        <field id="TNH4PHY"  long_name="TNH4PHY"                             unit="-"  />  
    326        <field id="TPHYDOM"  long_name="TPHYDOM"                             unit="-"  />  
    327        <field id="TPHYNH4"  long_name="TPHYNH4"                             unit="-"  />  
    328        <field id="TPHYZOO"  long_name="TPHYZOO"                             unit="-"  />  
    329        <field id="TPHYDET"  long_name="TPHYDET"                             unit="-"  />  
    330        <field id="TDETZOO"  long_name="TDETZOO"                             unit="-"  />  
    331        <field id="TZOODET"  long_name="TZOODET"                             unit="-"  />  
    332        <field id="TZOOBOD"  long_name="TZOOBOD"                             unit="-"  />  
    333        <field id="TZOONH4"  long_name="TZOONH4"                             unit="-"  />  
    334        <field id="TZOODOM"  long_name="TZOODOM"                             unit="-"  />  
    335        <field id="TNH4NO3"  long_name="TNH4NO3"                             unit="-"  />  
    336        <field id="TDOMNH4"  long_name="TDOMNH4"                             unit="-"  />  
    337        <field id="TDETNH4"  long_name="TDETNH4"                             unit="-"  />  
    338        <field id="TPHYTOT"  long_name="TPHYTOT"                             unit="-"  />  
    339        <field id="TZOOTOT"  long_name="TZOOTOT"                             unit="-"  />  
    340        <field id="SEDPOC"   long_name="SEDPOC"                              unit="-"  />  
    341        <field id="TDETSED"  long_name="TDETSED"                             unit="-"  />  
    342  
    343        <field id="qtrCFC11"     long_name="Air-sea flux of CFC-11"                   unit="mol/m2/s"   /> 
    344        <field id="qintCFC11"    long_name="Cumulative air-sea flux of CFC-11"        unit="mol/m2"     /> 
    345        <field id="qtrC14b"      long_name="Air-sea flux of Bomb C14"                 unit="mol/m2/s"   /> 
    346        <field id="qintC14b"     long_name="Cumulative air-sea flux of Bomb C14"      unit="mol/m2"     /> 
    347        <field id="fdecay"       long_name="Radiactive decay of Bomb C14"             unit="mol/m3"  grid_ref="grid_T_3D"  /> 
     341       <field id="Ironsed"     long_name="Iron deposition from sediment"           unit="mol/m2/s"  grid_ref="grid_T_3D "/> 
     342 
     343       <!-- PISCES with Kriest parametisation : variables available with key_kriest --> 
     344       <field id="POCFlx"      long_name="Particulate organic C flux"              unit="mol/m2/s"   grid_ref="grid_T_3D" /> 
     345       <field id="NumFlx"      long_name="Particle number flux"                    unit="nbr/m2/s"   grid_ref="grid_T_3D" /> 
     346       <field id="SiFlx"       long_name="Biogenic Si flux"                        unit="mol/m2/s"   grid_ref="grid_T_3D" /> 
     347       <field id="CaCO3Flx"    long_name="CaCO3 flux"                              unit="mol/m2/s"   grid_ref="grid_T_3D" /> 
     348       <field id="xnum"        long_name="Number of particles in aggregats"        unit="-"          grid_ref="grid_T_3D" /> 
     349       <field id="W1"          long_name="sinking speed of mass flux"              unit="m2/s"       grid_ref="grid_T_3D" /> 
     350       <field id="W2"          long_name="sinking speed of number flux"            unit="m2/s"       grid_ref="grid_T_3D" /> 
     351 
     352       <!-- PISCES light : variables available with key_pisces_reduced --> 
     353       <field id="FNO3PHY"     long_name="FNO3PHY"                                 unit="-"          grid_ref="grid_T_3D" />  
     354       <field id="FNH4PHY"     long_name="FNH4PHY"                                 unit="-"          grid_ref="grid_T_3D" />  
     355       <field id="FNH4NO3"     long_name="FNH4NO3"                                 unit="-"          grid_ref="grid_T_3D" />  
     356       <field id="TNO3PHY"     long_name="TNO3PHY"                                 unit="-"  />  
     357       <field id="TNH4PHY"     long_name="TNH4PHY"                                 unit="-"  />  
     358       <field id="TPHYDOM"     long_name="TPHYDOM"                                 unit="-"  />  
     359       <field id="TPHYNH4"     long_name="TPHYNH4"                                 unit="-"  />  
     360       <field id="TPHYZOO"     long_name="TPHYZOO"                                 unit="-"  />  
     361       <field id="TPHYDET"     long_name="TPHYDET"                                 unit="-"  />  
     362       <field id="TDETZOO"     long_name="TDETZOO"                                 unit="-"  />  
     363       <field id="TZOODET"     long_name="TZOODET"                                 unit="-"  />  
     364       <field id="TZOOBOD"     long_name="TZOOBOD"                                 unit="-"  />  
     365       <field id="TZOONH4"     long_name="TZOONH4"                                 unit="-"  />  
     366       <field id="TZOODOM"     long_name="TZOODOM"                                 unit="-"  />  
     367       <field id="TNH4NO3"     long_name="TNH4NO3"                                 unit="-"  />  
     368       <field id="TDOMNH4"     long_name="TDOMNH4"                                 unit="-"  />  
     369       <field id="TDETNH4"     long_name="TDETNH4"                                 unit="-"  />  
     370       <field id="TPHYTOT"     long_name="TPHYTOT"                                 unit="-"  />  
     371       <field id="TZOOTOT"     long_name="TZOOTOT"                                 unit="-"  />  
     372       <field id="SEDPOC"      long_name="SEDPOC"                                  unit="-"  />  
     373       <field id="TDETSED"     long_name="TDETSED"                                 unit="-"  />  
     374 
     375       <!-- CFC11 : variables available with key_cfc --> 
     376       <field id="qtrCFC11"    long_name="Air-sea flux of CFC-11"                   unit="mol/m2/s"   /> 
     377       <field id="qintCFC11"   long_name="Cumulative air-sea flux of CFC-11"        unit="mol/m2"     /> 
     378       <!-- Bomb C14 : variables available with key_c14b --> 
     379       <field id="qtrC14b"     long_name="Air-sea flux of Bomb C14"                 unit="mol/m2/s"   /> 
     380       <field id="qintC14b"    long_name="Cumulative air-sea flux of Bomb C14"      unit="mol/m2"     /> 
     381       <field id="fdecay"      long_name="Radiactive decay of Bomb C14"             unit="mol/m3"  grid_ref="grid_T_3D"  /> 
    348382     </field_group> 
    349383 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/NST_SRC/agrif_opa_sponge.F90

    r3698 r4153  
    185185      INTEGER  :: ji,jj,jk 
    186186      INTEGER  :: ispongearea, ilci, ilcj 
    187       REAL(wp) :: z1spongearea 
    188       REAL(wp), POINTER, DIMENSION(:,:) :: zlocalviscsponge 
     187      LOGICAL  :: ll_spdone 
     188      REAL(wp) :: z1spongearea, zramp 
     189      REAL(wp), POINTER, DIMENSION(:,:) :: ztabramp 
    189190 
    190191#if defined SPONGE || defined SPONGE_TOP 
    191  
    192       CALL wrk_alloc( jpi, jpj, zlocalviscsponge ) 
    193  
    194       ispongearea  = 2 + 2 * Agrif_irhox() 
    195       ilci = nlci - ispongearea 
    196       ilcj = nlcj - ispongearea  
    197       z1spongearea = 1._wp / REAL( ispongearea - 2 ) 
    198       spbtr2(:,:) = 1. / ( e1t(:,:) * e2t(:,:) ) 
     192      ll_spdone=.TRUE. 
     193      IF (( .NOT. spongedoneT ).OR.( .NOT. spongedoneU )) THEN 
     194         ! Define ramp from boundaries towards domain interior 
     195         ! at T-points 
     196         ! Store it in ztabramp 
     197         ll_spdone=.FALSE. 
     198 
     199         CALL wrk_alloc( jpi, jpj, ztabramp ) 
     200 
     201         ispongearea  = 2 + 2 * Agrif_irhox() 
     202         ilci = nlci - ispongearea 
     203         ilcj = nlcj - ispongearea  
     204         z1spongearea = 1._wp / REAL( ispongearea - 2 ) 
     205         spbtr2(:,:) = 1. / ( e1t(:,:) * e2t(:,:) ) 
     206 
     207         ztabramp(:,:) = 0. 
     208 
     209         IF( (nbondi == -1) .OR. (nbondi == 2) ) THEN 
     210            DO jj = 1, jpj 
     211               IF ( umask(2,jj,1) == 1._wp ) THEN 
     212                 DO ji = 2, ispongearea                   
     213                    ztabramp(ji,jj) = ( ispongearea-ji ) * z1spongearea 
     214                 END DO 
     215               ENDIF 
     216            ENDDO 
     217         ENDIF 
     218 
     219         IF( (nbondi == 1) .OR. (nbondi == 2) ) THEN 
     220            DO jj = 1, jpj 
     221               IF ( umask(nlci-2,jj,1) == 1._wp ) THEN 
     222                  DO ji = ilci+1,nlci-1 
     223                     zramp = (ji - (ilci+1) ) * z1spongearea 
     224                     ztabramp(ji,jj) = MAX( ztabramp(ji,jj), zramp ) 
     225                  ENDDO 
     226               ENDIF 
     227            ENDDO 
     228         ENDIF 
     229 
     230         IF( (nbondj == -1) .OR. (nbondj == 2) ) THEN 
     231            DO ji = 1, jpi 
     232               IF ( vmask(ji,2,1) == 1._wp ) THEN 
     233                  DO jj = 2, ispongearea 
     234                     zramp = ( ispongearea-jj ) * z1spongearea 
     235                     ztabramp(ji,jj) = MAX( ztabramp(ji,jj), zramp ) 
     236                  END DO 
     237               ENDIF 
     238            ENDDO 
     239         ENDIF 
     240 
     241         IF( (nbondj == 1) .OR. (nbondj == 2) ) THEN 
     242            DO ji = 1, jpi 
     243               IF ( vmask(ji,nlcj-2,1) == 1._wp ) THEN 
     244                  DO jj = ilcj+1,nlcj-1 
     245                     zramp = (jj - (ilcj+1) ) * z1spongearea 
     246                     ztabramp(ji,jj) = MAX( ztabramp(ji,jj), zramp ) 
     247                  END DO 
     248               ENDIF 
     249            ENDDO 
     250         ENDIF 
     251 
     252      ENDIF 
    199253 
    200254      ! Tracers 
    201255      IF( .NOT. spongedoneT ) THEN 
    202          zlocalviscsponge(:,:) = 0. 
    203256         spe1ur(:,:) = 0. 
    204257         spe2vr(:,:) = 0. 
    205258 
    206259         IF( (nbondi == -1) .OR. (nbondi == 2) ) THEN 
    207             DO ji = 2, ispongearea 
    208                zlocalviscsponge(ji,:) = visc_tra * ( ispongearea-ji ) * z1spongearea 
    209             ENDDO 
    210             spe1ur(2:ispongearea-1,:      ) = 0.5 * ( zlocalviscsponge(2:ispongearea-1,:      )   & 
    211                &                         +            zlocalviscsponge(3:ispongearea  ,:      ) ) & 
    212                &                         * e2u(2:ispongearea-1,:      ) / e1u(2:ispongearea-1,:      ) 
    213             spe2vr(2:ispongearea  ,1:jpjm1) = 0.5 * ( zlocalviscsponge(2:ispongearea  ,1:jpjm1)   & 
    214                &                         +            zlocalviscsponge(2:ispongearea,2  :jpj  ) ) & 
    215                &                         * e1v(2:ispongearea  ,1:jpjm1) / e2v(2:ispongearea  ,1:jpjm1) 
     260            spe1ur(2:ispongearea-1,:       ) = visc_tra                                        & 
     261               &                             *    0.5 * (  ztabramp(2:ispongearea-1,:      )   & 
     262               &                                         + ztabramp(3:ispongearea  ,:      ) ) & 
     263               &                             * e2u(2:ispongearea-1,:) / e1u(2:ispongearea-1,:) 
     264 
     265            spe2vr(2:ispongearea  ,1:jpjm1 ) = visc_tra                                        & 
     266               &                             *    0.5 * (  ztabramp(2:ispongearea  ,1:jpjm1)   & 
     267               &                                         + ztabramp(2:ispongearea,2  :jpj  ) ) & 
     268               &                             * e1v(2:ispongearea,1:jpjm1) / e2v(2:ispongearea,1:jpjm1) 
    216269         ENDIF 
    217270 
    218271         IF( (nbondi == 1) .OR. (nbondi == 2) ) THEN 
    219             DO ji = ilci+1,nlci-1 
    220                zlocalviscsponge(ji,:) = visc_tra * (ji - (ilci+1) ) * z1spongearea 
    221             ENDDO 
    222    
    223             spe1ur(ilci+1:nlci-2,:      ) = 0.5 * (  zlocalviscsponge(ilci+1:nlci-2,:)    &  
    224                &                          +          zlocalviscsponge(ilci+2:nlci-1,:) )  & 
    225                &                          * e2u(ilci+1:nlci-2,:) / e1u(ilci+1:nlci-2,:) 
    226  
    227             spe2vr(ilci+1:nlci-1,1:jpjm1) = 0.5 * (  zlocalviscsponge(ilci+1:nlci-1,1:jpjm1)    &  
    228                &                            +        zlocalviscsponge(ilci+1:nlci-1,2:jpj  )  ) &  
    229                &                                   * e1v(ilci+1:nlci-1,1:jpjm1) / e2v(ilci+1:nlci-1,1:jpjm1) 
     272            spe1ur(ilci+1:nlci-2,:        ) = visc_tra                                   & 
     273               &                            * 0.5 * (  ztabramp(ilci+1:nlci-2,:      )   &  
     274               &                                     + ztabramp(ilci+2:nlci-1,:      ) ) & 
     275               &                            * e2u(ilci+1:nlci-2,:) / e1u(ilci+1:nlci-2,:) 
     276 
     277            spe2vr(ilci+1:nlci-1,1:jpjm1  )  = visc_tra                                  & 
     278               &                            * 0.5 * (  ztabramp(ilci+1:nlci-1,1:jpjm1)   &  
     279               &                                     + ztabramp(ilci+1:nlci-1,2:jpj  ) ) &  
     280               &                            * e1v(ilci+1:nlci-1,1:jpjm1) / e2v(ilci+1:nlci-1,1:jpjm1) 
    230281         ENDIF 
    231282 
    232283         IF( (nbondj == -1) .OR. (nbondj == 2) ) THEN 
    233             DO jj = 2, ispongearea 
    234                zlocalviscsponge(:,jj) = visc_tra * ( ispongearea-jj ) * z1spongearea 
    235             ENDDO 
    236             spe1ur(1:jpim1,2:ispongearea  ) = 0.5 * ( zlocalviscsponge(1:jpim1,2:ispongearea  ) &  
    237                &                            +         zlocalviscsponge(2:jpi  ,2:ispongearea) ) & 
     284            spe1ur(1:jpim1,2:ispongearea  ) = visc_tra                                     & 
     285               &                            * 0.5 * (  ztabramp(1:jpim1,2:ispongearea  )   &  
     286               &                                     + ztabramp(2:jpi  ,2:ispongearea  ) ) & 
    238287               &                            * e2u(1:jpim1,2:ispongearea) / e1u(1:jpim1,2:ispongearea) 
    239288    
    240             spe2vr(:      ,2:ispongearea-1) = 0.5 * ( zlocalviscsponge(:,2:ispongearea-1)       & 
    241                &                            +         zlocalviscsponge(:,3:ispongearea  )     ) & 
     289            spe2vr(:      ,2:ispongearea-1) = visc_tra                                     & 
     290               &                            * 0.5 * (  ztabramp(:      ,2:ispongearea-1)   & 
     291               &                                     + ztabramp(:      ,3:ispongearea  ) ) & 
    242292               &                            * e1v(:,2:ispongearea-1) / e2v(:,2:ispongearea-1) 
    243293         ENDIF 
    244294 
    245295         IF( (nbondj == 1) .OR. (nbondj == 2) ) THEN 
    246             DO jj = ilcj+1,nlcj-1 
    247                zlocalviscsponge(:,jj) = visc_tra * (jj - (ilcj+1) ) * z1spongearea 
    248             ENDDO 
    249             spe1ur(1:jpim1,ilcj+1:nlcj-1) = 0.5 * ( zlocalviscsponge(1:jpim1,ilcj+1:nlcj-1)   & 
    250                &                          +         zlocalviscsponge(2:jpi  ,ilcj+1:nlcj-1) ) & 
     296            spe1ur(1:jpim1,ilcj+1:nlcj-1) = visc_tra                                   & 
     297               &                          * 0.5 * (  ztabramp(1:jpim1,ilcj+1:nlcj-1)   & 
     298               &                                   + ztabramp(2:jpi  ,ilcj+1:nlcj-1) ) & 
    251299               &                                * e2u(1:jpim1,ilcj+1:nlcj-1) / e1u(1:jpim1,ilcj+1:nlcj-1) 
    252             spe2vr(:      ,ilcj+1:nlcj-2) = 0.5 * ( zlocalviscsponge(:,ilcj+1:nlcj-2      )   & 
    253                &                          +         zlocalviscsponge(:,ilcj+2:nlcj-1)     )   & 
     300 
     301            spe2vr(:      ,ilcj+1:nlcj-2) = visc_tra                                   & 
     302               &                          * 0.5 * (  ztabramp(:      ,ilcj+1:nlcj-2)   & 
     303               &                                   + ztabramp(:      ,ilcj+2:nlcj-1) ) & 
    254304               &                                * e1v(:,ilcj+1:nlcj-2) / e2v(:,ilcj+1:nlcj-2) 
    255305         ENDIF 
    … …  
    259309      ! Dynamics 
    260310      IF( .NOT. spongedoneU ) THEN 
    261          zlocalviscsponge(:,:) = 0. 
    262311         spe1ur2(:,:) = 0. 
    263312         spe2vr2(:,:) = 0. 
    264313 
    265314         IF( (nbondi == -1) .OR. (nbondi == 2) ) THEN 
    266             DO ji = 2, ispongearea 
    267                zlocalviscsponge(ji,:) = visc_dyn * ( ispongearea-ji ) * z1spongearea 
    268             ENDDO 
    269             spe1ur2(2:ispongearea-1,:      ) = 0.5 * ( zlocalviscsponge(2:ispongearea-1,:      ) & 
    270                                              &     +   zlocalviscsponge(3:ispongearea,:    ) ) 
    271             spe2vr2(2:ispongearea  ,1:jpjm1) = 0.5 * ( zlocalviscsponge(2:ispongearea  ,1:jpjm1) & 
    272                                              &     +   zlocalviscsponge(2:ispongearea,2:jpj) )  
     315            spe1ur2(2:ispongearea-1,:      ) = visc_dyn                                   & 
     316               &                             * 0.5 * (  ztabramp(2:ispongearea-1,:      ) & 
     317               &                                      + ztabramp(3:ispongearea  ,:      ) ) 
     318            spe2vr2(2:ispongearea  ,1:jpjm1) = visc_dyn                                   & 
     319               &                             * 0.5 * (  ztabramp(2:ispongearea  ,1:jpjm1) & 
     320               &                                      + ztabramp(2:ispongearea  ,2:jpj  ) )  
    273321         ENDIF 
    274322 
    275323         IF( (nbondi == 1) .OR. (nbondi == 2) ) THEN 
    276             DO ji = ilci+1,nlci-1 
    277                zlocalviscsponge(ji,:) = visc_dyn * (ji - (ilci+1) ) * z1spongearea 
    278             ENDDO 
    279             spe1ur2(ilci+1:nlci-2,:      ) = 0.5 * (  zlocalviscsponge(ilci+1:nlci-2,:) & 
    280                                            &        + zlocalviscsponge(ilci+2:nlci-1,:) )   
    281             spe2vr2(ilci+1:nlci-1,1:jpjm1) = 0.5 * (  zlocalviscsponge(ilci+1:nlci-1,1:jpjm1) & 
    282                                            &        + zlocalviscsponge(ilci+1:nlci-1,2:jpj  )  )  
     324            spe1ur2(ilci+1:nlci-2  ,:      ) = visc_dyn                                   & 
     325               &                             * 0.5 * (  ztabramp(ilci+1:nlci-2, :       ) & 
     326               &                                      + ztabramp(ilci+2:nlci-1, :       ) )                       
     327            spe2vr2(ilci+1:nlci-1  ,1:jpjm1) = visc_dyn                                   & 
     328               &                             * 0.5 * (  ztabramp(ilci+1:nlci-1,1:jpjm1  ) & 
     329               &                                      + ztabramp(ilci+1:nlci-1,2:jpj    ) )  
    283330         ENDIF 
    284331 
    285332         IF( (nbondj == -1) .OR. (nbondj == 2) ) THEN 
    286             DO jj = 2, ispongearea 
    287                zlocalviscsponge(:,jj) = visc_dyn * ( ispongearea-jj ) * z1spongearea 
    288             ENDDO 
    289             spe1ur2(1:jpim1,2:ispongearea  ) = 0.5 * ( zlocalviscsponge(1:jpim1,2:ispongearea) & 
    290                                              &      + zlocalviscsponge(2:jpi,2:ispongearea) )  
    291             spe2vr2(:      ,2:ispongearea-1) = 0.5 * ( zlocalviscsponge(:,2:ispongearea-1)     & 
    292                                              &      + zlocalviscsponge(:,3:ispongearea)     ) 
     333            spe1ur2(1:jpim1,2:ispongearea  ) = visc_dyn                                   &   
     334               &                             * 0.5 * (  ztabramp(1:jpim1,2:ispongearea  ) & 
     335               &                                      + ztabramp(2:jpi  ,2:ispongearea  ) )  
     336            spe2vr2(:      ,2:ispongearea-1) = visc_dyn                                   & 
     337               &                             * 0.5 * (  ztabramp(:      ,2:ispongearea-1) & 
     338               &                                      + ztabramp(:      ,3:ispongearea  ) ) 
    293339         ENDIF 
    294340 
    295341         IF( (nbondj == 1) .OR. (nbondj == 2) ) THEN 
    296             DO jj = ilcj+1,nlcj-1 
    297                zlocalviscsponge(:,jj) = visc_dyn * (jj - (ilcj+1) ) * z1spongearea 
    298             ENDDO 
    299             spe1ur2(1:jpim1,ilcj+1:nlcj-1) = 0.5 * ( zlocalviscsponge(1:jpim1,ilcj+1:nlcj-1) & 
    300                                            &         + zlocalviscsponge(2:jpi,ilcj+1:nlcj-1) )  
    301             spe2vr2(:      ,ilcj+1:nlcj-2) = 0.5 * ( zlocalviscsponge(:,ilcj+1:nlcj-2      ) & 
    302                                            &         + zlocalviscsponge(:,ilcj+2:nlcj-1)     ) 
     342            spe1ur2(1:jpim1,ilcj+1:nlcj-1  ) = visc_dyn                                   & 
     343               &                             * 0.5 * (  ztabramp(1:jpim1,ilcj+1:nlcj-1  ) & 
     344               &                                      + ztabramp(2:jpi  ,ilcj+1:nlcj-1  ) )  
     345            spe2vr2(:      ,ilcj+1:nlcj-2  ) = visc_dyn                                   & 
     346               &                             * 0.5 * (  ztabramp(:      ,ilcj+1:nlcj-2  ) & 
     347               &                                      + ztabramp(:      ,ilcj+2:nlcj-1  ) ) 
    303348         ENDIF 
    304349         spongedoneU = .TRUE. 
    … …  
    306351      ENDIF 
    307352      ! 
    308       CALL wrk_dealloc( jpi, jpj, zlocalviscsponge ) 
     353      IF (.NOT.ll_spdone) CALL wrk_dealloc( jpi, jpj, ztabramp ) 
    309354      ! 
    310355#endif 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/BDY/bdydyn.F90

    r3294 r4153  
    3030   USE lbclnk          ! ocean lateral boundary conditions (or mpp link) 
    3131   USE in_out_manager  ! 
     32   USE domvvl          ! variable volume 
    3233 
    3334   IMPLICIT NONE 
    … …  
    8485      pu2d(:,:) = 0.e0 
    8586      pv2d(:,:) = 0.e0 
    86       DO jk = 1, jpkm1   !! Vertically integrated momentum trends 
    87           pu2d(:,:) = pu2d(:,:) + fse3u(:,:,jk) * umask(:,:,jk) * ua(:,:,jk) 
    88           pv2d(:,:) = pv2d(:,:) + fse3v(:,:,jk) * vmask(:,:,jk) * va(:,:,jk) 
    89       END DO 
    90       pu2d(:,:) = pu2d(:,:) * phur(:,:) 
    91       pv2d(:,:) = pv2d(:,:) * phvr(:,:) 
     87      IF (lk_vvl) THEN 
     88         DO jk = 1, jpkm1   !! Vertically integrated momentum trends 
     89            pu2d(:,:) = pu2d(:,:) + fse3u_a(:,:,jk) * umask(:,:,jk) * ua(:,:,jk) 
     90            pv2d(:,:) = pv2d(:,:) + fse3v_a(:,:,jk) * vmask(:,:,jk) * va(:,:,jk) 
     91         END DO 
     92         pu2d(:,:) = pu2d(:,:) / ( hu_0(:,:) + sshu_a(:,:) + 1._wp - umask(:,:,1) ) 
     93         pv2d(:,:) = pv2d(:,:) / ( hv_0(:,:) + sshv_a(:,:) + 1._wp - vmask(:,:,1) ) 
     94      ELSE 
     95         DO jk = 1, jpkm1   !! Vertically integrated momentum trends 
     96            pu2d(:,:) = pu2d(:,:) + fse3u(:,:,jk) * umask(:,:,jk) * ua(:,:,jk) 
     97            pv2d(:,:) = pv2d(:,:) + fse3v(:,:,jk) * vmask(:,:,jk) * va(:,:,jk) 
     98         END DO 
     99         pu2d(:,:) = pu2d(:,:) * phur(:,:) 
     100         pv2d(:,:) = pv2d(:,:) * phvr(:,:) 
     101      ENDIF 
    92102      DO jk = 1 , jpkm1 
    93          ua(:,:,jk) = ua(:,:,jk) - pu2d(:,:) 
    94          va(:,:,jk) = va(:,:,jk) - pv2d(:,:) 
     103         ua(:,:,jk) = ua(:,:,jk) - pu2d(:,:) * umask(:,:,jk) 
     104         va(:,:,jk) = va(:,:,jk) - pv2d(:,:) * vmask(:,:,jk) 
    95105      END DO 
    96106 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/C1D/step_c1d.F90

    r3680 r4153  
    5959 
    6060                             indic = 0                ! reset to no error condition 
     61      IF( kstp == nit000 )   CALL iom_init            ! iom_put initialization (must be done after nemo_init for AGRIF+XIOS+OASIS) 
    6162      IF( kstp /= nit000 )   CALL day( kstp )         ! Calendar (day was already called at nit000 in day_init) 
    62                              CALL iom_setkt( kstp )   ! say to iom that we are at time step kstp 
     63                             CALL iom_setkt( kstp - nit000 + 1 )   ! say to iom that we are at time step kstp 
    6364 
    6465      !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    … …  
    106107      !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< 
    107108                         CALL dia_wri( kstp )       ! ocean model: outputs 
     109      IF( lk_diahth  )   CALL dia_hth( kstp )       ! Thermocline depth (20°C) 
     110 
    108111 
    109112#if defined key_top 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/DIA/diadct.F90

    r4147 r4153  
    4242#endif 
    4343#if defined key_lim3 
    44   USE ice_3 
     44  USE par_ice 
     45  USE ice 
    4546#endif 
    4647  USE domvvl 
    … …  
    490491                 ijglo = secs(jsec)%listPoint(jpt)%J + jpjzoom - 1 + njmpp - 1 
    491492                 WRITE(numout,*)'         # I J : ',iiglo,ijglo 
     493                 CALL FLUSH(numout) 
    492494              ENDDO 
    493495           ENDIF 
    … …  
    612614     
    613615     !! * Local variables 
    614      INTEGER             :: jk, jseg, jclass,                    &!loop on level/segment/classes   
     616     INTEGER             :: jk, jseg, jclass,jl,                 &!loop on level/segment/classes/ice categories 
    615617                            isgnu, isgnv                          !  
    616618     REAL(wp)            :: zumid, zvmid,                        &!U/V velocity on a cell segment  
    … …  
    777779    
    778780              zTnorm=zumid_ice*e2u(k%I,k%J)+zvmid_ice*e1v(k%I,k%J) 
    779     
     781 
     782#if defined key_lim2    
    780783              transports_2d(1,jsec,jseg) = transports_2d(1,jsec,jseg) + (zTnorm)*   &  
    781784                                   (1.0 - frld(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J))  &  
    … …  
    784787              transports_2d(2,jsec,jseg) = transports_2d(2,jsec,jseg) + (zTnorm)*   &  
    785788                                    (1.0 -  frld(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J)) 
     789#endif 
     790#if defined key_lim3 
     791              DO jl=1,jpl 
     792                 transports_2d(1,jsec,jseg) = transports_2d(1,jsec,jseg) + (zTnorm)*     & 
     793                                   a_i(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J,jl) * & 
     794                                  ( ht_i(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J,jl) +  & 
     795                                    ht_s(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J,jl) ) 
     796                                    
     797                 transports_2d(2,jsec,jseg) = transports_2d(2,jsec,jseg) + (zTnorm)*   & 
     798                                   a_i(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J,jl) 
     799              ENDDO 
     800#endif 
    786801    
    787802           ENDIF !end of ice case 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/DOM/domvvl.F90

    r3294 r4153  
    192192      INTEGER  ::   iku, ikv     ! local integers     
    193193      INTEGER  ::   ii0, ii1, ij0, ij1   ! temporary integers 
    194       REAL(wp) ::   zvt          ! local scalars 
     194      REAL(wp) ::   zvt, zvtip1, zvtjp1  ! local scalars 
    195195      !!---------------------------------------------------------------------- 
    196196      ! 
    … …  
    202202         WRITE(numout,*) '~~~~~~~~~ ' 
    203203         pe3u_b(:,:,jpk) = fse3u_0(:,:,jpk) 
    204          pe3v_b(:,:,jpk) = fse3u_0(:,:,jpk) 
     204         pe3v_b(:,:,jpk) = fse3v_0(:,:,jpk) 
    205205      ENDIF 
    206206       
    … …  
    208208         DO jj = 2, jpjm1 
    209209            DO ji = fs_2, fs_jpim1 
    210                zvt = fse3t_b(ji,jj,jk) * e1e2t(ji,jj) 
    211                pe3u_b(ji,jj,jk) = 0.5_wp * ( zvt + fse3t_b(ji+1,jj,jk) * e1e2t(ji+1,jj) ) / ( e1u(ji,jj) * e2u(ji,jj) ) 
    212                pe3v_b(ji,jj,jk) = 0.5_wp * ( zvt + fse3t_b(ji,jj+1,jk) * e1e2t(ji,jj+1) ) / ( e1v(ji,jj) * e2v(ji,jj) ) 
     210               zvt    = ( fse3t_b(ji  ,jj  ,jk) - fse3t_0(ji  ,jj  ,jk) ) * e1e2t(ji  ,jj  ) 
     211               zvtip1 = ( fse3t_b(ji+1,jj  ,jk) - fse3t_0(ji+1,jj  ,jk) ) * e1e2t(ji+1,jj  ) 
     212               zvtjp1 = ( fse3t_b(ji  ,jj+1,jk) - fse3t_0(ji  ,jj+1,jk) ) * e1e2t(ji  ,jj+1) 
     213               pe3u_b(ji,jj,jk) = fse3u_0(ji,jj,jk) + 0.5_wp * ( zvt + zvtip1 ) / ( e1u(ji,jj) * e2u(ji,jj) ) 
     214               pe3v_b(ji,jj,jk) = fse3v_0(ji,jj,jk) + 0.5_wp * ( zvt + zvtjp1 ) / ( e1v(ji,jj) * e2v(ji,jj) ) 
    213215            END DO 
    214216         END DO 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/DOM/domzgr.F90

    r4148 r4153  
    11061106      INTEGER  ::   ios                      ! Local integer output status for namelist read 
    11071107      REAL(wp) ::   zrmax, ztaper   ! temporary scalars 
    1108       REAL(wp) ::   zrfact   ! temporary scalars 
    1109       REAL(wp), POINTER, DIMENSION(:,:  ) :: ztmpi1, ztmpi2, ztmpj1, ztmpj2 
    1110  
    1111       ! 
    1112       REAL(wp), POINTER, DIMENSION(:,:  ) :: zenv, zri, zrj, zhbat 
     1108      ! 
     1109      REAL(wp), POINTER, DIMENSION(:,:  ) :: zenv, ztmp, zmsk, zri, zrj, zhbat 
    11131110 
    11141111      NAMELIST/namzgr_sco/ln_s_sh94, ln_s_sf12, ln_sigcrit, rn_sbot_min, rn_sbot_max, rn_hc, rn_rmax,rn_theta, & 
    … …  
    11181115      IF( nn_timing == 1 )  CALL timing_start('zgr_sco') 
    11191116      ! 
    1120       CALL wrk_alloc( jpi, jpj,      ztmpi1, ztmpi2, ztmpj1, ztmpj2         ) 
    1121       CALL wrk_alloc( jpi, jpj,      zenv, zri, zrj, zhbat     ) 
    1122      ! 
     1117      CALL wrk_alloc( jpi, jpj,      zenv, ztmp, zmsk, zri, zrj, zhbat                           ) 
     1118      ! 
    11231119      REWIND( numnam_ref )              ! Namelist namzgr_sco in reference namelist : Sigma-stretching parameters 
    11241120      READ  ( numnam_ref, namzgr_sco, IOSTAT = ios, ERR = 901) 
    … …  
    11731169      !                                        ! ============================= 
    11741170      ! use r-value to create hybrid coordinates 
    1175 !     DO jj = 1, jpj 
    1176 !        DO ji = 1, jpi 
    1177 !           zenv(ji,jj) = MAX( bathy(ji,jj), 0._wp ) 
    1178 !        END DO 
    1179 !     END DO 
    1180 !     CALL lbc_lnk( zenv, 'T', 1._wp ) 
    1181       zenv(:,:) = bathy(:,:) 
     1171      DO jj = 1, jpj 
     1172         DO ji = 1, jpi 
     1173            zenv(ji,jj) = MAX( bathy(ji,jj), rn_sbot_min ) 
     1174         END DO 
     1175      END DO 
    11821176      !  
    11831177      ! Smooth the bathymetry (if required) 
    … …  
    11871181      jl = 0 
    11881182      zrmax = 1._wp 
    1189       !      
    1190       ! set scaling factor used in reducing vertical gradients 
    1191       zrfact = ( 1._wp - rn_rmax ) / ( 1._wp + rn_rmax )  
    1192       ! 
    1193       ! initialise temporary evelope depth arrays 
    1194       ztmpi1(:,:) = zenv(:,:) 
    1195       ztmpi2(:,:) = zenv(:,:) 
    1196       ztmpj1(:,:) = zenv(:,:) 
    1197       ztmpj2(:,:) = zenv(:,:) 
    1198       ! 
    1199       ! initialise temporary r-value arrays 
    1200       zri(:,:) = 1._wp 
    1201       zrj(:,:) = 1._wp 
    1202       !                                                            ! ================ ! 
    1203       DO WHILE( jl <= 10000 .AND. ( zrmax - rn_rmax ) > 1.e-8_wp ) !  Iterative loop  ! 
    1204          !                                                         ! ================ ! 
     1183      !                                                     ! ================ ! 
     1184      DO WHILE( jl <= 10000 .AND. zrmax > rn_rmax )         !  Iterative loop  ! 
     1185         !                                                  ! ================ ! 
    12051186         jl = jl + 1 
    12061187         zrmax = 0._wp 
    1207          ! we set zrmax from previous r-values (zri abd zrj) first 
    1208          ! if set after current r-value calculation (as previously) 
    1209          ! we could exit DO WHILE prematurely before checking r-value 
    1210          ! of current zenv 
    1211          DO jj = 1, nlcj 
    1212             DO ji = 1, nlci 
    1213                zrmax = MAX( zrmax, ABS(zri(ji,jj)), ABS(zrj(ji,jj)) ) 
    1214             END DO 
    1215          END DO 
    1216          zri(:,:) = 0._wp 
    1217          zrj(:,:) = 0._wp 
     1188         zmsk(:,:) = 0._wp 
    12181189         DO jj = 1, nlcj 
    12191190            DO ji = 1, nlci 
    12201191               iip1 = MIN( ji+1, nlci )      ! force zri = 0 on last line (ji=ncli+1 to jpi) 
    12211192               ijp1 = MIN( jj+1, nlcj )      ! force zrj = 0 on last raw  (jj=nclj+1 to jpj) 
    1222                IF( (zenv(ji,jj) > 0._wp) .AND. (zenv(iip1,jj) > 0._wp)) THEN 
    1223                   zri(ji,jj) = ( zenv(iip1,jj  ) - zenv(ji,jj) ) / ( zenv(iip1,jj  ) + zenv(ji,jj) ) 
    1224                END IF 
    1225                IF( (zenv(ji,jj) > 0._wp) .AND. (zenv(ji,ijp1) > 0._wp)) THEN 
    1226                   zrj(ji,jj) = ( zenv(ji  ,ijp1) - zenv(ji,jj) ) / ( zenv(ji  ,ijp1) + zenv(ji,jj) ) 
    1227                END IF 
    1228                IF( zri(ji,jj) >  rn_rmax )   ztmpi1(ji  ,jj  ) = zenv(iip1,jj  ) * zrfact 
    1229                IF( zri(ji,jj) < -rn_rmax )   ztmpi2(iip1,jj  ) = zenv(ji  ,jj  ) * zrfact  
    1230                IF( zrj(ji,jj) >  rn_rmax )   ztmpj1(ji  ,jj  ) = zenv(ji  ,ijp1) * zrfact 
    1231                IF( zrj(ji,jj) < -rn_rmax )   ztmpj2(ji  ,ijp1) = zenv(ji  ,jj  ) * zrfact 
     1193               zri(ji,jj) = ABS( zenv(iip1,jj  ) - zenv(ji,jj) ) / ( zenv(iip1,jj  ) + zenv(ji,jj) ) 
     1194               zrj(ji,jj) = ABS( zenv(ji  ,ijp1) - zenv(ji,jj) ) / ( zenv(ji  ,ijp1) + zenv(ji,jj) ) 
     1195               zrmax = MAX( zrmax, zri(ji,jj), zrj(ji,jj) ) 
     1196               IF( zri(ji,jj) > rn_rmax )   zmsk(ji  ,jj  ) = 1._wp 
     1197               IF( zri(ji,jj) > rn_rmax )   zmsk(iip1,jj  ) = 1._wp 
     1198               IF( zrj(ji,jj) > rn_rmax )   zmsk(ji  ,jj  ) = 1._wp 
     1199               IF( zrj(ji,jj) > rn_rmax )   zmsk(ji  ,ijp1) = 1._wp 
    12321200            END DO 
    12331201         END DO 
    12341202         IF( lk_mpp )   CALL mpp_max( zrmax )   ! max over the global domain 
     1203         ! lateral boundary condition on zmsk: keep 1 along closed boundary (use of MAX) 
     1204         ztmp(:,:) = zmsk(:,:)   ;   CALL lbc_lnk( zmsk, 'T', 1._wp ) 
     1205         DO jj = 1, nlcj 
     1206            DO ji = 1, nlci 
     1207                zmsk(ji,jj) = MAX( zmsk(ji,jj), ztmp(ji,jj) ) 
     1208            END DO 
     1209         END DO 
    12351210         ! 
    1236          IF(lwp)WRITE(numout,*) 'zgr_sco :   iter= ',jl, ' rmax= ', zrmax 
     1211         IF(lwp)WRITE(numout,*) 'zgr_sco :   iter= ',jl, ' rmax= ', zrmax, ' nb of pt= ', INT( SUM(zmsk(:,:) ) ) 
    12371212         ! 
    12381213         DO jj = 1, nlcj 
    12391214            DO ji = 1, nlci 
    1240                zenv(ji,jj) = MAX(zenv(ji,jj), ztmpi1(ji,jj), ztmpi2(ji,jj), ztmpj1(ji,jj), ztmpj2(ji,jj) ) 
     1215               iip1 = MIN( ji+1, nlci )     ! last  line (ji=nlci) 
     1216               ijp1 = MIN( jj+1, nlcj )     ! last  raw  (jj=nlcj) 
     1217               iim1 = MAX( ji-1,  1  )      ! first line (ji=nlci) 
     1218               ijm1 = MAX( jj-1,  1  )      ! first raw  (jj=nlcj) 
     1219               IF( zmsk(ji,jj) == 1._wp ) THEN 
     1220                  ztmp(ji,jj) =   (                                                                                   & 
     1221             &      zenv(iim1,ijp1)*zmsk(iim1,ijp1) + zenv(ji,ijp1)*zmsk(ji,ijp1) + zenv(iip1,ijp1)*zmsk(iip1,ijp1)   & 
     1222             &    + zenv(iim1,jj  )*zmsk(iim1,jj  ) + zenv(ji,jj  )*    2._wp     + zenv(iip1,jj  )*zmsk(iip1,jj  )   & 
     1223             &    + zenv(iim1,ijm1)*zmsk(iim1,ijm1) + zenv(ji,ijm1)*zmsk(ji,ijm1) + zenv(iip1,ijm1)*zmsk(iip1,ijm1)   & 
     1224             &                    ) / (                                                                               & 
     1225             &                      zmsk(iim1,ijp1) +               zmsk(ji,ijp1) +                 zmsk(iip1,ijp1)   & 
     1226             &    +                 zmsk(iim1,jj  ) +                   2._wp     +                 zmsk(iip1,jj  )   & 
     1227             &    +                 zmsk(iim1,ijm1) +               zmsk(ji,ijm1) +                 zmsk(iip1,ijm1)   & 
     1228             &                        ) 
     1229               ENDIF 
    12411230            END DO 
    12421231         END DO 
    12431232         ! 
    1244          CALL lbc_lnk( zenv, 'T', 1._wp ) 
     1233         DO jj = 1, nlcj 
     1234            DO ji = 1, nlci 
     1235               IF( zmsk(ji,jj) == 1._wp )   zenv(ji,jj) = MAX( ztmp(ji,jj), bathy(ji,jj) ) 
     1236            END DO 
     1237         END DO 
     1238         ! 
     1239         ! Apply lateral boundary condition   CAUTION: keep the value when the lbc field is zero 
     1240         ztmp(:,:) = zenv(:,:)   ;   CALL lbc_lnk( zenv, 'T', 1._wp ) 
     1241         DO jj = 1, nlcj 
     1242            DO ji = 1, nlci 
     1243               IF( zenv(ji,jj) == 0._wp )   zenv(ji,jj) = ztmp(ji,jj) 
     1244            END DO 
     1245         END DO 
    12451246         !                                                  ! ================ ! 
    12461247      END DO                                                !     End loop     ! 
    12471248      !                                                     ! ================ ! 
    12481249      ! 
    1249 !     DO jj = 1, jpj 
    1250 !        DO ji = 1, jpi 
    1251 !           zenv(ji,jj) = MAX( zenv(ji,jj), rn_sbot_min ) ! set all points to avoid undefined scale values 
    1252 !        END DO 
    1253 !     END DO 
     1250      ! Fill ghost rows with appropriate values to avoid undefined e3 values with some mpp decompositions 
     1251      DO ji = nlci+1, jpi  
     1252         zenv(ji,1:nlcj) = zenv(nlci,1:nlcj) 
     1253      END DO 
     1254      ! 
     1255      DO jj = nlcj+1, jpj 
     1256         zenv(:,jj) = zenv(:,nlcj) 
     1257      END DO 
    12541258      ! 
    12551259      ! Envelope bathymetry saved in hbatt 
    12561260      hbatt(:,:) = zenv(:,:)  
    1257  
    12581261      IF( MINVAL( gphit(:,:) ) * MAXVAL( gphit(:,:) ) <= 0._wp ) THEN 
    12591262         CALL ctl_warn( ' s-coordinates are tapered in vicinity of the Equator' ) 
    12601263         DO jj = 1, jpj 
    12611264            DO ji = 1, jpi 
    1262                ztaper = EXP( -(gphit(ji,jj)/8._wp)**2 ) 
     1265               ztaper = EXP( -(gphit(ji,jj)/8._wp)**2._wp ) 
    12631266               hbatt(ji,jj) = rn_sbot_max * ztaper + hbatt(ji,jj) * ( 1._wp - ztaper ) 
    12641267            END DO 
    … …  
    13751378      fsde3w(:,:,:) = gdep3w(:,:,:) 
    13761379      ! 
    1377       where (e3t   (:,:,:).eq.0.0)  e3t(:,:,:) = 1.0 
    1378       where (e3u   (:,:,:).eq.0.0)  e3u(:,:,:) = 1.0 
    1379       where (e3v   (:,:,:).eq.0.0)  e3v(:,:,:) = 1.0 
    1380       where (e3f   (:,:,:).eq.0.0)  e3f(:,:,:) = 1.0 
    1381       where (e3w   (:,:,:).eq.0.0)  e3w(:,:,:) = 1.0 
    1382       where (e3uw  (:,:,:).eq.0.0)  e3uw(:,:,:) = 1.0 
    1383       where (e3vw  (:,:,:).eq.0.0)  e3vw(:,:,:) = 1.0 
    1384  
     1380      where (e3t   (:,:,:).eq.0.0)  e3t(:,:,:) = 1._wp 
     1381      where (e3u   (:,:,:).eq.0.0)  e3u(:,:,:) = 1._wp 
     1382      where (e3v   (:,:,:).eq.0.0)  e3v(:,:,:) = 1._wp 
     1383      where (e3f   (:,:,:).eq.0.0)  e3f(:,:,:) = 1._wp 
     1384      where (e3w   (:,:,:).eq.0.0)  e3w(:,:,:) = 1._wp 
     1385      where (e3uw  (:,:,:).eq.0.0)  e3uw(:,:,:) = 1._wp 
     1386      where (e3vw  (:,:,:).eq.0.0)  e3vw(:,:,:) = 1._wp 
     1387 
     1388#if defined key_agrif 
     1389      ! Ensure meaningful vertical scale factors in ghost lines/columns 
     1390      IF( .NOT. Agrif_Root() ) THEN 
     1391         !   
     1392         IF((nbondi == -1).OR.(nbondi == 2)) THEN 
     1393            e3u(1,:,:) = e3u(2,:,:) 
     1394         ENDIF 
     1395         ! 
     1396         IF((nbondi ==  1).OR.(nbondi == 2)) THEN 
     1397            e3u(nlci-1,:,:) = e3u(nlci-2,:,:) 
     1398         ENDIF 
     1399         ! 
     1400         IF((nbondj == -1).OR.(nbondj == 2)) THEN 
     1401            e3v(:,1,:) = e3v(:,2,:) 
     1402         ENDIF 
     1403         ! 
     1404         IF((nbondj ==  1).OR.(nbondj == 2)) THEN 
     1405            e3v(:,nlcj-1,:) = e3v(:,nlcj-2,:) 
     1406         ENDIF 
     1407         ! 
     1408      ENDIF 
     1409#endif 
    13851410 
    13861411      fsdept(:,:,:) = gdept (:,:,:) 
    … …  
    14311456         WRITE(numout,"(10x,i4,4f9.2)") ( jk, fsdept(1,1,jk), fsdepw(1,1,jk),     & 
    14321457            &                                 fse3t (1,1,jk), fse3w (1,1,jk), jk=1,jpk ) 
    1433          DO jj = mj0(20), mj1(20) 
    1434             DO ji = mi0(20), mi1(20) 
     1458         iip1 = MIN(20, jpiglo-1)  ! for config with i smaller than 20 points 
     1459         ijp1 = MIN(20, jpjglo-1)  ! for config with j smaller than 20 points 
     1460         DO jj = mj0(ijp1), mj1(ijp1) 
     1461            DO ji = mi0(iip1), mi1(iip1) 
    14351462               WRITE(numout,*) 
    1436                WRITE(numout,*) ' domzgr: vertical coordinates : point (20,20,k)   bathy = ', bathy(ji,jj), hbatt(ji,jj) 
     1463               WRITE(numout,*) ' domzgr: vertical coordinates : point (',iip1,',',ijp1,',k)   bathy = ',  & 
     1464                  &                                              bathy(ji,jj), hbatt(ji,jj) 
    14371465               WRITE(numout,*) ' ~~~~~~  --------------------' 
    14381466               WRITE(numout,"(9x,' level   gdept    gdepw    gde3w     e3t      e3w  ')") 
    … …  
    14411469            END DO 
    14421470         END DO 
    1443          DO jj = mj0(74), mj1(74) 
    1444             DO ji = mi0(100), mi1(100) 
     1471         iip1 = MIN(  74, jpiglo-1) 
     1472         ijp1 = MIN( 100, jpjglo-1) 
     1473         DO jj = mj0(ijp1), mj1(ijp1) 
     1474            DO ji = mi0(iip1), mi1(iip1) 
    14451475               WRITE(numout,*) 
    1446                WRITE(numout,*) ' domzgr: vertical coordinates : point (100,74,k)   bathy = ', bathy(ji,jj), hbatt(ji,jj) 
     1476               WRITE(numout,*) ' domzgr: vertical coordinates : point (',iip1,',',ijp1,',k)   bathy = ',  & 
     1477                  &                                              bathy(ji,jj), hbatt(ji,jj) 
    14471478               WRITE(numout,*) ' ~~~~~~  --------------------' 
    14481479               WRITE(numout,"(9x,' level   gdept    gdepw    gde3w     e3t      e3w  ')") 
    … …  
    15011532      END DO 
    15021533      ! 
    1503       CALL wrk_dealloc( jpi, jpj,      zenv, ztmpi1, ztmpi2, ztmpj1, ztmpj2, zri, zrj, zhbat                           )      ! 
     1534      CALL wrk_dealloc( jpi, jpj,      zenv, ztmp, zmsk, zri, zrj, zhbat                           ) 
     1535      ! 
    15041536      IF( nn_timing == 1 )  CALL timing_stop('zgr_sco') 
    15051537      ! 
    … …  
    17301762      ENDDO 
    17311763      ! 
    1732       CALL lbc_lnk(e3t ,'T',1.) ; CALL lbc_lnk(e3u ,'T',1.) 
    1733       CALL lbc_lnk(e3v ,'T',1.) ; CALL lbc_lnk(e3f ,'T',1.) 
    1734       CALL lbc_lnk(e3w ,'T',1.) 
    1735       CALL lbc_lnk(e3uw,'T',1.) ; CALL lbc_lnk(e3vw,'T',1.) 
    1736       ! 
    17371764      !                                               ! ============= 
    17381765 
    … …  
    18311858      !!---------------------------------------------------------------------- 
    18321859      ! 
    1833       pf =   (   TANH( rn_theta * ( -(pk-0.5_wp) / REAL(jpkm1) + rn_thetb )  )   & 
     1860      pf =   (   TANH( rn_theta * ( -(pk-0.5_wp) / REAL(jpkm1,wp) + rn_thetb )  )   & 
    18341861         &     - TANH( rn_thetb * rn_theta                                )  )   & 
    18351862         & * (   COSH( rn_theta                           )                      & 
    … …  
    18571884      ! 
    18581885      IF ( rn_theta == 0 ) then      ! uniform sigma 
    1859          pf1 = - ( pk1 - 0.5_wp ) / REAL( jpkm1 ) 
     1886         pf1 = - ( pk1 - 0.5_wp ) / REAL( jpkm1,wp ) 
    18601887      ELSE                        ! stretched sigma 
    1861          pf1 =   ( 1._wp - pbb ) * ( SINH( rn_theta*(-(pk1-0.5_wp)/REAL(jpkm1)) ) ) / SINH( rn_theta )              & 
    1862             &  + pbb * (  (TANH( rn_theta*( (-(pk1-0.5_wp)/REAL(jpkm1)) + 0.5_wp) ) - TANH( 0.5_wp * rn_theta )  )  & 
     1888         pf1 =   ( 1._wp - pbb ) * ( SINH( rn_theta*(-(pk1-0.5_wp)/REAL(jpkm1,wp)) ) ) / SINH( rn_theta )              & 
     1889            &  + pbb * (  (TANH( rn_theta*( (-(pk1-0.5_wp)/REAL(jpkm1,wp)) + 0.5_wp) ) - TANH( 0.5_wp * rn_theta )  )  & 
    18631890            &        / ( 2._wp * TANH( 0.5_wp * rn_theta ) )  ) 
    18641891      ENDIF 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/DYN/dynadv_ubs.F90

    r3294 r4153  
    2929 
    3030   REAL(wp), PARAMETER :: gamma1 = 1._wp/3._wp  ! =1/4 quick      ; =1/3  3rd order UBS 
    31    REAL(wp), PARAMETER :: gamma2 = 1._wp/8._wp  ! =0   2nd order  ; =1/8 4th order centred 
     31   REAL(wp), PARAMETER :: gamma2 = 1._wp/32._wp ! =0   2nd order  ; =1/32 4th order centred 
    3232 
    3333   PUBLIC   dyn_adv_ubs   ! routine called by step.F90 
    … …  
    5757      !!                       = 1/3  3rd order Upstream biased scheme 
    5858      !!                gamma2 = 0    2nd order finite differencing  
    59       !!                       = 1/8 4th order finite differencing 
     59      !!                       = 1/32 4th order finite differencing 
    6060      !!      For stability reasons, the first term of the fluxes which cor- 
    6161      !!      responds to a second order centered scheme is evaluated using   
    … …  
    6464      !!      before velocity (forward in time).  
    6565      !!      Default value (hard coded in the begining of the module) are  
    66       !!      gamma1=1/3 and gamma2=1/8. 
     66      !!      gamma1=1/3 and gamma2=1/32. 
    6767      !! 
    6868      !! ** Action : - (ua,va) updated with the 3D advective momentum trends 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/DYN/dynspg_flt.F90

    r4147 r4153  
    109109      INTEGER  ::   ji, jj, jk   ! dummy loop indices 
    110110      REAL(wp) ::   z2dt, z2dtg, zgcb, zbtd, ztdgu, ztdgv   ! local scalars 
    111       REAL(wp), POINTER, DIMENSION(:,:,:) ::  zub, zvb 
    112111      !!---------------------------------------------------------------------- 
    113112      ! 
    114113      IF( nn_timing == 1 )  CALL timing_start('dyn_spg_flt') 
    115114      ! 
    116       CALL wrk_alloc( jpi,jpj,jpk, zub, zvb ) 
    117115      ! 
    118116      IF( kt == nit000 ) THEN 
    … …  
    213211         DO jk = 1, jpkm1 
    214212            DO ji = 1, jpij 
    215                spgu(ji,1) = spgu(ji,1) + fse3u(ji,1,jk) * ua(ji,1,jk) 
    216                spgv(ji,1) = spgv(ji,1) + fse3v(ji,1,jk) * va(ji,1,jk) 
     213               spgu(ji,1) = spgu(ji,1) + fse3u_a(ji,1,jk) * ua(ji,1,jk) 
     214               spgv(ji,1) = spgv(ji,1) + fse3v_a(ji,1,jk) * va(ji,1,jk) 
    217215            END DO 
    218216         END DO 
    … …  
    221219            DO jj = 2, jpjm1 
    222220               DO ji = 2, jpim1 
    223                   spgu(ji,jj) = spgu(ji,jj) + fse3u(ji,jj,jk) * ua(ji,jj,jk) 
    224                   spgv(ji,jj) = spgv(ji,jj) + fse3v(ji,jj,jk) * va(ji,jj,jk) 
     221                  spgu(ji,jj) = spgu(ji,jj) + fse3u_a(ji,jj,jk) * ua(ji,jj,jk) 
     222                  spgv(ji,jj) = spgv(ji,jj) + fse3v_a(ji,jj,jk) * va(ji,jj,jk) 
    225223               END DO 
    226224            END DO 
    … …  
    360358      IF( lrst_oce ) CALL flt_rst( kt, 'WRITE' ) 
    361359      ! 
    362       CALL wrk_dealloc( jpi,jpj,jpk, zub, zvb ) 
    363360      ! 
    364361      IF( nn_timing == 1 )  CALL timing_stop('dyn_spg_flt') 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/ICB/icb_oce.F90

    r4147 r4153  
    3737   USE par_oce   ! ocean parameters 
    3838   USE lib_mpp   ! MPP library 
    39    USE fldread   ! read input fields (FLD type) 
    4039 
    4140   IMPLICIT NONE 
    … …  
    148147   REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:)   :: griddata                           !: work array for icbrst 
    149148 
    150    TYPE(FLD), PUBLIC, ALLOCATABLE     , DIMENSION(:)       ::   sf_icb   !: structure: file information, fields read 
    151  
    152149   !!---------------------------------------------------------------------- 
    153150   !! NEMO/OPA 3.3 , NEMO Consortium (2011) 
    … …  
    165162      ! 
    166163      icb_alloc = 0 
    167 !!      ALLOCATE( berg_grid                      ,                                               & 
    168       ALLOCATE(                                                                                & 
    169          &      berg_grid%calving    (jpi,jpj) , berg_grid%calving_hflx (jpi,jpj)          ,   & 
     164      ALLOCATE( berg_grid%calving    (jpi,jpj) , berg_grid%calving_hflx (jpi,jpj)          ,   & 
    170165         &      berg_grid%stored_heat(jpi,jpj) , berg_grid%floating_melt(jpi,jpj)          ,   & 
    171166         &      berg_grid%maxclass   (jpi,jpj) , berg_grid%stored_ice   (jpi,jpj,nclasses) ,   & 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/ICB/icbini.F90

    r4147 r4153  
    3535   PUBLIC   icb_init  ! routine called in nemogcm.F90 module 
    3636 
    37    CHARACTER(len=100) ::   cn_dir          ! Root directory for location of icb files 
    38    TYPE(FLD_N)        ::   sn_icb          ! information about the calving file to be read 
    39  
     37   CHARACTER(len=100)                                 ::   cn_dir = './'   !: Root directory for location of icb files 
     38   TYPE(FLD_N)                                        ::   sn_icb          !: information about the calving file to be read 
     39   TYPE(FLD), PUBLIC, ALLOCATABLE     , DIMENSION(:)  ::   sf_icb          !: structure: file information, fields read 
     40                                                                           !: used in icbini and icbstp 
    4041   !!---------------------------------------------------------------------- 
    4142   !! NEMO/OPA 3.3 , NEMO Consortium (2011) 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/ICB/icbstp.F90

    r3614 r4153  
    2424   USE lib_mpp 
    2525   USE iom 
     26   USE fldread 
    2627   USE timing         ! timing 
    2728 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/IOM/iom.F90

    r4152 r4153  
    3131   USE sbc_oce, ONLY :   nn_fsbc         ! ocean space and time domain 
    3232   USE trc_oce, ONLY :   nn_dttrc        !  !: frequency of step on passive tracers 
     33   USE icb_oce, ONLY :   class_num       !  !: iceberg classes 
    3334   USE domngb          ! ocean space and time domain 
    3435   USE phycst          ! physical constants 
    … …  
    9697      clname = cdname 
    9798      IF( TRIM(Agrif_CFixed()) /= '0' )   clname = TRIM(Agrif_CFixed())//"_"//TRIM(cdname) 
     99# if defined key_mpp_mpi 
    98100      CALL xios_context_initialize(TRIM(clname), mpi_comm_opa) 
     101# else 
     102      CALL xios_context_initialize(TRIM(clname), 0) 
     103# endif 
    99104      CALL iom_swap( cdname ) 
    100105 
    … …  
    136141      CALL iom_set_axis_attr( "depthw", gdepw_0 ) 
    137142# if defined key_floats 
    138       CALL iom_set_axis_attr( "nfloat", (ji, ji=1,nfloat) ) 
     143      CALL iom_set_axis_attr( "nfloat", (/ (REAL(ji,wp), ji=1,nfloat) /) ) 
    139144# endif 
     145      CALL iom_set_axis_attr( "icbcla", class_num ) 
    140146       
    141147      ! automatic definitions of some of the xml attributs 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/LBC/lbclnk.F90

    r4152 r4153  
    281281   END SUBROUTINE lbc_lnk_3d 
    282282 
    283    SUBROUTINE lbc_bdy_lnk_3d( pt3d, cd_type, psgn, ib_bdy ) 
    284       !!--------------------------------------------------------------------- 
    285       !!                  ***  ROUTINE lbc_bdy_lnk  *** 
    286       !! 
    287       !! ** Purpose :   wrapper rountine to 'lbc_lnk_3d'. This wrapper is used 
    288       !!                to maintain the same interface with regards to the mpp case 
    289       !! 
    290       !!---------------------------------------------------------------------- 
    291       CHARACTER(len=1)                , INTENT(in   )           ::   cd_type   ! nature of pt3d grid-points 
    292       REAL(wp), DIMENSION(jpi,jpj,jpk), INTENT(inout)           ::   pt3d      ! 3D array on which the lbc is applied 
    293       REAL(wp)                        , INTENT(in   )           ::   psgn      ! control of the sign  
    294       INTEGER                                                   ::   ib_bdy    ! BDY boundary set 
    295       !! 
    296       CALL lbc_lnk_3d( pt3d, cd_type, psgn) 
    297  
    298    END SUBROUTINE lbc_bdy_lnk_3d 
    299  
    300    SUBROUTINE lbc_bdy_lnk_2d( pt2d, cd_type, psgn, ib_bdy ) 
    301       !!--------------------------------------------------------------------- 
    302       !!                  ***  ROUTINE lbc_bdy_lnk  *** 
    303       !! 
    304       !! ** Purpose :   wrapper rountine to 'lbc_lnk_3d'. This wrapper is used 
    305       !!                to maintain the same interface with regards to the mpp case 
    306       !! 
    307       !!---------------------------------------------------------------------- 
    308       CHARACTER(len=1)                , INTENT(in   )           ::   cd_type   ! nature of pt3d grid-points 
    309       REAL(wp), DIMENSION(jpi,jpj),     INTENT(inout)           ::   pt2d      ! 3D array on which the lbc is applied 
    310       REAL(wp)                        , INTENT(in   )           ::   psgn      ! control of the sign  
    311       INTEGER                                                   ::   ib_bdy    ! BDY boundary set 
    312       !! 
    313       CALL lbc_lnk_2d( pt2d, cd_type, psgn) 
    314  
    315    END SUBROUTINE lbc_bdy_lnk_2d 
    316  
    317283   SUBROUTINE lbc_lnk_2d( pt2d, cd_type, psgn, cd_mpp, pval ) 
    318284      !!--------------------------------------------------------------------- 
    … …  
    401367   END SUBROUTINE lbc_lnk_2d 
    402368 
     369#endif 
     370 
     371 
     372   SUBROUTINE lbc_bdy_lnk_3d( pt3d, cd_type, psgn, ib_bdy ) 
     373      !!--------------------------------------------------------------------- 
     374      !!                  ***  ROUTINE lbc_bdy_lnk  *** 
     375      !! 
     376      !! ** Purpose :   wrapper rountine to 'lbc_lnk_3d'. This wrapper is used 
     377      !!                to maintain the same interface with regards to the mpp 
     378      !case 
     379      !! 
     380      !!---------------------------------------------------------------------- 
     381      CHARACTER(len=1)                , INTENT(in   )           ::   cd_type   ! nature of pt3d grid-points 
     382      REAL(wp), DIMENSION(jpi,jpj,jpk), INTENT(inout)           ::   pt3d      ! 3D array on which the lbc is applied 
     383      REAL(wp)                        , INTENT(in   )           ::   psgn      ! control of the sign  
     384      INTEGER                                                   ::   ib_bdy    ! BDY boundary set 
     385      !! 
     386      CALL lbc_lnk_3d( pt3d, cd_type, psgn) 
     387 
     388   END SUBROUTINE lbc_bdy_lnk_3d 
     389 
     390   SUBROUTINE lbc_bdy_lnk_2d( pt2d, cd_type, psgn, ib_bdy ) 
     391      !!--------------------------------------------------------------------- 
     392      !!                  ***  ROUTINE lbc_bdy_lnk  *** 
     393      !! 
     394      !! ** Purpose :   wrapper rountine to 'lbc_lnk_3d'. This wrapper is used 
     395      !!                to maintain the same interface with regards to the mpp 
     396      !case 
     397      !! 
     398      !!---------------------------------------------------------------------- 
     399      CHARACTER(len=1)                , INTENT(in   )           ::   cd_type   ! nature of pt3d grid-points 
     400      REAL(wp), DIMENSION(jpi,jpj),     INTENT(inout)           ::   pt2d      ! 3D array on which the lbc is applied 
     401      REAL(wp)                        , INTENT(in   )           ::   psgn      ! control of the sign  
     402      INTEGER                                                   ::   ib_bdy    ! BDY boundary set 
     403      !! 
     404      CALL lbc_lnk_2d( pt2d, cd_type, psgn) 
     405 
     406   END SUBROUTINE lbc_bdy_lnk_2d 
     407 
     408 
    403409   SUBROUTINE lbc_lnk_2d_e( pt2d, cd_type, psgn, jpri, jprj ) 
    404410      !!--------------------------------------------------------------------- 
    … …  
    425431   END SUBROUTINE lbc_lnk_2d_e 
    426432 
    427 # endif 
    428433#endif 
    429434 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/LBC/lib_mpp.F90

    r4152 r4153  
    21842184!!gm Remark : this is very time consumming!!! 
    21852185      !                                         ! ------------------------ ! 
    2186             IF( ijpt0 > ijpt1 .OR. iipt0 > iipt1 ) THEN 
     2186        IF(((nbondi .ne. 0) .AND. (ktype .eq. 2)) .OR. ((nbondj .ne. 0) .AND. (ktype .eq. 1))) THEN 
    21872187            ! there is nothing to be migrated 
    21882188               lmigr = .FALSE. 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/LBC/mppini_2.h90

    r4147 r4153  
    129129      irestj = 1 + MOD( jpjglo - nrecj -1 , jpnj ) 
    130130 
     131#if defined key_nemocice_decomp 
     132      ! Change padding to be consistent with CICE 
     133      ilci(1:jpni-1      ,:) = jpi 
     134      ilci(jpni          ,:) = jpiglo - (jpni - 1) * (jpi - nreci) 
     135 
     136      ilcj(:,      1:jpnj-1) = jpj 
     137      ilcj(:,          jpnj) = jpjglo - (jpnj - 1) * (jpj - nrecj) 
     138#else 
    131139      ilci(1:iresti      ,:) = jpi 
    132140      ilci(iresti+1:jpni ,:) = jpi-1 
    … …  
    134142      ilcj(:,      1:irestj) = jpj 
    135143      ilcj(:, irestj+1:jpnj) = jpj-1 
     144#endif 
    136145 
    137146      IF(lwp) WRITE(numout,*) 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/SBC/sbcmod.F90

    r4152 r4153  
    229229 
    230230      ! 
    231                           CALL sbc_ssm_init 
     231                          CALL sbc_ssm_init               ! Sea-surface mean fields initialisation 
    232232      ! 
    233233      IF( ln_ssr      )   CALL sbc_ssr_init               ! Sea-Surface Restoring initialisation 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/SOL/solmat.F90

    r3609 r4153  
    3030   USE lbclnk          ! lateral boudary conditions 
    3131   USE lib_mpp         ! distributed memory computing 
     32   USE c1d               ! 1D vertical configuration 
    3233   USE in_out_manager  ! I/O manager 
    3334   USE timing          ! timing 
    … …  
    271272       
    272273      ! SOR and PCG solvers 
     274      IF( lk_c1d ) CALL lbc_lnk( gcdmat, 'T', 1._wp ) ! 1D case bmask =/0  but gcdmat not define everywhere  
    273275      DO jj = 1, jpj 
    274276         DO ji = 1, jpi 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/OPA_SRC/step.F90

    r4152 r4153  
    284284      IF( lk_cpl           )   CALL sbc_cpl_snd( kstp )     ! coupled mode : field exchanges 
    285285      ! 
    286       IF( kstp == nitend   )  THEN 
     286#if defined key_iomput 
     287      IF( kstp == nitend .OR. indic < 0 ) THEN  
    287288                      CALL iom_context_finalize( "nemo"     ) ! needed for XIOS+AGRIF 
    288289         IF( ln_crs ) CALL iom_context_finalize( "nemo_crs" ) !  
    289290      ENDIF 
     291#endif 
    290292      ! 
    291293      IF( nn_timing == 1 .AND.  kstp == nit000  )   CALL timing_reset 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zfechem.F90

    r4148 r4153  
    129129                  zoxy   = trn(ji,jj,jk,jpoxy) * ( rhop(ji,jj,jk) / 1.e3 ) 
    130130                  ! Fe2+ oxydation rate from Santana-Casiano et al. (2005) 
    131                   zkox   = 35.407 - 6.7109 * zph + 0.5342 * zph * zph - 5362.6 / ( tsn(ji,jj,1,jp_tem) + 273.15 )  & 
     131                  zkox   = 35.407 - 6.7109 * zph + 0.5342 * zph * zph - 5362.6 / ( tsn(ji,jj,jk,jp_tem) + 273.15 )  & 
    132132                    &    - 0.04406 * SQRT( tsn(ji,jj,jk,jp_sal) ) - 0.002847 * tsn(ji,jj,jk,jp_sal) 
    133133                  zkox   = ( 10.** zkox ) * spd 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zsms.F90

    r4152 r4153  
    433433#endif 
    434434            &                    + trn(:,:,:,jpsfe)                     & 
    435             &                    + trn(:,:,:,jpzoo)                     & 
     435            &                    + trn(:,:,:,jpzoo) * ferat3            & 
    436436            &                    + trn(:,:,:,jpmes) * ferat3            ) * cvol(:,:,:)  ) 
    437437 

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/SETTE/iodef_sette.xml

    r4147 r4153  
    2121    --> 
    2222     
    23     <file_definition type="multiple_file" sync_freq="1d" min_digits="4"> 
     23    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4"> 
    2424     
    2525      <file_group id="1h" output_freq="1h"  output_level="10" enabled=".FALSE."/> <!-- 1h files --> 
    … …  
    5454     
    5555   <axis_definition>   
    56       <axis id="deptht" long_name="Vertical T levels" unit="m"  /><!-- positive=".FALSE." --> 
    57       <axis id="depthu" long_name="Vertical U levels" unit="m"  /><!-- positive=".FALSE." --> 
    58       <axis id="depthv" long_name="Vertical V levels" unit="m"  /><!-- positive=".FALSE." --> 
    59       <axis id="depthw" long_name="Vertical W levels" unit="m"  /><!-- positive=".FALSE." --> 
     56      <axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" /> 
     57      <axis id="depthu" long_name="Vertical U levels" unit="m" positive="down" /> 
     58      <axis id="depthv" long_name="Vertical V levels" unit="m" positive="down" /> 
     59      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" /> 
    6060      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
     61      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
    6162   </axis_definition>  
    6263     

  • branches/2013/dev_LOCEAN_2013/NEMOGCM/TOOLS/MISCELLANEOUS/chk_iomput.sh

    r2404 r4153  
    3535       echo ' --insrc              only print all variable definitions found in the source code' 
    3636       echo 'Examples' 
    37        echo '      chk_iomput.sh' 
    38        echo '      chk_iomput.sh --help' 
    39        echo '      chk_iomput.sh ../../CONFIG/ORCA2_LIM/EXP00/iodef.xml "../../NEMO/OPA_SRC/ ../../NEMO/LIM_SRC_2/"' 
     37       echo '      ./chk_iomput.sh' 
     38       echo '      ./chk_iomput.sh --help' 
     39       echo '      ./chk_iomput.sh ../../CONFIG/ORCA2_LIM/EXP00/iodef.xml "../../NEMO/OPA_SRC/ ../../NEMO/LIM_SRC_2/"' 
    4040       echo 
    4141       exit ;; 
    … …  
    5959#------------------------------------------------ 
    6060# 
    61 [ $inxml -eq 1 ] && grep "< *field * id *=" $xmlfile 
     61external=$( grep -c "<field_definition.* src=" $xmlfile ) 
     62if [ $external -eq 1 ] 
     63then 
     64    xmlfield_def=$( grep "<field_definition.* src=" $xmlfile | sed -e 's/.*src="\([^"]*\)".*/\1/' ) 
     65    xmlfield_def=$( dirname $xmlfile )/$xmlfield_def    
     66else 
     67    xmlfield_def=$xmlfile 
     68fi 
     69[ $inxml -eq 1 ] && grep "< *field * id *=" $xmlfield_def 
    6270[ $insrc -eq 1 ] && find $srcdir -name "*.[Ffh]90" -exec grep -iH "^[^\!]*call  *iom_put *(" {} \; 
    6371[ $(( $insrc + $inxml )) -ge 1 ] && exit 
    … …  
    7179# list of variables used in "CALL iom_put" 
    7280# 
    73 varlistsrc=$( find $srcdir -name "*.[Ffh]90" -exec grep -i  "^[^\!]*call  *iom_put *(" {} \; | sed -e "s/.*iom_put *( *[\"\']\([^\"\']*\)[\"\'] *,.*/\1/" | sort -d ) 
     81badvarsrc=$( find $srcdir -name "*.[Ffh]90" -exec grep -i  "^[^\!]*call  *iom_put *(" {} \; | sed -e "s/.*iom_put *( *[\"\']\([^\"\']*\)[\"\'] *,.*/\1/" | grep -ic iom_put ) 
     82if [ $badvarsrc -ne 0 ] 
     83then 
     84    echo "The following call to iom_put cannot be checked" 
     85    echo 
     86    find $srcdir -name "*.[Ffh]90" -exec grep -i  "^[^\!]*call  *iom_put *(" {} \; | sed -e "s/.*iom_put *( *[\"\']\([^\"\']*\)[\"\'] *,.*/\1/" | grep -i iom_put | sort -d  
     87    echo 
     88fi 
     89varlistsrc=$( find $srcdir -name "*.[Ffh]90" -exec grep -i  "^[^\!]*call  *iom_put *(" {} \; | sed -e "s/.*iom_put *( *[\"\']\([^\"\']*\)[\"\'] *,.*/\1/" | grep -vi iom_put | sort -d ) 
    7490# 
    7591# list of variables defined in the xml file 
    7692# 
    77 varlistxml=$( grep "< *field * id *=" $xmlfile  | sed -e "s/^.*< *field * id *= *[\"\']\([^\"\']*\)[\"\'].*/\1/" | sort -d ) 
     93varlistxml=$( grep "< *field.* id *=" $xmlfield_def  | sed -e "s/^.*< *field.* id *= *[\"\']\([^\"\']*\)[\"\'].*/\1/" | sort -d ) 
    7894# 
    7995# list of variables to be outputed in the xml file 
    8096# 
    81 varlistout=$( grep "< *field * ref *=" $xmlfile  | sed -e "s/^.*< *field * ref *= *[\"\']\([^\"\']*\)[\"\'].*/\1/" | sort -d ) 
     97varlistout=$( grep "< *field.* field_ref *=" $xmlfile  | sed -e "s/^.*< *field.* field_ref *= *[\"\']\([^\"\']*\)[\"\'].*/\1/" | sort -d ) 
    8298# 
    8399echo "--------------------------------------------------" 
    84100echo  check if all iom_put found in $srcdir 
    85 echo  have a corresponding variable definition in $xmlfile 
     101echo  have a corresponding variable definition in $xmlfield_def 
    86102echo "--------------------------------------------------" 
    87103for var in $varlistsrc 
    … …  
    90106    if [ $tst -ne 1 ]  
    91107    then 
    92    echo "problem with $var: $tst lines corresponding to its definition in $xmlfile, but defined in the code in" 
     108   echo "problem with $var: $tst lines corresponding to its definition in $xmlfield_def, but defined in the code in" 
    93109   for f in $srclist 
    94110   do 
Note: See TracChangeset for help on using the changeset viewer.