Changeset 4258 for branches

branches/2013/dev_r3858_NOC_ZTC/DOC/NEMO_book.tex

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23	23	\usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption} % Gives small font for captions
24	24	\usepackage{enumitem} % allows non-bold description items
	25	\usepackage{longtable} % allows multipage tables
25	26	%\usepackage{colortbl} % gives coloured panels behind table columns
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branches/2013/dev_r3858_NOC_ZTC/DOC/TexFiles/Chapters/Chap_DIA.tex

-                      r3764
+                      r4258
 % ================================================================
 % Chapter Ñ I/O & Diagnostics
+% Chapter I/O & Diagnostics
 % ================================================================
 \chapter{Ouput and Diagnostics (IOM, DIA, TRD, FLO)}
 …
 The model outputs are of three types: the restart file, the output listing,
 and the output file(s). The restart file is used internally by the code when
+and the diagnostic output file(s). The restart file is used internally by the code when
 the user wants to start the model with initial conditions defined by a
 previous simulation. It contains all the information that is necessary in
 …
 that it is saved in the same binary format as the one used by the computer
 that is to read it (in particular, 32 bits binary IEEE format must not be used for
+this file). The output listing and file(s) are predefined but should be checked
+this file).
+The output listing and file(s) are predefined but should be checked
 and eventually adapted to the user's needs. The output listing is stored in
 the $ocean.output$ file. The information is printed from within the code on the
 …
 "\textit{grep -i numout}" in the source code directory.
+In the standard configuration, the user will find the model results in
+NetCDF files containing mean values (or instantaneous values if
+\key{diainstant} is defined) for every time-step where output is demanded.
+These outputs are defined in the \mdl{diawri} module.
+When defining \key{dimgout}, the output are written in DIMG format,
+an IEEE output format.
+Since version 3.2, an I/O server has been added which provides more
+flexibility in the choice of the fields to be output as well as how the
+writing work is distributed over the processors in massively parallel
+computing. It is presented in next section.
+By default, diagnostic output files are written in NetCDF format but an IEEE binary output format, called DIMG, can be choosen by 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 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.
+By 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).
 %\gmcomment{                    % start of gmcomment
 …
+Since version 3.2, iom\_put is the NEMO output interface. It was designed to be simple to use,
+flexible and efficient. Two main functionalities are covered by iom\_put:
+(1) the control of the output files through an external xml file defined by the user ;
+(2) the distribution (or not) of all task related to output files on dedicated processors.
+The first functionality allows the user to specify, without touching anything into the code,
+the way he want to output data: \\
+- choice of output frequencies that can be different for each file (including real months and years) \\
+- choice of file contents: decide which data will be written in which file (the same data can be
+outputted in different files)  \\
+- possibility to extract a subdomain (for example all TAO-PIRATA-RAMA moorings are already defined)  \\
+- choice of the temporal operation to perform: mean, instantaneous, min, max  \\
+- extremely large choice of data available   \\
+- redefine variables name and long\_name  \\
+In addition, iom\_put allows the user to output any variable (scalar, 2D or 3D) in the code
+in a very easy way. All details of iom\_put functionalities are listed in the following subsections.
+An example of the iodef.xml file that control the outputs can be found here:
+NEMOGCM/CONFIG/ORCA2\_LIM/EXP00/iodef.xml
+The second functionality targets outputs performances when running on a very large number of processes.
+The idea is to dedicate N specific processes to write the outputs, where N is defined by the user.
+In the current version, this functionality is technically working however, its performance are usually poor
+(for known reasons). Users can therefore test this functionality but they must be aware that expected
+performance improvement will not be achieved before the release 3.4.
+An example of xmlio\_server.def NEMOGCM/CONFIG/ORCA2\_LIM/EXP00/xmlio\_server.def
+\subsection{Basic knowledge}
+Since 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:
+\begin{enumerate}
+\item The complete and flexible control of the output files through external XML files adapted by the user from standard templates.
+\item To achieve high performance and scalable output through the optional distribution of all diagnostic output related tasks to dedicated processes.
+\end{enumerate}
+The first functionality allows the user to specify, without code changes or recompilation, aspects of the diagnostic output stream, such as:
+\begin{itemize}
+\item The choice of output frequencies that can be different for each file (including real months and years).
+\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).
+\item The possibility to split output files at a choosen frequency.
+\item The possibility to extract a vertical or an horizontal subdomain.
+\item The choice of the temporal operation to perform, e.g.: average, accumulate, instantaneous, min, max and once.
+\item Control over metadata via a large XML "database" of possible output fields.
+\end{itemize}
+In 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:
+\begin{alltt}
+\begin{verbatim}
+  NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml
+  NEMOGCM/CONFIG/SHARED/field_def.xml
+  and
+  NEMOGCM/CONFIG/SHARED/domain_def.xml.
+\end{verbatim}
+\end{alltt}
+The second functionality targets output performance when running in parallel (\key{mpp\_mpi}). Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO processes) to collect and write the outputs. With an appropriate choice of N by the user, the bottleneck associated with the writing of the output files can be greatly reduced.
+Since version 3.5, the iom\_put interface depends on an external code called \href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}. This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to create a single output file and therefore to bypass the rebuilding phase. Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to an HDF5 library that has been correctly compiled (i.e. with the configure option $--$enable-parallel). Note that the files created by iomput through XIOS are incompatible with NetCDF3. All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3.
+Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers, where N is typically much less than the number of NEMO processors, will reduce the number of output files created. This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors. Note that for smaller configurations, the rebuilding phase can be avoided, even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server.
+\subsection{XIOS: the IO\_SERVER}
+\subsubsection{Attached or detached mode?}
+Iomput 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''.
+In 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.
+In 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.
+\subsubsection{Number of cpu used by XIOS in detached mode}
+The 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:
+\texttt{ mpirun -np 62 ./nemo.exe : -np 2 ./xios\_server.exe }
+\subsubsection{Control of XIOS: the XIOS context in iodef.xml}
+As 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.
+\begin{tabular}{|p{4cm}|p{6.0cm}|p{2.0cm}|}
+   \hline
+   variable name &
+   description &
+   example \\
+   \hline
+   \hline
+   buffer\_size &
+   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 &
+   25000000 \\
+   \hline
+   buffer\_server\_factor\_size &
+   ratio between NEMO and XIOS buffer size. Should be 2. &
+\\
+   \hline
+   info\_level &
+   verbosity level (0 to 100) &
+\\
+   \hline
+   using\_server &
+   activate attached(false) or detached(true) mode &
+   true \\
+   \hline
+   using\_oasis &
+   XIOS is used with OASIS(true) or not (false) &
+   false \\
+   \hline
+   oasis\_codes\_id &
+   when using oasis, define the identifier of NEMO in the namcouple. Note that the identifier of XIOS is xios.x &
+   oceanx \\
+   \hline
+\end{tabular}
+\subsection{Practical issues}
+\subsubsection{Installation}
+As 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
+\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.
+\subsubsection{Add your own outputs}
+It 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.
+\begin{description}
+\item[1.] in NEMO code, add a \\
+\texttt{      CALL iom\_put( 'identifier', array ) } \\
+where you want to output a 2D or 3D array.
+\item[2.] If necessary, add \\
+\texttt{   USE iom\ \ \ \ \ \ \ \ \ \ \ \ ! I/O manager library }  \\
+to the list of used modules in the upper part of your module.
+\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:
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <field_definition>
+      <!-- T grid -->
+     <field_group id="grid_T" grid_ref="grid_T_3D">
+      ...
+      <field id="identifier" long_name="blabla" ... />
+      ...
+   </field_definition>
+\end{verbatim}
+}}\end{alltt}
+Note 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.:
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+     <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/>
+\end{verbatim}
+}}\end{alltt}
+Note, if your array is computed within the surface module each nn\_fsbc time\_step,
+add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$ which has been defined with the correct frequency of operations (iom\_set\_field\_attr in iom.F90)
+\item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules)   \\
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <file id="file1" .../>
+      ...
+      <field field_ref="identifier" />
+      ...
+   </file>
+\end{verbatim}
+}}\end{alltt}
+\end{description}
+\subsection{XML fundamentals}
 \subsubsection{ XML basic rules}
 …
 \subsubsection{Structure of the xml file used in NEMO}
+The xml file is split into 3 parts:
+\begin{description}
+\item[field definition]: define all variables that can be output \\
+all lines in between the following two tags\\
+\verb?   <field\_definition ...> ?  \\
+\verb?   </field\_definition ...> ?
+\item[file definition]: define the netcdf files to be created and the variables they will contain \\
+all lines in between the following two tags \\
+\verb?   <field\_definition> ?  \\
+\verb?   </field\_definition> ?
+\item[axis and grid definitions]: define the horizontal and vertical grids \\
+all lines in between the following two set of two tags\\
+\verb?   <axis\_definition ...> ?  \\
+\verb?   </axis\_definition ...> ?
+and \\
+\verb?   <grid\_definition ...> ?  \\
+\verb?   </grid\_definition ...> ?
+\end{description}
+\subsubsection{Inheritance and group }
+ Xml extensively uses the concept of inheritance. \\
+The 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):
 \\
+example 1: \\
+\vspace{-30pt}
+\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|}
+   \hline
+   flavor &
+   description &
+   example \\
+   \hline
+   \hline
+   root &
+   declaration of the root element that can contain element groups or elements &
+   {\scriptsize \verb? < file_definition ... >?} \\
+   \hline
+   group &
+   declaration of a group element that can contain element groups or elements &
+   {\scriptsize \verb? < file_group ... >?} \\
+   \hline
+   element &
+   declaration of an element that can contain elements &
+   {\scriptsize \verb? < file ... >?} \\
+   \hline
+\end{tabular}
+\\
+Each 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.
+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):\\
+\\
+\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|}
+   \hline
+   context &
+   description &
+   example \\
+   \hline
+   \hline
+   context xios &
+   context containing information for XIOS &
+   {\scriptsize \verb? <context id="xios" ...  ?} \\
+   \hline
+   context nemo &
+   context containing IO information for NEMO (mother grid when using AGRIF) &
+   {\scriptsize \verb? <context id="nemo" ... ?} \\
+   \hline
+   context 1\_nemo &
+   context containing IO information for NEMO child grid 1 (when using AGRIF) &
+   {\scriptsize \verb? <context id="1_nemo" ...  ?} \\
+   \hline
+   context n\_nemo &
+   context containing IO information for NEMO child grid n (when using AGRIF) &
+   {\scriptsize \verb? <context id="n_nemo" ...  ?} \\
+   \hline
+\end{tabular}
+\\
+\noindent The xios context contains only 1 tag:
+\\
+\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|}
+   \hline
+   context tag &
+   description &
+   example \\
+   \hline
+   \hline
+   variable\_definition &
+   define variables needed by XIOS. This can be seen as a kind of namelist for XIOS. &
+   {\scriptsize \verb? <variable_definition ... ?} \\
+   \hline
+\end{tabular}
+\\
+\noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts (that can be defined in any order):\\
+\\
+\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|}
+   \hline
+   context tag &
+   description &
+   example \\
+   \hline
+   \hline
+   field\_definition &
+   define all variables that can potentially be outputted &
+   {\scriptsize \verb? <field_definition ... ?} \\
+   \hline
+   file\_definition &
+   define the netcdf files to be created and the variables they will contain &
+   {\scriptsize \verb? <file_definition ... ?} \\
+   \hline
+   axis\_definition &
+   define vertical axis &
+   {\scriptsize \verb? <axis_definition ... ?} \\
+   \hline
+   domain\_definition &
+   define the horizontal grids &
+   {\scriptsize \verb? <domain_definition ... ?} \\
+   \hline
+   grid\_definition &
+   define the 2D and 3D grids (association of an axis and a domain) &
+   {\scriptsize \verb? <grid_definition ... ?} \\
+   \hline
+\end{tabular}
+\\
+\subsubsection{Nesting XML files}
+The 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: \\
+{\scriptsize \verb? <context src="./nemo_def.xml" /> ?}\\
+\noindent In NEMO, by default, the field and domain definition is done in 2 separate files:
+{\scriptsize \tt
+\begin{verbatim}
+NEMOGCM/CONFIG/SHARED/field_def.xml
+and
+NEMOGCM/CONFIG/SHARED/domain_def.xml
+\end{verbatim}
+}
+\noindent that are included in the main iodef.xml file through the following commands: \\
+{\scriptsize \verb? <field_definition src="./field_def.xml" /> ? \\
+\verb? <domain_definition src="./domain_def.xml" /> ? }
+\subsubsection{Use of inheritance}
+XML 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.  \\
+\\
+example 1: Direct inheritance.
+\vspace{-20pt}
 \begin{alltt}  {{\scriptsize
 \begin{verbatim}
    <field_definition operation="ave(X)" >
       <field id="sst"                    />   <!-- averaged      sst -->
       <field id="sss" operation="inst(X)"/>   <!-- instantaneous sss -->
+   <field_definition operation="average" >
+     <field id="sst"                    />   <!-- averaged      sst -->
+     <field id="sss" operation="instant"/>   <!-- instantaneous sss -->
    </field_definition>
 \end{verbatim}
 }}\end{alltt}
 The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''ave(X)''
 of the attribute ''operation'' from its parent ''field definition''. Note that a child can overwrite
+The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average''
+of the attribute ''operation'' from its parent. Note that a child can overwrite
 the attribute definition inherited from its parents. In the example above, the field ''sss'' will
+therefore output instantaneous values instead of average values.
 example 2: Use (or overwrite) attributes value of a field when listing the variables included in a file
+for example output instantaneous values instead of average values. \\
+\\
+example 2: Inheritance by reference.
 \vspace{-20pt}
 \begin{alltt}  {{\scriptsize
 \begin{verbatim}
    <field_definition>
       <field id="sst" description="sea surface temperature" />
       <field id="sss" description="sea surface salinity"    />
+     <field id="sst" long_name="sea surface temperature" />
+     <field id="sss" long_name="sea surface salinity"    />
    </field_definition>
    <file_definition>
       <file id="file_1" />
             <field ref="sst"                              />  <!-- default def -->
             <field ref="sss" description="my description" />  <!-- overwrite   -->
       </file>
+     <file id="myfile" output_freq="1d" />
+       <field field_ref="sst"                            />  <!-- default def -->
+       <field field_ref="sss" long_name="my description" />  <!-- overwrite   -->
+     </file>
    </file_definition>
 \end{verbatim}
 }}\end{alltt}
+With the help of the inheritance, the concept of group allow to define a set of attributes
+for several fields or files.
+example 3, group of fields: define a group ''T\_grid\_variables'' identified with the name
+''grid\_T''. By default variables of this group have no vertical axis but, following inheritance
+rules, ''axis\_ref'' can be redefined for the field ''toce'' that is a 3D variable.
+\vspace{-30pt}
+Inherit (and overwrite, if needed) the attributes of a tag you are refering to.
+\subsubsection{Use of Groups}
+Groups 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''.
+\vspace{-20pt}
 \begin{alltt}  {{\scriptsize
 \begin{verbatim}
+   <field_definition>
+      <group id="grid_T" axis_ref="none" grid_ref="T_grid_variables">
+            <field id="sst"/>
+            <field id="sss"/>
+            <field id="toce" axis_ref="deptht"/>  <!-- overwrite axis def -->
+      </group>
+   </field_definition>
+   <field_group id="grid_T" grid_ref="grid_T_2D">
+    <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/>
+    <field id="sst"  long_name="sea surface temperature" unit="degC"                     />
+    <field id="sss"  long_name="sea surface salinity"    unit="psu"                      />
+    <field id="ssh"  long_name="sea surface height"      unit="m"                        />
+         ...
 \end{verbatim}
 }}\end{alltt}
+example 4, group of files: define a group of file with the attribute output\_freq equal to 432000 (5 days)
 \vspace{-30pt}
+Secondly, 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:
+\vspace{-20pt}
 \begin{alltt}  {{\scriptsize
 \begin{verbatim}
+   <file_definition>
+      <group id="5d" output_freq="432000">    <!-- 5d files -->
+         <file id="5d_grid_T" name="auto">   <!-- T grid file -->
+   <field_group id="groupU" >
+    <field field_ref="uoce"  />
+    <field field_ref="suoce" />
+    <field field_ref="utau"  />
+   </field_group>
+\end{verbatim}
+}}\end{alltt}
+that can be directly included in a file through the following syntax:
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <file id="myfile_U" output_freq="1d" />
+    <field_group group_ref="groupU"/>
+    <field field_ref="uocetr_eff"  />  <!-- add another field -->
+   </file>
+\end{verbatim}
+}}\end{alltt}
+\subsection{Detailed functionalities }
+The 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.
+\subsubsection{Define horizontal subdomains}
+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 {\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).
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <domain_group id="grid_T">
+    <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" />
+\end{verbatim}
+}}\end{alltt}
+The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. For example:
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <file id="myfile_vzoom" output_freq="1d" >
+      <field field_ref="toce" domain_ref="myzoom"/>
+   </file>
+\end{verbatim}
+}}\end{alltt}
+Moorings 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'' ...)
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <file id="myfile_vzoom" output_freq="1d" >
+      <field field_ref="toce" domain_ref="0n180wT"/>
+   </file>
+\end{verbatim}
+}}\end{alltt}
+Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if you use the ''multiple\_file'' type for your output files, you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat, \href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}). We are therefore advising to use the ''one\_file'' type in this case.
+\subsubsection{Define vertical zooms}
+Vertical zooms are defined through the attributs zoom\_begin and zoom\_end of the tag family axis. It must therefore be done in the axis part of the XML file. For example, in NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml, we provide the following example:
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" >
+      <axis id="deptht" />
+      <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" />
+\end{verbatim}
+}}\end{alltt}
+The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. For example:
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <file id="myfile_hzoom" output_freq="1d" >
+      <field field_ref="toce" axis_ref="deptht_myzoom"/>
+   </file>
+\end{verbatim}
+}}\end{alltt}
+\subsubsection{Control of the output file names}
+The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. for example:
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <file_group id="1d" output_freq="1d" name="myfile_1d" >
+      <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA"  -->
          ...
          </file>
          <file id="5d_grid_U" name="auto">   <!-- U grid file -->
+      </file>
+      <file id="myfileB" name_suffix="_BBB" > <!-- will create file "myfile_1d_BBB" -->
          ...
+         </file>
+      </group>
+   </file_definition>
+      </file>
+   </file_group>
 \end{verbatim}
 }}\end{alltt}
+\subsubsection{Control of the xml attributes from NEMO}
+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).
+Here is the list of these attributes: \\
+However it is often very convienent to define the file name with the name of the experiment, the output file frequency and the date of the beginning and the end of the simulation (which are informations stored either in the namelist or in the XML file). To do so, we added the following rule: if the id of the tag file is ''fileN''(where N = 1 to 99) or one of the predefined sections or moorings (see next subsection), the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by:\\
+\\
+\begin{tabular}{|p{4cm}|p{8cm}|}
+   \hline
+   \centering placeholder string & automatically  replaced by \\
+   \hline
+   \hline
+   \centering @expname@ &
+   the experiment name (from cn\_exp in the namelist) \\
+   \hline
+   \centering @freq@ &
+   output frequency (from attribute output\_freq) \\
+   \hline
+   \centering @startdate@  &
+   starting date of the simulation (from nn\_date0 in the restart or the namelist). \verb?yyyymmdd? format \\
+   \hline
+   \centering @startdatefull@  &
+   starting date of the simulation (from nn\_date0 in the restart or the namelist). \verb?yyyymmdd_hh:mm:ss? format \\
+   \hline
+   \centering @enddate@  &
+   ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \verb?yyyymmdd? format \\
+   \hline
+   \centering @enddatefull@  &
+   ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \verb?yyyymmdd_hh:mm:ss? format \\
+   \hline
+\end{tabular}\\
+\\
+\noindent For example,
+{{\scriptsize
+\begin{verbatim}
+   <file id="myfile_hzoom" name="myfile_@expname@_@startdate@_freq@freq@" output_freq="1d" >
+\end{verbatim}
+}}
+\noindent with the namelist:
+{{\scriptsize
+\begin{verbatim}
+   cn_exp      =  "ORCA2"
+   nn_date0    =  19891231
+   ln_rstart   = .false.
+\end{verbatim}
+}}
+\noindent will give the following file name radical:
+{{\scriptsize
+\begin{verbatim}
+   myfile_ORCA2_19891231_freq1d
+\end{verbatim}
+}}
+\subsubsection{Other controls of the xml attributes from NEMO}
+The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in iom.F90). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary).
+Here is the list of these attributes:\\
 \\
 \begin{tabular}{|l|c|c|c|}
 …
     \multicolumn{2}{|c|}{field\_definition} & freq\_op & \np{rn\_rdt} \\
    \hline
+    \multicolumn{2}{|c|}{SBC}                  & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_fsbc} \\
+   \hline
+h, 2h, 3h, 4h, 6h, 12h & \_grid\_T, \_grid\_U,  &  name & filename defined by   \\
+d, 3d, 5d                     & \_grid\_V, \_grid\_W, &            & a call to rou{dia\_nam}  \\
+m, 2m, 3m, 4m, 6m    & \_icemod, \_ptrc\_T,  &            & following NEMO \\
+y, 2y, 5y, 10y               &  \_diad\_T, \_scalar   &            & nomenclature \\
+    \multicolumn{2}{|c|}{SBC}               & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_fsbc}  \\
+   \hline
+    \multicolumn{2}{|c|}{ptrc\_T}           & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\
+   \hline
+    \multicolumn{2}{|c|}{diad\_T}           & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\
    \hline
     \multicolumn{2}{|c|}{EqT, EqU, EqW} & jbegin, ni,      & according to the grid    \\
     \multicolumn{2}{|c|}{                         } & name\_suffix &                                      \\
    \hline
     \multicolumn{2}{|c|}{TAO, RAMA and PIRATA moorings} & ibegin, jbegin,      & according to the grid    \\
+   \multicolumn{2}{|c|}{TAO, RAMA and PIRATA moorings} & zoom\_ibegin, zoom\_jbegin, & according to the grid    \\
     \multicolumn{2}{|c|}{                                                       } & name\_suffix &                                      \\
    \hline
 …
 \subsection{ Detailed functionalities }
+\subsection{XML reference tables}
 \subsubsection{Tag list}
+\begin{description}
+\item[context]: define the model using the xml file. Id is the only attribute accepted.
+Its value must be ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom. Child of simulation tag.
+\item[field]: define the field to be output. Accepted attributes are axis\_ref, description, enable,
+freq\_op, grid\_ref, id (if child of field\_definition), level, operation, name, ref (if child of file),
+unit, zoom\_ref. Child of field\_definition, file or group of fields tag.
+\item[field\_definition]: definition of the part of the xml file corresponding to the field definition.
+Accept the same attributes as field tag. Child of context tag.
+\item[group]: define a group of file or field. Accept the same attributes as file or field.
+\item[file]: define the output file's characteristics. Accepted attributes are description, enable,
+output\_freq, output\_level, id, name, name\_suffix. Child of file\_definition or group of files tag.
+\item[file\_definition]: definition of the part of the xml file corresponding to the file definition.
+Accept the same attributes as file tag. Child of context tag.
+\item[axis]: definition of the vertical axis. Accepted attributes are description, id, positive, size, unit.
+Child of axis\_definition tag.
+\item[axis\_definition]: definition of the part of the xml file corresponding to the vertical axis definition.
+Accept the same attributes as axis tag. Child of context tag
+\item[grid]: definition of the horizontal grid. Accepted attributes are description and id.
+Child of axis\_definition tag.
+\item[grid\_definition]: definition of the part of the xml file corresponding to the horizontal grid definition.
+Accept the same attributes as grid tag. Child of context tag
+\item[zoom]: definition of a subdomain of an horizontal grid. Accepted attributes are description, id,
+i/jbegin, ni/j. Child of grid tag.
+\end{description}
+\begin{longtable}{|p{2.2cm}|p{2.5cm}|p{3.5cm}|p{2.2cm}|p{1.6cm}|}
+   \hline
+   tag name &
+   description &
+   accepted attribute &
+   child of &
+   parent of \endhead
+   \hline
+   simulation &
+   this tag is the root tag which encapsulates all the content of the xml file &
+   none &
+   none &
+   context \\
+   \hline
+   context &
+   encapsulates parts of the xml file dedicated to different codes or different parts of a code &
+   id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin &
+   simulation &
+   all root tags: ... \_definition \\
+   \hline
+   \hline
+   field\_definition &
+   encapsulates the definition of all the fields that can potentially be outputted &
+   axis\_ref, default\_value, domain\_ref, enabled, grid\_ref, level, operation, prec, src &
+   context &
+   field or field\_group \\
+   \hline
+   field\_group &
+   encapsulates a group of fields &
+   axis\_ref, default\_value, domain\_ref, enabled, group\_ref, grid\_ref, id, level, operation, prec, src &
+   field\_definition, field\_group, file &
+   field or field\_group \\
+   \hline
+   field &
+   define a specific field &
+   axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref, id, level, long\_name, name, operation, prec, standard\_name, unit &
+   field\_definition, field\_group, file &
+   none \\
+   \hline
+   \hline
+   file\_definition &
+   encapsulates the definition of all the files that will be outputted &
+   enabled, min\_digits, name, name\_suffix, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src &
+   context &
+   file or file\_group \\
+   \hline
+   file\_group &
+   encapsulates a group of files that will be outputted &
+   enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src &
+   file\_definition, file\_group &
+   file or file\_group \\
+   \hline
+   file &
+   define the contents of a file to be outputted &
+   enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src &
+   file\_definition, file\_group &
+   field \\
+   \hline
+   axis\_definition &
+   define all the vertical axis potentially used by the variables &
+   src &
+   context &
+   axis\_group, axis \\
+   \hline
+   axis\_group &
+   encapsulates a group of vertical axis &
+   id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
+   axis\_definition, axis\_group &
+   axis\_group, axis \\
+   \hline
+   axis &
+   define a vertical axis &
+   id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
+   axis\_definition, axis\_group  &
+   none \\
+   \hline
+   \hline
+   domain\_\-definition &
+   define all the horizontal domains potentially used by the variables &
+   src &
+   context &
+   domain\_\-group, domain \\
+   \hline
+   domain\_group &
+   encapsulates a group of horizontal domains &
+   id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj &
+   domain\_\-definition, domain\_group &
+   domain\_\-group, domain \\
+   \hline
+   domain &
+   define an horizontal domain &
+   id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj &
+   domain\_\-definition, domain\_group &
+   none \\
+   \hline
+   \hline
+   grid\_definition &
+   define all the grid (association of a domain and/or an axis) potentially used by the variables &
+   src &
+   context &
+   grid\_group, grid \\
+   \hline
+   grid\_group &
+   encapsulates a group of grids &
+   id, domain\_ref, axis\_ref &
+   grid\_definition, grid\_group &
+   grid\_group, grid \\
+   \hline
+   grid &
+   define a grid &
+   id, domain\_ref, axis\_ref &
+   grid\_definition, grid\_group &
+   none \\
+   \hline
+\end{longtable}
 \subsubsection{Attributes list}
+Applied to a tag or a group of tags.
+% table to be added ?
+Another table, perhaps?
+%%%%
+Attribute
+Applied to?
+Definition
+Comment
+axis\_ref
+field
+String defining the vertical axis of the variable. It refers to the id of the vertical axis defined in the axis tag.
+Use ''non'' if the variable has no vertical axis
+%%%%%%
+\begin{description}
+\item[axis\_ref]: field attribute. String defining the vertical axis of the variable.
+It refers to the id of the vertical axis defined in the axis tag.
+Use ''none'' if the variable has no vertical axis
+\item[description]: this attribute can be applied to all tags but it is used only with the field tag.
+In this case, the value of description will be used to define, in the output netcdf file,
+the attributes long\_name and standard\_name of the variable.
+\item[enabled]: field and file attribute. Logical to switch on/off the output of a field or a file.
+\item[freq\_op]: field attribute (automatically defined, see part 1.4 (''control of the xml attributes'')).
+An integer defining the frequency in seconds at which NEMO is calling iom\_put for this variable.
+It corresponds to the model time step (rn\_rdt in the namelist) except for the variables computed
+at the frequency of the surface boundary condition (rn\_rdt ? nn\_fsbc in the namelist).
+\item[grid\_ref]: field attribute. String defining the horizontal grid of the variable.
+It refers to the id of the grid tag.
+\item[ibegin]: zoom attribute. Integer defining the zoom starting point along x direction.
+Automatically defined for TAO/RAMA/PIRATA moorings (see part 1.4).
+\item[id]: exists for all tag. This is a string defining the name to a specific tag that will be used
+later to refer to this tag. Tags of the same category must have different ids.
+\item[jbegin]: zoom attribute. Integer defining the zoom starting point along y direction.
+Automatically defined for TAO/RAMA/PIRATA moorings and equatorial section (see part 1.4).
+\item[level]: field attribute. Integer from 0 to 10 defining the output priority of a field.
+See output\_level attribute definition
+\item[operation]: field attribute. String defining the type of temporal operation to perform on a variable.
+Possible choices are ''ave(X)'' for temporal mean, ''inst(X)'' for instantaneous, ''t\_min(X)'' for temporal min
+and ''t\_max(X)'' for temporal max.
+\item[output\_freq]: file attribute. Integer defining the operation frequency in seconds.
+For example 86400 for daily mean.
+\item[output\_level]: file attribute. Integer from 0 to 10 defining the output priority of variables in a file:
+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.
+\item[positive]: axis attribute (always .FALSE.). Logical defining the vertical axis convention used
+in \NEMO (positive downward). Define the attribute positive of the variable in the netcdf output file.
+\item[prec]: field attribute. Integer defining the output precision.
+Not implemented, we always output real4 arrays.
+\item[name]: field or file attribute. String defining the name of a variable or a file.
+If the name of a file is undefined, its id is used as a name. 2 files must have different names.
+Files with specific ids will have their name automatically defined (see part 1.4).
+Note that is name will be automatically completed by the cpu number (if needed) and ''.nc''
+\item[name\_suffix]: file attribute. String defining a suffix to be inserted after the name
+and before the cpu number and the ''.nc'' termination. Files with specific ids have an
+automatic definition of their suffix (see part 1.4).
+\item[ni]: zoom attribute. Integer defining the zoom extent along x direction.
+Automatically defined for equatorial sections (see part 1.4).
+\item[nj]: zoom attribute. Integer defining the zoom extent along x direction.
+\item[ref]: field attribute. String referring to the id of the field we want to add in a file.
+\item[size]: axis attribute. use unknown...
+\item[unit]: field attribute. String defining the unit of a variable and the associated
+attribute in the netcdf output file.
+\item[zoom\_ref]: field attribute. String defining the subdomain of data on which
+the file should be written (to ouput data only in a limited area).
+It refers to the id of a zoom defined in the zoom tag.
+\end{description}
+\subsection{IO\_SERVER}
+\subsubsection{Attached or detached mode?}
+Iom\_put is based on the io\_server developed by Yann Meurdesoif from IPSL
+(see \href{http://forge.ipsl.jussieu.fr/ioserver/browser}{here} for the source code or
+see its copy in NEMOGCM/EXTERNAL directory).
+This server can be used in ''attached mode'' (as a library) or in ''detached mode''
+(as an external executable on n cpus). In attached mode, each cpu of NEMO will output
+its own subdomain. In detached mode, the io\_server will gather data from NEMO
+and output them split over n files with n the number of cpu dedicated to the io\_server.
+\subsubsection{Control the io\_server: the namelist file xmlio\_server.def}
+%
+%Again, a small table might be more readable?
+%Name
+%Type
+%Description
+%Comment
+%Using_server
+%Logical
+%Switch to use the server in attached or detached mode
+%(.TRUE. corresponding to detached mode).
+The control of the use of the io\_server is done through the namelist file of the io\_server
+called xmlio\_server.def.
+\textbf{using\_server}: logical, switch to use the server in attached or detached mode
+(.TRUE. corresponding to detached mode).
+\textbf{using\_oasis}: logical, set to .TRUE. if NEMO is used in coupled mode.
+\textbf{client\_id} = ''oceanx'' : character, used only in coupled mode.
+Specify the id used in OASIS to refer to NEMO. The same id must be used to refer to NEMO
+in the \$NBMODEL part of OASIS namcouple in the call of prim\_init\_comp\_proto in cpl\_oasis3f90
+\textbf{server\_id} = ''ionemo'' : character, used only in coupled mode.
+Specify the id used in OASIS to refer to the IO\_SERVER when used in detached mode.
+Use the same id to refer to the io\_server in the \$NBMODEL part of OASIS namcouple.
+\textbf{global\_mpi\_buffer\_size}: integer; define the size in Mb of the MPI buffer used by the io\_server.
+\subsubsection{Number of cpu used by the io\_server in detached mode}
+The number of cpu used by the io\_server is specified only when launching the model.
+Here is an example of 2 cpus for the io\_server and 6 cpu for opa using mpirun:
+\texttt{ -p 2 -e ./ioserver}
+\texttt{ -p 6 -e ./opa }
+\subsection{Practical issues}
+\subsubsection{Add your own outputs}
+It is very easy to add you own outputs with iom\_put. 4 points must be followed.
+\begin{description}
+\item[1-] in NEMO code, add a \\
+\texttt{      CALL iom\_put( 'identifier', array ) } \\
+where you want to output a 2D or 3D array.
+\item[2-] don't forget to add \\
+\texttt{   USE iom            ! I/O manager library }  \\
+in the list of used modules in the upper part of your module.
+\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.
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <field_definition>
+      ...
+      <field id="identifier" description="blabla" />
+      ...
+   </field_definition>
+\end{verbatim}
+}}\end{alltt}
+attributes axis\_ref and grid\_ref must be consistent with the size of the array to pass to iom\_put.
+if your array is computed within the surface module each nn\_fsbc time\_step,
+add the field definition within the group defined with the id ''SBC'': $<$group id=''SBC''...$>$
+\item[4-] add your field in one of the output files   \\
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+   <file id="file_1" .../>
+      ...
+      <field ref="identifier" />
+      ...
+   </file>
+\end{verbatim}
+}}\end{alltt}
+\end{description}
+\subsubsection{Several time axes in the output file}
+If your output file contains variables with different operations (see operation definition),
+IOIPSL will create one specific time axis for each operation. Note that inst(X) will have
+a time axis corresponding to the end each output period whereas all other operators
+will have a time axis centred in the middle of the output periods.
+\subsubsection{Error/bug messages from IOIPSL}
+If you get the following error in the standard output file:
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+FATAL ERROR FROM ROUTINE flio_dom_set
+ --> too many domains simultaneously defined
+ --> please unset useless domains
+ --> by calling flio_dom_unset
+\end{verbatim}
+}}\end{alltt}
+You must increase the value of dom\_max\_nb in fliocom.f90 (multiply it by 10 for example).
+If you mix, in the same file, variables with different freq\_op (see definition above),
+like for example variables from the surface module with other variables,
+IOIPSL will print in the standard output file warning messages saying there may be a bug.
+\vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+WARNING FROM ROUTINE histvar_seq
+ --> There were 10 errors in the learned sequence of variables
+ --> for file   4
+ --> This looks like a bug, please report it.
+\end{verbatim}
+}}\end{alltt}
+Don't worry, there is no bug, everything is properly working!
+ %    }      %end  \gmcomment
+\begin{longtable}{|p{2.2cm}|p{4cm}|p{3.8cm}|p{2cm}|}
+   \hline
+   attribute name &
+   description &
+   example &
+   accepted by \endhead
+   \hline
+   axis\_ref &
+   refers to the id of a vertical axis &
+   axis\_ref="deptht" &
+   field, grid families \\
+   \hline
+   enabled &
+   switch on/off the output of a field or a file &
+   enabled=".TRUE." &
+   field, file families \\
+   \hline
+   default\_value &
+   missing\_value definition &
+   default\_value="1.e20" &
+   field family \\
+   \hline
+   description &
+   just for information, not used &
+   description="ocean T grid variables" &
+   all tags \\
+   \hline
+   domain\_ref &
+   refers to the id of a domain &
+   domain\_ref="grid\_T" &
+   field or grid families \\
+   \hline
+   field\_ref &
+   id of the field we want to add in a file &
+   field\_ref="toce" &
+   field \\
+   \hline
+   grid\_ref &
+   refers to the id of a grid &
+   grid\_ref="grid\_T\_2D" &
+   field family \\
+   \hline
+   group\_ref &
+   refer to a group of variables &
+   group\_ref="mooring" &
+   field\_group \\
+   \hline
+   id &
+   allow to identify a tag &
+   id="nemo" &
+   accepted by all tags except simulation \\
+   \hline
+   level &
+   output priority of a field: 0 (high) to 10 (low)&
+   level="1" &
+   field family \\
+   \hline
+   long\_name &
+   define the long\_name attribute in the NetCDF file &
+   long\_name="Vertical T levels" &
+   field \\
+   \hline
+   min\_digits &
+   specify the minimum of digits used in the core number in the name of the NetCDF file &
+   min\_digits="4" &
+   file family \\
+   \hline
+   name &
+   name of a variable or a file. If the name of a file is undefined, its id is used as a name &
+   name="tos" &
+   field or file families \\
+   \hline
+   name\_suffix &
+   suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file &
+   name\_suffix="\_myzoom" &
+   file family \\
+   \hline
+   attribute name &
+   description &
+   example &
+   accepted by \\
+   \hline
+   \hline
+   operation &
+   type of temporal operation: average, accumulate, instantaneous, min, max and once &
+   operation="average" &
+   field family \\
+   \hline
+   output\_freq &
+   operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. &
+   output\_freq="1d12h" &
+   field family \\
+   \hline
+   output\_level &
+   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. &
+   output\_level="10"&
+   file family \\
+   \hline
+   positive &
+   convention used for the orientation of vertival axis (positive downward in \NEMO). &
+   positive="down" &
+   axis family \\
+   \hline
+   prec &
+   output precision: real 4 or real 8 &
+   prec="4" &
+   field family \\
+   \hline
+   split\_freq &
+   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.&
+   split\_freq="1mo" &
+   file family \\
+   \hline
+   split\_freq\-\_format &
+   date format used in the name of temporally split output files. Can be specified
+   using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s &
+   split\_freq\_format= "\%y\%mo\%d" &
+   file family \\
+   \hline
+   src &
+   allow to include a file &
+   src="./field\_def.xml" &
+   accepted by all tags except simulation \\
+   \hline
+   standard\_name &
+   define the standard\_name attribute in the NetCDF file &
+   standard\_name= "Eastward\_Sea\_Ice\_Transport" &
+   field \\
+   \hline
+   sync\_freq &
+   NetCDF file synchronization frequency (update of the time\_counter). units can be ts (timestep), y, mo, d, h, mi, s. &
+   sync\_freq="10d" &
+   file family \\
+   \hline
+   attribute name &
+   description &
+   example &
+   accepted by \\
+   \hline
+   \hline
+   time\_origin &
+   specify the origin of the time counter &
+   time\_origin="1900-01-01 00:00:00"&
+   context \\
+   \hline
+   type (1)&
+   specify if the output files are to be split spatially (multiple\_file) or not (one\_file) &
+   type="multiple\_file" &
+   file familly \\
+   \hline
+   type (2)&
+   define the type of a variable tag &
+   type="boolean" &
+   variable \\
+   \hline
+   unit &
+   unit of a variable or the vertical axis &
+   unit="m" &
+   field and axis families \\
+   \hline
+   zoom\_ibegin &
+   starting point along x direction of the zoom. Automatically defined for TAO/RAMA/PIRATA moorings &
+   zoom\_ibegin="1" &
+   domain family \\
+   \hline
+   zoom\_jbegin &
+   starting point along y direction of the zoom. Automatically defined for TAO/RAMA/PIRATA moorings &
+   zoom\_jbegin="1" &
+   domain family \\
+   \hline
+   zoom\_ni &
+   zoom extent along x direction &
+   zoom\_ni="1" &
+   domain family \\
+   \hline
+   zoom\_nj &
+   zoom extent along y direction &
+   zoom\_nj="1" &
+   domain family \\
+   \hline
+\end{longtable}
 …
 domain size in any dimension. The algorithm used is:
+\vspace{-20pt}
 \begin{alltt}  {{\scriptsize
 \begin{verbatim}

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/ARCH/arch-PW7_METO.fcm

-                      r3834
+                      r4258
+%NCDF_INC            -I/home/nwp/ofrd/share/netcdf-3.6.0-p1_ec/include
+%NCDF_LIB            -L /home/nwp/ofrd/share/netcdf-3.6.0-p1_ec/lib -lnetcdf
+%NCDF_INC            -I/home/nwp/nm/frrj/lib/MTOOLS/include
+%NCDF_LIB            -L/home/nwp/nm/frrj/lib/MTOOLS/lib -lnetcdf -lhdf5 -lhdf5_hl -lhdf5_fortran -lz
+%XIOS_ROOT           /home/cr/ocean/hadcv/xios_r445
 %FC                  mpxlf90_r
 %FCFLAGS             -qrealsize=8 -qextname -qsuffix=f=f90 -qarch=pwr7 -qtune=pwr7 -NS32768 -I/home/nwp/ofrd/share/netcdf-3.6.0-p1_ex/include -g -O3 -qnostrict
 %FFLAGS              -qrealsize=8 -qextname -qsuffix=f=f90 -qarch=pwr7 -qtune=pwr7 -NS32768 -I/home/nwp/ofrd/share/netcdf-3.6.0-p1_ex/include -g -O3 -qnostrict
 %LD                  mpxlf90_r
 %LDFLAGS             -L /home/nwp/ofrd/share/netcdf-3.6.0-p1_ec/lib -lnetcdf -L/projects/um1/lib -lsig -O3 -L MASS
+%FCFLAGS             -qrealsize=8 -qextname -qsuffix=f=f90 -qarch=pwr7 -qtune=pwr7 -NS32768 -I/home/nwp/nm/frrj/lib/MTOOLS/include -g -O3 -qnostrict
+%FFLAGS              -qrealsize=8 -qextname -qsuffix=f=f90 -qarch=pwr7 -qtune=pwr7 -NS32768 -I/home/nwp/nm/frrj/lib/MTOOLS/include -g -O3 -qnostrict
+%LD                  mpCC_r
+%LDFLAGS             -lxlf90 -L/home/nwp/nm/frrj/lib/MTOOLS/lib -lnetcdf -L/projects/um1/lib -lsig -O3 -L MASS
 %FPPFLAGS            -E -P -traditional -I/opt/ibmhpc/pecurrent/ppe.poe/include -I/usr/lpp/ppe.poe/include/thread64
 %AR                  ar
 %ARFLAGS             rs
 %MK                  gmake
 %USER_INC            %NCDF_INC
 %USER_LIB            %NCDF_LIB
+%USER_INC            %NCDF_INC -I%XIOS_ROOT/inc
+%USER_LIB            %NCDF_LIB -L%XIOS_ROOT/lib -lxios

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/AMM12/EXP00/iodef.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="10d" min_digits="4">
+      <file_group id="1ts" output_freq="1ts"  output_level="10" enabled=".TRUE."/> <!-- 1 time step files -->
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
       <file_group id="2h" output_freq="2h"  output_level="10" enabled=".TRUE."/> <!-- 2h files -->
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/GYRE/EXP00/iodef.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="one_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4">
+      <file_group id="1ts" output_freq="1ts"  output_level="10" enabled=".TRUE."/> <!-- 1 time step files -->
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
       <file_group id="2h" output_freq="2h"  output_level="10" enabled=".TRUE."/> <!-- 2h files -->
 …
       <file_group id="5d" output_freq="5d"  output_level="10" enabled=".TRUE.">  <!-- 5d files -->
         <file id="5d_grid_T" name="auto" description="ocean T grid variables" >
+   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
      <field field_ref="toce"         name="votemper"  />
      <field field_ref="soce"         name="vosaline"  />
 …
         </file>
         <file id="5d_grid_U" name="auto" description="ocean U grid variables" >
+   <file id="file2" name_suffix="_grid_U" description="ocean U grid variables" >
           <field field_ref="uoce"         name="vozocrtx"  />
           <field field_ref="utau"         name="sozotaux"  />
         </file>
         <file id="5d_grid_V" name="auto" description="ocean V grid variables" >
+   <file id="file3" name_suffix="_grid_V" description="ocean V grid variables" >
           <field field_ref="voce"         name="vomecrty"  />
           <field field_ref="vtau"         name="sometauy"  />
         </file>
         <file id="5d_grid_W" name="auto" description="ocean W grid variables" >
+   <file id="file4" name_suffix="_grid_W" description="ocean W grid variables" >
           <field field_ref="woce"         name="vovecrtz" />
           <field field_ref="avt"          name="votkeavt" />
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>
 …
      <variable id="buffer_server_factor_size" type="integer">2</variable>
      <variable id="info_level"                type="integer">0</variable>
      <variable id="using_server"              type="boolean">true</variable>
+     <variable id="using_server"              type="boolean">false</variable>
      <variable id="using_oasis"               type="boolean">false</variable>
      <variable id="oasis_codes_id"            type="string" >oceanx</variable>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/GYRE_BFM/EXP00/iodef.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="10d" min_digits="4">
+      <file_group id="1ts" output_freq="1ts"  output_level="10" enabled=".TRUE."/> <!-- 1 time step files -->
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
       <file_group id="2h" output_freq="2h"  output_level="10" enabled=".TRUE."/> <!-- 2h files -->
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/iodef.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="10d" min_digits="4">
+      <file_group id="1ts" output_freq="1ts"  output_level="10" enabled=".TRUE."/> <!-- 1 time step files -->
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
       <file_group id="2h" output_freq="2h"  output_level="10" enabled=".TRUE."/> <!-- 2h files -->
 …
       <file_group id="5d" output_freq="5d"  output_level="10" enabled=".TRUE.">  <!-- 5d files -->
         <file id="5d_grid_T" name="auto" description="ocean T grid variables" >
+        <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
      <field field_ref="toce"         name="votemper"  />
      <field field_ref="soce"         name="vosaline"  />
 …
         </file>
         <file id="5d_grid_U" name="auto" description="ocean U grid variables" >
+        <file id="file2" name_suffix="_grid_U" description="ocean U grid variables" >
           <field field_ref="uoce"         name="vozocrtx"  />
           <field field_ref="utau"         name="sozotaux"  />
         </file>
         <file id="5d_grid_V" name="auto" description="ocean V grid variables" >
+        <file id="file3" name_suffix="_grid_V" description="ocean V grid variables" >
           <field field_ref="voce"         name="vomecrty"  />
           <field field_ref="vtau"         name="sometauy"  />
         </file>
         <file id="5d_grid_W" name="auto" description="ocean W grid variables" >
+        <file id="file4" name_suffix="_grid_W" description="ocean W grid variables" >
           <field field_ref="woce"         name="vovecrtz" />
           <field field_ref="avt"          name="votkeavt" />
 …
         </file>
    <file id="5d_ptrc_T" name="auto" description="lobster sms variables" >
+   <file id="file5" name="_ptrc_T" description="lobster sms variables" >
           <field field_ref="DET"      />
           <field field_ref="ZOO"      />
 …
       <file_group id="1y"  output_freq="1y" output_level="10" enabled=".TRUE."> <!-- real yearly files -->
    <file id="1y_diad_T" name="auto" description="additional lobster diagnostics" >
+   <file id="file6" name_suffix="_diad_T" description="additional lobster diagnostics" >
           <field field_ref="FNO3PHY"   />
           <field field_ref="FNH4PHY"   />
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/1_namelist

-                      r3795
+                      r4258
    cn_exp      = "Agulhas" !  experience name
    nn_it000    =       1   !  first time step
    nn_itend    =   10950   !  last  time step
+   nn_itend    =     480   !  last  time step
    nn_date0    =  010101   !  date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1)
    nn_leapy    =       0   !  Leap year calendar (1) or not (0)
 …
    sn_tem  = 'data_1m_potential_temperature_nomask', -1,'votemper',  .true.  , .true., 'yearly'   , ' '      , ' '
    sn_sal  = 'data_1m_salinity_nomask'             , -1,'vosaline',  .true.  , .true., 'yearly'   , ''       , ' '
+   cn_dir        = './'      !  root directory for the location of the runoff files
+   ln_tsd_init   = .true.    !  Initialisation of ocean T & S with T &S input data (T) or not (F)
+   ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
 !!======================================================================

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef_ar5.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" output_level="10" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" output_level="10" sync_freq="2mo" min_digits="4">
       <!--
 +++++++++++++++++++++++++++++++++++++++++++++++   daily   ++++++++++++++++++++++++++++++++++++++++++++++++++
         -->
       <file_group id="1d" output_freq="1d"  enabled=".TRUE.">                      <!-- 1d files -->
    <file id="1d_grid_T" name="auto" name_suffix="_table2.2" >         <!-- grid T  -->
+   <file id="file1" name_suffix="_grid_T_table2.2" >         <!-- grid T  -->
      <field field_ref="sst"          name='tos'      long_name="sea_surface_temperature"                              level="2"                      />
      <field field_ref="sst2"         name='tossq'    long_name="square_of_sea_surface_temperature"                    level="2"                      />
 …
    <!--
 ..............................................    grid T   .................................................
+     -->
+   <file_group id="1m_grid_T" name="auto" >                                                        <!-- grid T -->
+     <file id="1m grid_T table 2.2" name_suffix="_table2.2" >
+       <field field_ref="botpres"      name="pbo"      long_name="sea_water_pressure_at_sea_floor"                               />
+       <!-- pso : sea_water_pressure_at_sea_water_surface = 0 -->
+       <field field_ref="ssh"          name="zos"      long_name="sea_surface_height_above_geoid"                                 />
+       <field field_ref="ssh2"         name="zossq"    long_name="square_of_sea_surface_height_above_geoid"             level="2" />
+       <!-- masscello : sea_water_mass_per_unit_area = cellthc*rau0                                          no time changes -->
+       <field field_ref="cellthc"      name="thkcello" long_name="cell_thickness"                                                 /> <!-- no time changes -->
+       <field field_ref="toce"         name="thetao"   long_name="sea_water_potential_temperature"                                />
+       <field field_ref="sst"          name="tos"      long_name="sea_surface_temperature"                              level="1" />
+       <field field_ref="sst2"         name="tossq"    long_name="square_of_sea_surface_temperature"                    level="2" />
+       <field field_ref="soce"         name="so"       long_name="sea_water_salinity"                                             />
+       <field field_ref="sss"          name="sos"      long_name="sea_surface_salinity"                                 level="1" />
+       <field field_ref="rhop"         name="rhopoto"  long_name="sea_water_potential_density"                          level="2" />
+       <!-- no agessc : sea_water_age_since_surface_contact -->
+       <!-- no cfc11  : moles_per_unit_mass_of_cfc11_in_sea_water -->
+       <!-- msftbarot : ocean_barotropic_mass_streamfunction : offline -->
+       <!-- mlotst    :           ocean_mixed_layer_thickness_defined_by_sigma_t : must be done offline -->
+       <!-- mlotstsq  : square_of_ocean_mixed_layer_thickness_defined_by_sigma_t : must be done offline -->
+       <field field_ref="mldkz5"       name='omlmax'   long_name="ocean_mixed_layer_thickness_defined_by_mixing_scheme" level="2" operation="maximum" />
+     </file>
+     <file id="1m grid_T table 2.5" name_suffix="_table2.5" >
+       <field field_ref="rain"         name="pr"       long_name="rainfall_flux"                                           level="1" />
+       <field field_ref="snow_ao_cea"  name="prsn"     long_name="snowfall_flux"                                           level="1" />
+       <field field_ref="evap_ao_cea"  name="evs"      long_name="water_evaporation_flux"                                  level="1" />
+       <field field_ref="runoffs"      name="friver"   long_name="water_flux_into_sea_water_from_rivers"                   level="1" />
+       <field field_ref="calving"      name="ficeberg" long_name="water_flux_into_sea_water_from_icebergs"                 level="1" />
+       <field field_ref="isnwmlt_cea"  name="fsitherm" long_name="water_flux_into_sea_water_due_to_sea_ice_thermodynamics" level="1" />
+       <field field_ref="empmr"        name="wfo"      long_name="water_flux_into_sea_water"                               level="1" />
+       <!-- wfonocorr : water_flux_into_sea_water_without_flux_correction : emp - erp -->
+       <field field_ref="erp"          name="wfcorr"   long_name="water_flux_correction"                                   level="1" /> <!-- usually = 0 -->
+     </file>
+     <file id="1m grid_T table 2.6" name_suffix="_table2.6" >
+       <!-- vsfpr    : virtual_salt_flux_into_sea_water_due_to_rainfall    = 0 -->
+       <!-- vsfevap  : virtual_salt_flux_into_sea_water_due_to_evaporation = 0 -->
+       <!-- vsfriver : virtual_salt_flux_into_sea_water_from_rivers        = 0 -->
+       <field field_ref="fsal_virt_cea" name="vsfsit" long_name="virtual_salt_flux_into_sea_water_due_to_sea_ice_thermodynamics" level="1" />
+       <!-- vsf      : virtual_salt_flux_into_sea_water = fsal_virtual + fsal_real -->
+       <!-- wfcorr   : virtual_salt_flux_correction                        = 0 -->
+       <field field_ref="fsal_virt_cea" name="sfdsi"  long_name="downward_sea_ice_basal_salt_flux"                               level="1" />
+       <!-- sfriver  : salt_flux_into_sea_water_from_rivers                = 0 -->
+     </file>
+     <file id="1m grid_T table 2.7" name_suffix="_table2.7" >
+       <!-- hfgeou : upward_geothermal_heat_flux_at_sea_floor : cte, see nambbc and trabbc.F90 -->
+       <field field_ref="hflx_rain_cea" name="hfrainds"    long_name="temperature_flux_due_to_rainfall_expressed_as_heat_flux_into_sea_water"      level="1" />
+       <field field_ref="hflx_evap_cea" name="hfevapds"    long_name="temperature_flux_due_to_evaporation_expressed_as_heat_flux_out_of_sea_water" level="1" />
+       <field field_ref="hflx_rnf_cea"  name="hfrunoffds"  long_name="temperature_flux_due_to_runoff_expressed_as_heat_flux_into_sea_water"        level="1" />
+       <field field_ref="hflx_snow_cea" name="hfsnthermds" long_name="heat_flux_into_sea_water_due_to_snow_thermodynamics"                         level="1" />
+       <field field_ref="hflx_ice_cea"  name="hfsithermds" long_name="heat_flux_into_sea_water_due_to_sea_ice_thermodynamics"                      level="1" />
+       <field field_ref="hflx_cal_cea"  name="hfibthermds" long_name="heat_flux_into_sea_water_due_to_iceberg_thermodynamics"                      level="1" />
+       <!-- rlds   : surface_net_downward_longwave_flux : not available -->
+       <!-- hfls   : surface_downward_latent_heat_flux  : not available -->
+       <!-- hfss   : surface_downward_sensible_heat_flux: not available -->
+       <field field_ref="qns"           name="nshfls"      long_name="surface_net_downward_non_solar_flux"                                         level="1" />
+       <field field_ref="qsr"           name="rsntds"      long_name="surface_net_downward_shortwave_flux"                                         level="1" />
+       <field field_ref="qsr3d"         name="rsds"        long_name="downwelling_shortwave_flux_in_sea_water"                                     level="1" />
+       <field field_ref="qrp"           name="hfcorr"      long_name="heat_flux_correction"                                                        level="1" />
+     </file>
+   </file_group>
+     -->
+   <file id="file2" name_suffix="_grid_T_table2.2" >
+     <field field_ref="botpres"      name="pbo"      long_name="sea_water_pressure_at_sea_floor"                               />
+     <!-- pso : sea_water_pressure_at_sea_water_surface = 0 -->
+     <field field_ref="ssh"          name="zos"      long_name="sea_surface_height_above_geoid"                                 />
+     <field field_ref="ssh2"         name="zossq"    long_name="square_of_sea_surface_height_above_geoid"             level="2" />
+     <!-- masscello : sea_water_mass_per_unit_area = cellthc*rau0                                          no time changes -->
+     <field field_ref="cellthc"      name="thkcello" long_name="cell_thickness"                                                 /> <!-- no time changes -->
+     <field field_ref="toce"         name="thetao"   long_name="sea_water_potential_temperature"                                />
+     <field field_ref="sst"          name="tos"      long_name="sea_surface_temperature"                              level="1" />
+     <field field_ref="sst2"         name="tossq"    long_name="square_of_sea_surface_temperature"                    level="2" />
+     <field field_ref="soce"         name="so"       long_name="sea_water_salinity"                                             />
+     <field field_ref="sss"          name="sos"      long_name="sea_surface_salinity"                                 level="1" />
+     <field field_ref="rhop"         name="rhopoto"  long_name="sea_water_potential_density"                          level="2" />
+     <!-- no agessc : sea_water_age_since_surface_contact -->
+     <!-- no cfc11  : moles_per_unit_mass_of_cfc11_in_sea_water -->
+     <!-- msftbarot : ocean_barotropic_mass_streamfunction : offline -->
+     <!-- mlotst    :           ocean_mixed_layer_thickness_defined_by_sigma_t : must be done offline -->
+     <!-- mlotstsq  : square_of_ocean_mixed_layer_thickness_defined_by_sigma_t : must be done offline -->
+     <field field_ref="mldkz5"       name='omlmax'   long_name="ocean_mixed_layer_thickness_defined_by_mixing_scheme" level="2" operation="maximum" />
+   </file>
+   <file id="file3" name_suffix="_grid_T_table2.5" >
+     <field field_ref="rain"         name="pr"       long_name="rainfall_flux"                                           level="1" />
+     <field field_ref="snow_ao_cea"  name="prsn"     long_name="snowfall_flux"                                           level="1" />
+     <field field_ref="evap_ao_cea"  name="evs"      long_name="water_evaporation_flux"                                  level="1" />
+     <field field_ref="runoffs"      name="friver"   long_name="water_flux_into_sea_water_from_rivers"                   level="1" />
+     <field field_ref="calving"      name="ficeberg" long_name="water_flux_into_sea_water_from_icebergs"                 level="1" />
+     <field field_ref="isnwmlt_cea"  name="fsitherm" long_name="water_flux_into_sea_water_due_to_sea_ice_thermodynamics" level="1" />
+     <field field_ref="empmr"        name="wfo"      long_name="water_flux_into_sea_water"                               level="1" />
+     <!-- wfonocorr : water_flux_into_sea_water_without_flux_correction : emp - erp -->
+     <field field_ref="erp"          name="wfcorr"   long_name="water_flux_correction"                                   level="1" /> <!-- usually = 0 -->
+   </file>
+   <file id="file4" name_suffix="_grid_T_table2.6" >
+     <!-- vsfpr    : virtual_salt_flux_into_sea_water_due_to_rainfall    = 0 -->
+     <!-- vsfevap  : virtual_salt_flux_into_sea_water_due_to_evaporation = 0 -->
+     <!-- vsfriver : virtual_salt_flux_into_sea_water_from_rivers        = 0 -->
+     <field field_ref="fsal_virt_cea" name="vsfsit" long_name="virtual_salt_flux_into_sea_water_due_to_sea_ice_thermodynamics" level="1" />
+     <!-- vsf      : virtual_salt_flux_into_sea_water = fsal_virtual + fsal_real -->
+     <!-- wfcorr   : virtual_salt_flux_correction                        = 0 -->
+     <field field_ref="fsal_virt_cea" name="sfdsi"  long_name="downward_sea_ice_basal_salt_flux"                               level="1" />
+     <!-- sfriver  : salt_flux_into_sea_water_from_rivers                = 0 -->
+   </file>
+   <file id="file5" name_suffix="_grid_T_table2.7" >
+     <!-- hfgeou : upward_geothermal_heat_flux_at_sea_floor : cte, see nambbc and trabbc.F90 -->
+     <field field_ref="hflx_rain_cea" name="hfrainds"    long_name="temperature_flux_due_to_rainfall_expressed_as_heat_flux_into_sea_water"      level="1" />
+     <field field_ref="hflx_evap_cea" name="hfevapds"    long_name="temperature_flux_due_to_evaporation_expressed_as_heat_flux_out_of_sea_water" level="1" />
+     <field field_ref="hflx_rnf_cea"  name="hfrunoffds"  long_name="temperature_flux_due_to_runoff_expressed_as_heat_flux_into_sea_water"        level="1" />
+     <field field_ref="hflx_snow_cea" name="hfsnthermds" long_name="heat_flux_into_sea_water_due_to_snow_thermodynamics"                         level="1" />
+     <field field_ref="hflx_ice_cea"  name="hfsithermds" long_name="heat_flux_into_sea_water_due_to_sea_ice_thermodynamics"                      level="1" />
+     <field field_ref="hflx_cal_cea"  name="hfibthermds" long_name="heat_flux_into_sea_water_due_to_iceberg_thermodynamics"                      level="1" />
+     <!-- rlds   : surface_net_downward_longwave_flux : not available -->
+     <!-- hfls   : surface_downward_latent_heat_flux  : not available -->
+     <!-- hfss   : surface_downward_sensible_heat_flux: not available -->
+     <field field_ref="qns"           name="nshfls"      long_name="surface_net_downward_non_solar_flux"                                         level="1" />
+     <field field_ref="qsr"           name="rsntds"      long_name="surface_net_downward_shortwave_flux"                                         level="1" />
+     <field field_ref="qsr3d"         name="rsds"        long_name="downwelling_shortwave_flux_in_sea_water"                                     level="1" />
+     <field field_ref="qrp"           name="hfcorr"      long_name="heat_flux_correction"                                                        level="1" />
+   </file>
    <!--
 ..............................................    grid U   .................................................
+     -->
+   <file_group id="1m_grid_U" name="auto" >                                                        <!-- grid U -->
+     <file id="1m grid_U table 2.3" name_suffix="_table2.3" >
+       <field field_ref="uoce"         name="uo"      long_name="sea_water_x_velocity"                                       />
+       <field field_ref="u_masstr"     name="umo"     long_name="ocean_mass_x_transport"                           level="1" />
+       <field field_ref="u_heattr"     name="hfx"     long_name="ocean_heat_x_transport"                           level="1" />
+       <field field_ref="ueiv_heattr"  name="hfxba"   long_name="ocean_heat_x_transport_due_to_bolus_advection"    level="2" />
+       <field field_ref="udiff_heattr" name="hfxdiff" long_name="ocean_heat_x_transport_due_to_diffusion"          level="2" />
+     </file>
+     <file id="1m grid_U table 2.8" name_suffix="_table2.8" >
+       <field field_ref="utau"         name="tauuo" long_name="surface_downward_x_stress"                          level="1" />
+       <!-- tauucorr : surface_downward_x_stress_correction = 0 -->
+     </file>
+   </file_group>
+   -->
+   <file id="file6" name_suffix="_grid_U_table2.3" >
+     <field field_ref="uoce"         name="uo"      long_name="sea_water_x_velocity"                                       />
+     <field field_ref="u_masstr"     name="umo"     long_name="ocean_mass_x_transport"                           level="1" />
+     <field field_ref="u_heattr"     name="hfx"     long_name="ocean_heat_x_transport"                           level="1" />
+     <field field_ref="ueiv_heattr"  name="hfxba"   long_name="ocean_heat_x_transport_due_to_bolus_advection"    level="2" />
+     <field field_ref="udiff_heattr" name="hfxdiff" long_name="ocean_heat_x_transport_due_to_diffusion"          level="2" />
+   </file>
+   <file id="file7" name_suffix="_grid_U_table2.8" >
+     <field field_ref="utau"         name="tauuo" long_name="surface_downward_x_stress"                          level="1" />
+     <!-- tauucorr : surface_downward_x_stress_correction = 0 -->
+   </file>
    <!--
 ..............................................    grid V   .................................................
+     -->
+   <file_group id="1m_grid_V" name="auto" >                                                        <!-- grid V -->
+     <file id="1m grid_V table 2.3" name_suffix="_table2.3" >
+       <field field_ref="voce"         name="vo"      long_name="sea_water_y_velocity"                                       />
+       <field field_ref="v_masstr"     name="vmo"     long_name="ocean_mass_y_transport"                           level="1" />
+       <field field_ref="v_heattr"     name="hfy"     long_name="ocean_heat_y_transport"                           level="1" />
+       <field field_ref="veiv_heattr"  name="hfyba"   long_name="ocean_heat_y_transport_due_to_bolus_advection"    level="2" />
+       <field field_ref="vdiff_heattr" name="hfydiff" long_name="ocean_heat_y_transport_due_to_diffusion"          level="2" />
+     </file>
+     <file id="1m grid_V table 2.8" name_suffix="_table2.8" >
+       <field field_ref="vtau"         name="tauvo" long_name="surface_downward_y_stress"                          level="1" />
+       <!-- tauvcorr : surface_downward_y_stress_correction = 0 -->
+     </file>
+   </file_group>
+   -->
+   <file id="file8" name_suffix="_grid_V_table2.3" >
+     <field field_ref="voce"         name="vo"      long_name="sea_water_y_velocity"                                       />
+     <field field_ref="v_masstr"     name="vmo"     long_name="ocean_mass_y_transport"                           level="1" />
+     <field field_ref="v_heattr"     name="hfy"     long_name="ocean_heat_y_transport"                           level="1" />
+     <field field_ref="veiv_heattr"  name="hfyba"   long_name="ocean_heat_y_transport_due_to_bolus_advection"    level="2" />
+     <field field_ref="vdiff_heattr" name="hfydiff" long_name="ocean_heat_y_transport_due_to_diffusion"          level="2" />
+   </file>
+   <file id="file9" name_suffix="_grid_V_table2.8" >
+     <field field_ref="vtau"         name="tauvo" long_name="surface_downward_y_stress"                          level="1" />
+     <!-- tauvcorr : surface_downward_y_stress_correction = 0 -->
+   </file>
    <!--
 ..............................................    grid W   .................................................
+     -->
+   <file_group id="1m_grid_W" name="auto" >                                                        <!-- grid W -->
+     <file id="1m grid_W table 2.3" name_suffix="_table2.3" >
+       <field field_ref="w_masstr"   name="wmo"   long_name="upward_ocean_mass_transport"                                    />
+       <field field_ref="w_masstr2"  name="wmosq" long_name="square_pf_upward_ocean_mass_transport"                          />
+     </file>
+     <file id="1m grid_W table 2.9" name_suffix="_table2.9" >
+       <field field_ref="avt"     name="difvho"   long_name="ocean_vertical_heat_diffusivity"                  level="2" />
+       <field field_ref="avs"     name="difvso"   long_name="ocean_vertical_salt_diffusivity"                  level="2" />
+       <!-- difvtrbo : ocean_vertical_tracer_diffusivity_due_to_background : cte with time, see namelist parameters nn_avb and  nn_havtb -->
+       <field field_ref="av_tide" name="difvtrto" long_name="ocean_vertical_tracer_diffusivity_due_to_tides"   level="2" />
+       <!-- tnpeo     : tendency_of_ocean_potential_energy_content                   : not available -->
+       <!-- tnpeot    : tendency_of_ocean_potential_energy_content_due_to_tides      : not available -->
+       <!-- tnpeotb   : tendency_of_ocean_potential_energy_content_due_to_background : not available -->
+       <field field_ref="avm"     name="difvmo"   long_name="ocean_vertical_momentum_diffusivity"              level="2" />
+       <!-- difvmbo : ocean_vertical_momentum_diffusivity_due_to_background : cte with time, see namelist parameters nn_avb -->
+       <field field_ref="av_tide" name="difvmto"  long_name="ocean_vertical_momentum_diffusivity_due_to_tides" level="2" /> <!-- same as tracer -->
+       <!-- difvmfdo : ocean_vertical_momentum_diffusivity_due_to_form_drag : ??? -->
+       <!-- dispkevfo : ocean_kinetic_energy_dissipation_per_unit_area_due_to_vertical_friction : not available -->
+     </file>
+     <file id="1m grid_W table 2.10" name_suffix="_table2.10" >
+       <!-- if ln_traldf_lap    =  .true. -->
+       <field field_ref="aht2d_eiv" name="diftrblo" long_name="ocean_tracer_bolus_laplacian_diffusivity"                     level="2" />
+       <!-- diftrelo : ocean_tracer_epineutral_laplacian_diffusivity : cte with time, see ln_traldf_iso -->
+       <!-- diftrxylo : ocean_tracer_xy_laplacian_diffusivity : cte with time -->
+       <!-- if ln_traldf_bilap  =  .true. -->
+       <!-- field field_ref="diftrbbo" name="aht2d_eiv" long_name="ocean_tracer_bolus_biharmonic_diffusivity"                    level="2" /-->
+       <!-- diftrebo : ocean_tracer_epineutral_biharmonic_diffusivity : cte with time, see ln_traldf_iso -->
+       <!-- diftrxybo : ocean_tracer_xy_biharmonic_diffusivity : cte with time -->
+       <!-- tnkebto : tendency_of_ocean_eddy_kinetic_energy_content_due_to_bolus_transport : not available -->
+       <!-- difmxylo : ocean_momentum_xy_laplacian_diffusivity : cte with time, see ln_dynldf_lap -->
+       <!-- difmxybo : ocean_momentum_xy_biharmonic_diffusivity : cte with time, see ln_dynldf_bilap -->
+       <!-- dispkexyfo : ocean_kinetic_energy_dissipation_per_unit_area_due_to_xy_friction : not available -->
+     </file>
+   </file_group>
+   -->
+   <file id="file10" name_suffix="_grid_W_table2.3" >
+     <field field_ref="w_masstr"   name="wmo"   long_name="upward_ocean_mass_transport"                                    />
+     <field field_ref="w_masstr2"  name="wmosq" long_name="square_pf_upward_ocean_mass_transport"                          />
+   </file>
+   <file id="file11" name_suffix="_grid_W_table2.9" >
+     <field field_ref="avt"     name="difvho"   long_name="ocean_vertical_heat_diffusivity"                  level="2" />
+     <field field_ref="avs"     name="difvso"   long_name="ocean_vertical_salt_diffusivity"                  level="2" />
+     <!-- difvtrbo : ocean_vertical_tracer_diffusivity_due_to_background : cte with time, see namelist parameters nn_avb and  nn_havtb -->
+     <field field_ref="av_tide" name="difvtrto" long_name="ocean_vertical_tracer_diffusivity_due_to_tides"   level="2" />
+     <!-- tnpeo     : tendency_of_ocean_potential_energy_content                   : not available -->
+     <!-- tnpeot    : tendency_of_ocean_potential_energy_content_due_to_tides      : not available -->
+     <!-- tnpeotb   : tendency_of_ocean_potential_energy_content_due_to_background : not available -->
+     <field field_ref="avm"     name="difvmo"   long_name="ocean_vertical_momentum_diffusivity"              level="2" />
+     <!-- difvmbo : ocean_vertical_momentum_diffusivity_due_to_background : cte with time, see namelist parameters nn_avb -->
+     <field field_ref="av_tide" name="difvmto"  long_name="ocean_vertical_momentum_diffusivity_due_to_tides" level="2" /> <!-- same as tracer -->
+     <!-- difvmfdo : ocean_vertical_momentum_diffusivity_due_to_form_drag : ??? -->
+     <!-- dispkevfo : ocean_kinetic_energy_dissipation_per_unit_area_due_to_vertical_friction : not available -->
+   </file>
+   <file id="file12" name_suffix="_grid_W_table2.10" >
+     <!-- if ln_traldf_lap    =  .true. -->
+     <field field_ref="aht2d_eiv" name="diftrblo" long_name="ocean_tracer_bolus_laplacian_diffusivity"                     level="2" />
+     <!-- diftrelo : ocean_tracer_epineutral_laplacian_diffusivity : cte with time, see ln_traldf_iso -->
+     <!-- diftrxylo : ocean_tracer_xy_laplacian_diffusivity : cte with time -->
+     <!-- if ln_traldf_bilap  =  .true. -->
+     <!-- field field_ref="diftrbbo" name="aht2d_eiv" long_name="ocean_tracer_bolus_biharmonic_diffusivity"                    level="2" /-->
+     <!-- diftrebo : ocean_tracer_epineutral_biharmonic_diffusivity : cte with time, see ln_traldf_iso -->
+     <!-- diftrxybo : ocean_tracer_xy_biharmonic_diffusivity : cte with time -->
+     <!-- tnkebto : tendency_of_ocean_eddy_kinetic_energy_content_due_to_bolus_transport : not available -->
+     <!-- difmxylo : ocean_momentum_xy_laplacian_diffusivity : cte with time, see ln_dynldf_lap -->
+     <!-- difmxybo : ocean_momentum_xy_biharmonic_diffusivity : cte with time, see ln_dynldf_bilap -->
+     <!-- dispkexyfo : ocean_kinetic_energy_dissipation_per_unit_area_due_to_xy_friction : not available -->
+   </file>
    <!--
 ..............................................    scalar   .................................................
      -->
    <file id="1m_scalar" name="auto" name_suffix="_table2.2" >         <!-- scalar -->
+   -->
+   <file id="file13" name_suffix="_scalar_table2.2" >         <!-- scalar -->
      <field field_ref="masstot"    name="masso"    long_name="sea_water_mass"                                />
      <field field_ref="voltot"     name="volo"     long_name="sea_water_volume"                              />
 …
    <!--
 ..............................................    icemod   .................................................
      -->
    <file id="1m_icemod" name="auto" name_suffix="_table2.2" >         <!-- scalar -->
+   -->
+   <file id="file14" name_suffix="_icemod_table2.2" >         <!-- scalar -->
      <field field_ref="ice_pres"                     />
      <field field_ref="ice_cover"    name="sic"        long_name="sea_ice_area_fraction"                            />
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef_default.xml

Property svn:mime-type deleted
Property svn:keywords set to Id

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="10d" min_digits="4">
+      <file_group id="1ts" output_freq="1ts"  output_level="10" enabled=".TRUE."/> <!-- 1 time step files -->
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
       <file_group id="2h" output_freq="2h"  output_level="10" enabled=".TRUE."/> <!-- 2h files -->
 …
       <file_group id="1d" output_freq="1d"  output_level="10" enabled=".TRUE."> <!-- 1d files -->
    <file id="1d_grid_T" name="auto" description="ocean T grid variables" >
+   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
      <field field_ref="sst"          name="tos"      long_name="sea_surface_temperature"                       />
      <field field_ref="sss"          name="sos"      long_name="sea_surface_salinity"                          />
 …
    </file>
    <file id="1d_grid_U" name="auto" description="ocean U grid variables" >
+   <file id="file2" name_suffix="_grid_U" description="ocean U grid variables" >
      <field field_ref="suoce"        name="uos"     long_name="sea_surface_x_velocity"    />
    </file>
    <file id="1d_grid_V" name="auto" description="ocean V grid variables" >
+   <file id="file3" name_suffix="_grid_V" description="ocean V grid variables" >
      <field field_ref="svoce"        name="vos"     long_name="sea_surface_y_velocity"    />
    </file>
       </file_group>
       <file_group id="3d" output_freq="3d"  output_level="10" enabled=".TRUE."/> <!-- 3d files -->
       <file_group id="5d" output_freq="5d"  output_level="10" enabled=".TRUE.">  <!-- 5d files -->
    <file id="5d_grid_T" name="auto" description="ocean T grid variables" >
+   <file id="file4" name_suffix="_grid_T" description="ocean T grid variables" >
      <field field_ref="toce"         name="thetao"   long_name="sea_water_potential_temperature"               />
      <field field_ref="soce"         name="so"       long_name="sea_water_salinity"                            />
 …
    </file>
    <file id="5d_grid_U" name="auto" description="ocean U grid variables" >
+   <file id="file5" name_suffix="_grid_U" description="ocean U grid variables" >
      <field field_ref="uoce"         name="uo"      long_name="sea_water_x_velocity"      />
      <field field_ref="suoce"        name="uos"     long_name="sea_surface_x_velocity"    />
 …
    </file>
    <file id="5d_grid_V" name="auto" description="ocean V grid variables" >
+   <file id="file6" name_suffix="_grid_V" description="ocean V grid variables" >
      <field field_ref="voce"         name="vo"      long_name="sea_water_y_velocity"      />
      <field field_ref="svoce"        name="vos"     long_name="sea_surface_y_velocity"    />
 …
    </file>
    <file id="5d_grid_W" name="auto" description="ocean W grid variables" >
+   <file id="file7" name_suffix="_grid_W" description="ocean W grid variables" >
      <field field_ref="woce"         name="wo"      long_name="ocean vertical velocity"         />
      <field field_ref="avt"          name="difvho"  long_name="ocean_vertical_heat_diffusivity" />
    </file>
    <file id="5d_icemod" name="auto" description="ice variables" >
+   <file id="file8" name_suffix="_icemod" description="ice variables" >
      <field field_ref="ice_pres"                     />
      <field field_ref="snowthic_cea" name="snd"     long_name="surface_snow_thickness"   />
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef_demo.xml

Property svn:mime-type deleted
Property svn:keywords set to Id

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4">
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."> <!-- 1h files -->
    <file id="1h_grid_T" name="auto" description="ocean T grid variables" >
+   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
      <field field_ref="sst"  />
      <field field_ref="qsr"  />
 …
       <file_group id="1d" output_freq="1d"  output_level="10" enabled=".TRUE."> <!-- 1d files -->
+   <file_group id="1d_grid_T" name="auto" description="ocean T grid variables" >
+     <!-- example of "hand made" zoom  -->
+     <file id="blabla_1" name_suffix="_myzoom" >
+       <!-- group of variables sharing the same zoom. see zoom definition in domain_def.xml -->
+       <field_group id="blabla" domain_ref="myzoom" >
+         <field field_ref="toce" />
+         <field field_ref="soce" />
+       </field_group>
+     </file>
+     <!-- mooring: automatic definition of the file name suffix based on id="0n180wT"  -->
+     <!-- include a group of variables. see field_def.xml for mooring variables definition  -->
+     <file id="0n180wT" name_suffix="auto" >
+         <field_group group_ref="mooring"/>
+     </file>
+     <!-- Equatorial section: automatic definition of the file name suffix based on id="EqT" -->
+     <!-- Zoom over vertical axis. def of axis_ref in the axis_definition bellow -->
+     <file id="EqT" name_suffix="auto" >
+       <field_group id="EqT" domain_ref="EqT" >
+         <field field_ref="toce" name="votemper" axis_ref="deptht_zoom"  />
+       </field_group>
+     </file>
+     <!-- global file with different operations on data   -->
+     <file id="blabla_2" >
+       <field field_ref="toce"   default_value="-10" />    <!-- redefine the missing value -->
+       <field field_ref="sst"    name="sstmooring1" domain_ref="0n180wT"  />   <!-- include a mooring -->
+       <field field_ref="sst"    name="sst_1d_ave"  />                         <!-- mean -->
+       <field field_ref="sst"    name="sst_1d_inst" operation="instant" />     <!-- instant value -->
+       <field field_ref="sst"    name="sst_1d_max"  operation="maximum" />     <!-- max -->
+       <field field_ref="suoce"  />   <!-- include a U-grid variable in the list -->
+     </file>
+   </file_group>
+   <!-- example of "hand made" zoom  -->
+   <file id="file2" name_suffix="_grid_T_myzoom" >
+     <!-- group of variables sharing the same zoom. see zoom definition in domain_def.xml -->
+     <field_group id="blabla" domain_ref="myzoom" >
+       <field field_ref="toce" />
+       <field field_ref="soce" />
+     </field_group>
+   </file>
+   <!-- mooring: automatic definition of the file name suffix based on id="0n180wT"  -->
+   <!-- include a group of variables. see field_def.xml for mooring variables definition  -->
+   <file id="0n180wT">
+     <field_group group_ref="mooring" domain_ref="0n180wT" />
+   </file>
+   <!-- Equatorial section: automatic definition of the file name suffix based on id="EqT" -->
+   <!-- Zoom over vertical axis. def of axis_ref in the axis_definition bellow -->
+   <file id="EqT" >
+     <field_group id="EqT" domain_ref="EqT" >
+       <field field_ref="toce" name="votemper" axis_ref="deptht_myzoom"  />
+       <field field_ref="sss" />
+     </field_group>
+   </file>
+   <!-- global file with different operations on data   -->
+   <file id="file3" >
+     <field field_ref="toce"   default_value="-10" />    <!-- redefine the missing value -->
+     <field field_ref="sst"    name="sstmooring1" domain_ref="0n180wT"  />   <!-- include a mooring -->
+     <field field_ref="sst"    name="sst_1d_ave"  />                         <!-- mean -->
+     <field field_ref="sst"    name="sst_1d_inst" operation="instant" />     <!-- instant value -->
+     <field field_ref="sst"    name="sst_1d_max"  operation="maximum" />     <!-- max -->
+     <field field_ref="suoce"  />   <!-- include a U-grid variable in the list -->
+   </file>
       </file_group>
    </file_definition>
+    </file_definition>
     <!--
 …
      <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" >
        <axis id="deptht" />
        <axis id="deptht_zoom" zoom_begin="1" zoom_end="10" />
+       <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" />
      </axis_group>
       <axis id="depthu" long_name="Vertical U levels" unit="m" positive="down" />
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef_oldstyle.xml

Property svn:mime-type deleted
Property svn:keywords set to Id

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4">
+      <file_group id="1ts" output_freq="1ts"  output_level="10" enabled=".TRUE."/> <!-- 1 time step files -->
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
       <file_group id="2h" output_freq="2h"  output_level="10" enabled=".TRUE."/> <!-- 2h files -->
 …
       <file_group id="5d" output_freq="5d"  output_level="10" enabled=".TRUE.">  <!-- 5d files -->
    <file id="5d_grid_T" name="auto" description="ocean T grid variables" >
+   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
      <field field_ref="toce"         name="votemper"  />
      <field field_ref="soce"         name="vosaline"  />
 …
    </file>
    <file id="5d_grid_U" name="auto" description="ocean U grid variables" >
+   <file id="file2" name_suffix="_grid_U" description="ocean U grid variables" >
      <field field_ref="uoce"         name="vozocrtx"  />
      <field field_ref="uoce_eiv"     name="vozoeivu"  />
 …
    </file>
    <file id="5d_grid_V" name="auto" description="ocean V grid variables" >
+   <file id="file3" name_suffix="_grid_V" description="ocean V grid variables" >
      <field field_ref="voce"         name="vomecrty"  />
      <field field_ref="voce_eiv"     name="vomeeivv"  />
 …
    </file>
    <file id="5d_grid_W" name="auto" description="ocean W grid variables" >
+   <file id="file4" name_suffix="_grid_W" description="ocean V grid variables" >
      <field field_ref="woce"         name="vovecrtz" />
      <field field_ref="avt"          name="votkeavt" />
 …
    </file>
    <file id="5d_icemod" name="auto" description="ice variables" >
+   <file id="file5" name_suffix="_icemod" description="ocean V grid variables" >
      <field field_ref="ice_pres"                     />
      <field field_ref="snowthic_cea" name="isnowthi" />
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/namelist_ice_lim2

r2580	r4258
89	89	! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing !
90	90	sn_hicif = 'ice_damping', -1. , 'hicif' , .true. , .true. , 'yearly' , '' , ''
91		sn_~~cnf~~ = 'ice_damping', -1. , 'frld' , .true. , .true. , 'yearly' , '' , ''
	91	sn_frld = 'ice_damping', -1. , 'frld' , .true. , .true. , 'yearly' , '' , ''
92	92	!
93	93	cn_dir = './' ! root directory for the location of the runoff files

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM_CFC_C14b/EXP00/iodef.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4">
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM_PISCES/EXP00/iodef.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="10d" min_digits="4">
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
 …
       <file_group id="1d" output_freq="1d"  output_level="10" enabled=".TRUE."> <!-- 1d files -->
    <file id="1d_grid_T" name="auto" description="ocean T grid variables" >
+   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
      <field field_ref="sst"          name="sosstsst"  />
      <field field_ref="sss"          name="sosaline"  />
 …
    </file>
    <file id="1d_grid_U" name="auto" description="ocean U grid variables" >
+   <file id="file2" name_suffix="_grid_U" description="ocean U grid variables" >
      <field field_ref="suoce"         name="vozocrtx"  />
    </file>
    <file id="1d_grid_V" name="auto" description="ocean V grid variables" >
+   <file id="file3" name_suffix="_grid_V" description="ocean V grid variables" >
      <field field_ref="svoce"         name="vomecrty"  />
    </file>
 …
       <file_group id="5d" output_freq="5d"  output_level="10" enabled=".TRUE.">  <!-- 5d files -->
    <file id="5d_grid_T" name="auto" description="ocean T grid variables" >
+   <file id="file4" name_suffix="_grid_T" description="ocean T grid variables" >
      <field field_ref="toce"         name="votemper"  />
      <field field_ref="soce"         name="vosaline"  />
 …
      <field field_ref="qsr"          name="soshfldo"  />
           <field field_ref="saltflx"      name="sosfldow"  />
+          <field field_ref="fmmflx"       name="sofmflup"  />
      <field field_ref="qt"           name="sohefldo"  />
      <field field_ref="mldr10_1"     name="somxl010"  />
 …
    </file>
    <file id="5d_grid_U" name="auto" description="ocean U grid variables" >
+   <file id="file5" name_suffix="_grid_U" description="ocean U grid variables" >
      <field field_ref="uoce"         name="vozocrtx"  />
      <field field_ref="uoce_eiv"     name="vozoeivu"  />
 …
    </file>
    <file id="5d_grid_V" name="auto" description="ocean V grid variables" >
+   <file id="file6" name_suffix="_grid_V" description="ocean V grid variables" >
      <field field_ref="voce"         name="vomecrty"  />
      <field field_ref="voce_eiv"     name="vomeeivv"  />
 …
    </file>
    <file id="5d_grid_W" name="auto" description="ocean W grid variables" >
+   <file id="file7" name_suffix="_grid_W" description="ocean W grid variables" >
      <field field_ref="woce"         name="vovecrtz" />
      <field field_ref="avt"          name="votkeavt" />
 …
    </file>
    <file id="5d_icemod" name="auto" description="ice variables" >
+   <file id="file8" name_suffix="_icemod" description="ice variables" >
      <field field_ref="ice_pres"                     />
      <field field_ref="snowthic_cea" name="isnowthi" />
 …
       <file_group id="1m" output_freq="1mo" output_level="10" enabled=".TRUE."> <!-- real monthly files -->
    <file id="1m_ptrc_T" name="auto" description="pisces sms variables" >
+   <file id="file9" name_suffix="_ptrc_T" description="pisces sms variables" >
           <field field_ref="DIC"      />
           <field field_ref="Alkalini" />
 …
    </file>
    <file id="1m_diad_T" name="auto" description="additional pisces diagnostics" >
+   <file id="file10" name_suffix="_diad_T" description="additional pisces diagnostics" >
           <field field_ref="Cflx"     />
           <field field_ref="Dpco2"    />
 …
       <file_group id="1y"  output_freq="1y" output_level="10" enabled=".TRUE."> <!-- real yearly files -->
    <file id="1y_ptrc_T" name="auto" description="pisces sms variables" >
+   <file id="file11" name_suffix="_ptrc_T" description="pisces sms variables" >
           <field field_ref="DIC"      />
           <field field_ref="Alkalini" />
 …
    </file>
    <file id="1y_diad_T" name="auto" description="additional pisces diagnostics" >
+   <file id="file12" name_suffix="_diad_T" description="additional pisces diagnostics" >
           <field field_ref="PH"       />
           <field field_ref="CO3"      />
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_LIM_PISCES/EXP00/namelist_pisces

-                      r3824
+                      r4258
    cn_dir      = './'     !  root directory for the location of the dynamical files
+!
    ln_presatm  = .true.   ! constant atmopsheric pressure (F) or from a file (T)
+   ln_presatm  = .false.   ! constant atmopsheric pressure (F) or from a file (T)
+/
 !'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
 …
    xkmort     =  2.E-7    ! half saturation constant for mortality
    ferat3     =  10.E-6   ! Fe/C in zooplankton
    wsbio2     =  30.      ! Big particles sinking speed
+   wsbio2     =  50.      ! Big particles sinking speed
    niter1max  =  1        ! Maximum number of iterations for POC
    niter2max  =  1        ! Maximum number of iterations for GOC
 …
 !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    concnno3   =  1.e-6    ! Nitrate half saturation of nanophytoplankton
    concdno3   =  3.E-6   ! Phosphate half saturation for diatoms
+   concdno3   =  3.E-6    ! Phosphate half saturation for diatoms
    concnnh4   =  1.E-7    ! NH4 half saturation for phyto
    concdnh4   =  3.E-7   ! NH4 half saturation for diatoms
    concnfer   =  1.E-9     ! Iron half saturation for phyto
    concdfer   =  3.E-9   ! Iron half saturation for diatoms
+   concdnh4   =  3.E-7    ! NH4 half saturation for diatoms
+   concnfer   =  1.E-9    ! Iron half saturation for phyto
+   concdfer   =  3.E-9    ! Iron half saturation for diatoms
    concbfe    =  1.E-11   ! Half-saturation for Fe limitation of Bacteria
    concbnh4   =  2.5E-8   ! NH4 half saturation for phyto
 …
    xsizerd    =  3.0      ! Size ratio for diatoms
    xksi1      =  2.E-6    ! half saturation constant for Si uptake
    xksi2      =  20E-6  ! half saturation constant for Si/C
+   xksi2      =  20E-6    ! half saturation constant for Si/C
    xkdoc      =  417.E-6  ! half-saturation constant of DOC remineralization
    qnfelim    =  7.E-6    ! Optimal quota of phyto
 …
    excret2    =  0.05     ! excretion ratio of diatoms
    ln_newprod =  .true.   ! Enable new parame. of production (T/F)
    bresp      =  0.00333  ! Basal respiration rate
+   bresp      =  0.0333   ! Basal respiration rate
    chlcnm     =  0.033    ! Minimum Chl/C in nanophytoplankton
    chlcdm     =  0.05     ! Minimum Chl/C in diatoms
 …
    part2      =  0.75     ! part of calcite not dissolved in mesozoo guts
    grazrat2   =  0.75     ! maximal mesozoo grazing rate
    resrat2    =  0.005    ! exsudation rate of mesozooplankton
+   resrat2    =  0.01     ! exsudation rate of mesozooplankton
    mzrat2     =  0.03     ! mesozooplankton mortality rate
    xprefc     =  1.       ! zoo preference for phyto
 …
    xthresh2   =  3E-7     ! Food threshold for grazing
    xkgraz2    =  20.E-6   ! half sturation constant for meso grazing
    epsher2    =  0.3      ! Efficicency of Mesozoo growth
+   epsher2    =  0.4      ! Efficicency of Mesozoo growth
    sigma2     =  0.6      ! Fraction of mesozoo excretion as DOM
    unass2     =  0.3      ! non assimilated fraction of P by mesozoo
 …
    part       =  0.5      ! part of calcite not dissolved in microzoo gutsa
    grazrat    =  3.0      ! maximal zoo grazing rate
    resrat     =  0.03     ! exsudation rate of zooplankton
+   resrat     =  0.05     ! exsudation rate of zooplankton
    mzrat      =  0.004    ! zooplankton mortality rate
    xpref2c    =  0.1      ! Microzoo preference for POM
 …
    xthresh    =  3.E-7    ! Food threshold for feeding
    xkgraz     =  20.E-6   ! half sturation constant for grazing
    epsher     =  0.3      ! Efficiency of microzoo growth
+   epsher     =  0.4      ! Efficiency of microzoo growth
    sigma1     =  0.6      ! Fraction of microzoo excretion as DOM
    unass      =  0.3      ! non assimilated fraction of phyto by zoo
 …
 !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    ln_fechem =  .false.   ! complex iron chemistry ( T/F )
    ln_ligvar =  .true.   ! variable ligand concentration
+   ln_ligvar =  .false.   ! variable ligand concentration
    xlam1     =  0.005     ! scavenging rate of Iron
    xlamdust  =  150.0     ! Scavenging rate of dust
 …
 &nampisrem     !   parameters for remineralization
 !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    xremik    =  0.35      ! remineralization rate of DOC
+   xremik    =  0.3       ! remineralization rate of DOC
    xremip    =  0.025     ! remineralisation rate of POC
    nitrif    =  0.05      ! NH4 nitrification rate
 …
 &nampismass     !  Mass conservation
 !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    ln_check_mass =  .false.    !  Check mass conservation
+/
+   ln_check_mass =  .true.    !  Check mass conservation
+/

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/iodef.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4">
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
 …
       <file_group id="1m" output_freq="1mo" output_level="10" enabled=".TRUE."> <!-- real monthly files -->
    <file id="1m_ptrc_T" name="auto" description="pisces sms variables" >
+   <file id="file1" name_suffix="_ptrc_T" description="pisces sms variables" >
           <field field_ref="DIC"      />
           <field field_ref="Alkalini" />
 …
    </file>
    <file id="1m_diad_T" name="auto" description="additional pisces diagnostics" >
+   <file id="file2" name_suffix="_diad_T" description="additional pisces diagnostics" >
           <field field_ref="Cflx"     />
           <field field_ref="Dpco2"    />
 …
       <file_group id="1y"  output_freq="1y" output_level="10" enabled=".TRUE."> <!-- real yearly files -->
    <file id="1y_ptrc_T" name="auto" description="pisces sms variables" >
+   <file id="file3" name_suffix="_ptrc_T" description="pisces sms variables" >
           <field field_ref="DIC"      />
           <field field_ref="Alkalini" />
 …
    </file>
    <file id="1y_diad_T" name="auto" description="additional pisces diagnostics" >
+   <file id="file4" name_suffix="_diad_T" description="additional pisces diagnostics" >
           <field field_ref="PH"       />
           <field field_ref="CO3"      />
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist

r4254	r4258
665	665	sn_mld = 'dyna_grid_T' , 120 , 'somixhgt' , .true. , .true. , 'yearly' , '' , ''
666	666	sn_emp = 'dyna_grid_T' , 120 , 'sowaflup' , .true. , .true. , 'yearly' , '' , ''
667		sn_~~sfx = 'dyna_grid_T' , 120 , 'sowaflcd~~' , .true. , .true. , 'yearly' , '' , ''
	667	sn_fmf = 'dyna_grid_T' , 120 , 'iowaflup' , .true. , .true. , 'yearly' , '' , ''
668	668	sn_ice = 'dyna_grid_T' , 120 , 'soicecov' , .true. , .true. , 'yearly' , '' , ''
669	669	sn_qsr = 'dyna_grid_T' , 120 , 'soshfldo' , .true. , .true. , 'yearly' , '' , ''

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_pisces

-                      r3824
+                      r4258
    cn_dir      = './'     !  root directory for the location of the dynamical files
+!
    ln_presatm  = .true.   ! constant atmopsheric pressure (F) or from a file (T)
+   ln_presatm  = .false.   ! constant atmopsheric pressure (F) or from a file (T)
+/
 !'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
 …
    xkmort     =  2.E-7    ! half saturation constant for mortality
    ferat3     =  10.E-6   ! Fe/C in zooplankton
    wsbio2     =  30.      ! Big particles sinking speed
+   wsbio2     =  50.      ! Big particles sinking speed
    niter1max  =  1        ! Maximum number of iterations for POC
    niter2max  =  1        ! Maximum number of iterations for GOC
 …
 !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    concnno3   =  1.e-6    ! Nitrate half saturation of nanophytoplankton
    concdno3   =  3.E-6   ! Phosphate half saturation for diatoms
+   concdno3   =  3.E-6    ! Phosphate half saturation for diatoms
    concnnh4   =  1.E-7    ! NH4 half saturation for phyto
    concdnh4   =  3.E-7   ! NH4 half saturation for diatoms
    concnfer   =  1.E-9     ! Iron half saturation for phyto
    concdfer   =  3.E-9   ! Iron half saturation for diatoms
+   concdnh4   =  3.E-7    ! NH4 half saturation for diatoms
+   concnfer   =  1.E-9    ! Iron half saturation for phyto
+   concdfer   =  3.E-9    ! Iron half saturation for diatoms
    concbfe    =  1.E-11   ! Half-saturation for Fe limitation of Bacteria
    concbnh4   =  2.5E-8   ! NH4 half saturation for phyto
 …
    xsizerd    =  3.0      ! Size ratio for diatoms
    xksi1      =  2.E-6    ! half saturation constant for Si uptake
    xksi2      =  20E-6  ! half saturation constant for Si/C
+   xksi2      =  20E-6    ! half saturation constant for Si/C
    xkdoc      =  417.E-6  ! half-saturation constant of DOC remineralization
    qnfelim    =  7.E-6    ! Optimal quota of phyto
 …
    excret2    =  0.05     ! excretion ratio of diatoms
    ln_newprod =  .true.   ! Enable new parame. of production (T/F)
    bresp      =  0.00333  ! Basal respiration rate
+   bresp      =  0.0333   ! Basal respiration rate
    chlcnm     =  0.033    ! Minimum Chl/C in nanophytoplankton
    chlcdm     =  0.05     ! Minimum Chl/C in diatoms
 …
    part2      =  0.75     ! part of calcite not dissolved in mesozoo guts
    grazrat2   =  0.75     ! maximal mesozoo grazing rate
    resrat2    =  0.005    ! exsudation rate of mesozooplankton
+   resrat2    =  0.01     ! exsudation rate of mesozooplankton
    mzrat2     =  0.03     ! mesozooplankton mortality rate
    xprefc     =  1.       ! zoo preference for phyto
 …
    xthresh2   =  3E-7     ! Food threshold for grazing
    xkgraz2    =  20.E-6   ! half sturation constant for meso grazing
    epsher2    =  0.3      ! Efficicency of Mesozoo growth
+   epsher2    =  0.4      ! Efficicency of Mesozoo growth
    sigma2     =  0.6      ! Fraction of mesozoo excretion as DOM
    unass2     =  0.3      ! non assimilated fraction of P by mesozoo
 …
    part       =  0.5      ! part of calcite not dissolved in microzoo gutsa
    grazrat    =  3.0      ! maximal zoo grazing rate
    resrat     =  0.03     ! exsudation rate of zooplankton
+   resrat     =  0.05     ! exsudation rate of zooplankton
    mzrat      =  0.004    ! zooplankton mortality rate
    xpref2c    =  0.1      ! Microzoo preference for POM
 …
    xthresh    =  3.E-7    ! Food threshold for feeding
    xkgraz     =  20.E-6   ! half sturation constant for grazing
    epsher     =  0.3      ! Efficiency of microzoo growth
+   epsher     =  0.4      ! Efficiency of microzoo growth
    sigma1     =  0.6      ! Fraction of microzoo excretion as DOM
    unass      =  0.3      ! non assimilated fraction of phyto by zoo
 …
 !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    ln_fechem =  .false.   ! complex iron chemistry ( T/F )
    ln_ligvar =  .true.   ! variable ligand concentration
+   ln_ligvar =  .false.   ! variable ligand concentration
    xlam1     =  0.005     ! scavenging rate of Iron
    xlamdust  =  150.0     ! Scavenging rate of dust
 …
 &nampisrem     !   parameters for remineralization
 !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    xremik    =  0.35      ! remineralization rate of DOC
+   xremik    =  0.3       ! remineralization rate of DOC
    xremip    =  0.025     ! remineralisation rate of POC
    nitrif    =  0.05      ! NH4 nitrification rate
 …
 &nampismass     !  Mass conservation
 !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    ln_check_mass =  .false.    !  Check mass conservation
+/
+   ln_check_mass =  .true.    !  Check mass conservation
+/

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_SAS_LIM/EXP00/iodef.xml

-                      r3771
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4">
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".TRUE."/> <!-- 1h files -->
 …
       <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/ORCA2_SAS_LIM/EXP00/namelist_ice_lim2

r3331	r4258
89	89	! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing !
90	90	sn_hicif = 'ice_damping', -1. , 'hicif' , .true. , .true. , 'yearly' , '' , ''
91		sn_~~cnf~~ = 'ice_damping', -1. , 'frld' , .true. , .true. , 'yearly' , '' , ''
	91	sn_frld = 'ice_damping', -1. , 'frld' , .true. , .true. , 'yearly' , '' , ''
92	92	!
93	93	cn_dir = './' ! root directory for the location of the runoff files

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/SHARED/field_def.xml

-                      r3824
+                      r4258
          <field id="empmr"        long_name="Net Upward Water Flux"                                        unit="kg/m2/s"  />
+         <field id="saltflx"      long_name="Downward salt flux"                                          unit="PSU/m2/s"  />
+         <field id="saltflx"      long_name="Downward salt flux"                                           unit="PSU/m2/s"  />
+         <field id="fmmflx"       long_name="Water flux due to freezing/melting"                           unit="kg/m2/s"  />
          <field id="snowpre"      long_name="Snow precipitation"                                           unit="kg/m2/s"  />
          <field id="runoffs"      long_name="River Runoffs"                                                unit="Kg/m2/s"  />
 …
         <field id="traj_dens"  long_name="floats density"     unit="kg/m3" />
         <field id="traj_group" long_name="floats group"       unit="none"  />
+      </field_group>
+      <!-- variables available with iceberg trajectories -->
+      <field_group id="icbvar" domain_ref="grid_T"  >
+        <field id="berg_melt"          long_name="icb melt rate of icebergs"                     unit="kg/m2/s"   />
+        <field id="berg_buoy_melt"     long_name="icb buoyancy component of iceberg melt rate"   unit="kg/m2/s"   />
+        <field id="berg_eros_melt"     long_name="icb erosion component of iceberg melt rate"    unit="kg/m2/s"   />
+        <field id="berg_conv_melt"     long_name="icb convective component of iceberg melt rate" unit="kg/m2/s"   />
+        <field id="berg_virtual_area"  long_name="icb virtual coverage by icebergs"              unit="m2"        />
+        <field id="bits_src"           long_name="icb mass source of bergy bits"                 unit="kg/m2/s"   />
+        <field id="bits_melt"          long_name="icb melt rate of bergy bits"                   unit="kg/m2/s"   />
+        <field id="bits_mass"          long_name="icb bergy bit density field"                   unit="kg/m2"     />
+        <field id="berg_mass"          long_name="icb iceberg density field"                     unit="kg/m2"     />
+        <field id="calving"            long_name="icb calving mass input"                        unit="kg/s"      />
+        <field id="berg_floating_melt" long_name="icb melt rate of icebergs + bits"              unit="kg/m2/s"   />
+        <field id="berg_real_calving"  long_name="icb calving into iceberg class"                unit="kg/s"     axis_ref="icbcla" />
+        <field id="berg_stored_ice"    long_name="icb accumulated ice mass by class"             unit="kg"       axis_ref="icbcla" />
       </field_group>
 …
        <field id="NH4"      long_name="Ammonium Concentration"                   unit="mmol/m3" />
+       <!-- PISCES with Kriest parametisation : variables available with key_kriest -->
+       <field id="Num"      long_name="Number of organic particles"              unit="nbr" />
+       <!-- PISCES light : variables available with key_pisces_reduced -->
        <field id="DET"      long_name="Detritus"                                 unit="mmol-N/m3" />
        <field id="DOM"      long_name="Dissolved Organic Matter"                 unit="mmol-N/m3" />
+       <!-- CFC11 : variables available with key_cfc -->
        <field id="CFC11"    long_name="CFC-11 Concentration"                     unit="umol/L" />
+       <!-- Bomb C14 : variables available with key_c14b -->
        <field id="C14B"     long_name="Bomb C14 Concentration"                   unit="ration" />
      </field_group>
+      <!-- diad on T grid : variables available with key_diatrc -->
+      <!-- PISCES additional diagnostics on T grid  -->
      <field_group id="diad_T" grid_ref="grid_T_2D">
        <field id="PH"          long_name="PH"                                      unit="-"          grid_ref="grid_T_3D" />
 …
        <field id="Heup"        long_name="Euphotic layer depth"                    unit="m"                            />
        <field id="Irondep"     long_name="Iron deposition from dust"               unit="mol/m2/s"                     />
+       <field id="Ironsed"     long_name="Iron deposition from sediment"           unit="mol/m2/s"  grid_ref="grid_T_3D"  />
+       <field id="FNO3PHY"  long_name="FNO3PHY"                             unit="-"  grid_ref="grid_T_3D" />
+       <field id="FNH4PHY"  long_name="FNH4PHY"                             unit="-"  grid_ref="grid_T_3D" />
+       <field id="FNH4NO3"  long_name="FNH4NO3"                             unit="-"  grid_ref="grid_T_3D" />
+       <field id="TNO3PHY"  long_name="TNO3PHY"                             unit="-"  />
+       <field id="TNH4PHY"  long_name="TNH4PHY"                             unit="-"  />
+       <field id="TPHYDOM"  long_name="TPHYDOM"                             unit="-"  />
+       <field id="TPHYNH4"  long_name="TPHYNH4"                             unit="-"  />
+       <field id="TPHYZOO"  long_name="TPHYZOO"                             unit="-"  />
+       <field id="TPHYDET"  long_name="TPHYDET"                             unit="-"  />
+       <field id="TDETZOO"  long_name="TDETZOO"                             unit="-"  />
+       <field id="TZOODET"  long_name="TZOODET"                             unit="-"  />
+       <field id="TZOOBOD"  long_name="TZOOBOD"                             unit="-"  />
+       <field id="TZOONH4"  long_name="TZOONH4"                             unit="-"  />
+       <field id="TZOODOM"  long_name="TZOODOM"                             unit="-"  />
+       <field id="TNH4NO3"  long_name="TNH4NO3"                             unit="-"  />
+       <field id="TDOMNH4"  long_name="TDOMNH4"                             unit="-"  />
+       <field id="TDETNH4"  long_name="TDETNH4"                             unit="-"  />
+       <field id="TPHYTOT"  long_name="TPHYTOT"                             unit="-"  />
+       <field id="TZOOTOT"  long_name="TZOOTOT"                             unit="-"  />
+       <field id="SEDPOC"   long_name="SEDPOC"                              unit="-"  />
+       <field id="TDETSED"  long_name="TDETSED"                             unit="-"  />
+       <field id="qtrCFC11"     long_name="Air-sea flux of CFC-11"                   unit="mol/m2/s"   />
+       <field id="qintCFC11"    long_name="Cumulative air-sea flux of CFC-11"        unit="mol/m2"     />
+       <field id="qtrC14b"      long_name="Air-sea flux of Bomb C14"                 unit="mol/m2/s"   />
+       <field id="qintC14b"     long_name="Cumulative air-sea flux of Bomb C14"      unit="mol/m2"     />
+       <field id="fdecay"       long_name="Radiactive decay of Bomb C14"             unit="mol/m3"  grid_ref="grid_T_3D"  />
+       <field id="Ironsed"     long_name="Iron deposition from sediment"           unit="mol/m2/s"  grid_ref="grid_T_3D "/>
+       <!-- PISCES with Kriest parametisation : variables available with key_kriest -->
+       <field id="POCFlx"      long_name="Particulate organic C flux"              unit="mol/m2/s"   grid_ref="grid_T_3D" />
+       <field id="NumFlx"      long_name="Particle number flux"                    unit="nbr/m2/s"   grid_ref="grid_T_3D" />
+       <field id="SiFlx"       long_name="Biogenic Si flux"                        unit="mol/m2/s"   grid_ref="grid_T_3D" />
+       <field id="CaCO3Flx"    long_name="CaCO3 flux"                              unit="mol/m2/s"   grid_ref="grid_T_3D" />
+       <field id="xnum"        long_name="Number of particles in aggregats"        unit="-"          grid_ref="grid_T_3D" />
+       <field id="W1"          long_name="sinking speed of mass flux"              unit="m2/s"       grid_ref="grid_T_3D" />
+       <field id="W2"          long_name="sinking speed of number flux"            unit="m2/s"       grid_ref="grid_T_3D" />
+       <!-- PISCES light : variables available with key_pisces_reduced -->
+       <field id="FNO3PHY"     long_name="FNO3PHY"                                 unit="-"          grid_ref="grid_T_3D" />
+       <field id="FNH4PHY"     long_name="FNH4PHY"                                 unit="-"          grid_ref="grid_T_3D" />
+       <field id="FNH4NO3"     long_name="FNH4NO3"                                 unit="-"          grid_ref="grid_T_3D" />
+       <field id="TNO3PHY"     long_name="TNO3PHY"                                 unit="-"  />
+       <field id="TNH4PHY"     long_name="TNH4PHY"                                 unit="-"  />
+       <field id="TPHYDOM"     long_name="TPHYDOM"                                 unit="-"  />
+       <field id="TPHYNH4"     long_name="TPHYNH4"                                 unit="-"  />
+       <field id="TPHYZOO"     long_name="TPHYZOO"                                 unit="-"  />
+       <field id="TPHYDET"     long_name="TPHYDET"                                 unit="-"  />
+       <field id="TDETZOO"     long_name="TDETZOO"                                 unit="-"  />
+       <field id="TZOODET"     long_name="TZOODET"                                 unit="-"  />
+       <field id="TZOOBOD"     long_name="TZOOBOD"                                 unit="-"  />
+       <field id="TZOONH4"     long_name="TZOONH4"                                 unit="-"  />
+       <field id="TZOODOM"     long_name="TZOODOM"                                 unit="-"  />
+       <field id="TNH4NO3"     long_name="TNH4NO3"                                 unit="-"  />
+       <field id="TDOMNH4"     long_name="TDOMNH4"                                 unit="-"  />
+       <field id="TDETNH4"     long_name="TDETNH4"                                 unit="-"  />
+       <field id="TPHYTOT"     long_name="TPHYTOT"                                 unit="-"  />
+       <field id="TZOOTOT"     long_name="TZOOTOT"                                 unit="-"  />
+       <field id="SEDPOC"      long_name="SEDPOC"                                  unit="-"  />
+       <field id="TDETSED"     long_name="TDETSED"                                 unit="-"  />
+       <!-- CFC11 : variables available with key_cfc -->
+       <field id="qtrCFC11"    long_name="Air-sea flux of CFC-11"                   unit="mol/m2/s"   />
+       <field id="qintCFC11"   long_name="Cumulative air-sea flux of CFC-11"        unit="mol/m2"     />
+       <!-- Bomb C14 : variables available with key_c14b -->
+       <field id="qtrC14b"     long_name="Air-sea flux of Bomb C14"                 unit="mol/m2/s"   />
+       <field id="qintC14b"    long_name="Cumulative air-sea flux of Bomb C14"      unit="mol/m2"     />
+       <field id="fdecay"      long_name="Radiactive decay of Bomb C14"             unit="mol/m3"  grid_ref="grid_T_3D"  />
      </field_group>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/cfg.txt

-                      r3769
+                      r4258
 GYRE_PISCES OPA_SRC TOP_SRC
 ORCA2_LIM3 OPA_SRC LIM_SRC_3
-ORCA2_LIM_PISCES OPA_SRC LIM_SRC_2 NST_SRC TOP_SRC
-ORCA2_OFF_PISCES OPA_SRC OFF_SRC TOP_SRC
 ORCA2_SAS_LIM OPA_SRC SAS_SRC LIM_SRC_2 NST_SRC
 ORCA2_LIM_CFC_C14b OPA_SRC LIM_SRC_2 NST_SRC TOP_SRC
 ORCA2_LIM OPA_SRC LIM_SRC_2 NST_SRC
+ORCA2_OFF_PISCES OPA_SRC OFF_SRC TOP_SRC
+ORCA2_LIM_PISCES OPA_SRC LIM_SRC_2 NST_SRC TOP_SRC

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/CONFIG/makenemo

-                      r3764
+                      r4258
 export AGRIFUSE=10
 declare -a TAB
+list_key=0
+chk_key=1
 #-
 #- FCM and functions location ---
 …
 #-
 #- Choice of the options ---
 while getopts :hd:n:r:m:j:e:s:v:t: V
+while getopts :hd:n:r:m:j:e:s:v:t:k: V
 do
     case $V in
    (h) x_h=${OPTARG};
         echo "Usage   : "${b_n} \
        " [-h] [-n name] [-m arch] [-d "dir1 dir2"] [-r conf] [-s Path] [-e Path] [-j No] [-v No]";
+       " [-h] [-n name] [-m arch] [-d "dir1 dir2"] [-r conf] [-s Path] [-e Path] [-j No] [-v No] [-k 0/1]";
    echo " -h           : help";
    echo " -h institute : specific help for consortium members";
 …
         echo " -j No        : number of processes used to compile (0=nocompilation)";
         echo " -v No        : set verbosity level for compilation [0-3]";
+        echo " -k 0/1       : used cpp keys check (default = 1 -> check activated)";
    echo " -t dir       : temporary directory for compilation"
    echo "";
 …
    echo "Example to clean ";
    echo "./makenemo clean";
+   echo "";
+   echo "Example to list the available keys of a CONFIG ";
+   echo "./makenemo list_key";
    echo "";
    echo "Example to add and remove keys";
 …
    (j)  x_j=${OPTARG};;
    (t)  x_t=${OPTARG};;
+    (e)  x_e=${OPTARG};;
+    (s)  x_s=${OPTARG};;
+    (v)  x_v=${OPTARG};;
+   (e)  x_e=${OPTARG};;
+   (s)  x_s=${OPTARG};;
+   (v)  x_v=${OPTARG};;
+   (k)  chk_key=${OPTARG};;
    (:)  echo ${b_n}" : -"${OPTARG}" option : missing value" 1>&2;
    exit 2;;
 …
        export ${list_del_key}
        shift
+       ;;
+   list_key)
+       list_key=1
        ;;
    *)
 …
 [ "${CMP_NAM}" ==  help ] && . ${COMPIL_DIR}/Flist_archfile.sh all && exit
-#- When used for the first time, choose a compiler ---
-. ${COMPIL_DIR}/Fcheck_archfile.sh arch_nemo.fcm ${CMP_NAM} || exit
 #-
 #- Choose a default configuration if needed ---
 #- ORCA2_LIM or last one used ---
 . ${COMPIL_DIR}/Fcheck_config.sh cfg.txt ${NEW_CONF} || exit
 if [ ${#NEW_CONF} -eq 0 ] ; then
 …
 . ${COMPIL_DIR}/Fmake_bld.sh ${CONFIG_DIR} ${NEW_CONF}  ${NEMO_TDIR} || exit
+# build the complete list of the cpp keys of this configuration
+if [ $chk_key -eq 1 ] ; then
+    for i in $( grep "^ *#.* key_" ${NEW_CONF}/WORK/* )
+    do
+   echo $i | grep key_ | sed -e "s/=.*//"
+    done | sort -d | uniq > ${COMPIL_DIR}/full_key_list.txt
+    if [ $list_key -eq 1 ]; then
+   cat ${COMPIL_DIR}/full_key_list.txt
+   exit 0
+    fi
+fi
 #- At this stage new configuration has been added,
 #- We add or remove keys
 …
     . ${COMPIL_DIR}/Fdel_keys.sh ${NEW_CONF} del_key ${list_del_key}
 fi
+#- check that all keys are really existing...
+if [ $chk_key -eq 1 ] ; then
+    for kk in $( cat ${NEW_CONF}/cpp_${NEW_CONF}.fcm )
+    do
+   if [ "$( echo $kk | cut -c 1-4 )" == "key_" ]; then
+       kk=${kk/=*/}
+       nb=$( grep -c $kk ${COMPIL_DIR}/full_key_list.txt )
+       if [ $nb -eq 0 ]; then
+      echo
+      echo "E R R O R : key "$kk" is not found in ${NEW_CONF}/WORK routines..."
+      echo "we stop..."
+      echo
+      exit 1
+       fi
+   fi
+    done
+fi
+#- At this stage cpp keys have been updated. we can check the arch file
+#- When used for the first time, choose a compiler ---
+. ${COMPIL_DIR}/Fcheck_archfile.sh arch_nemo.fcm cpp.fcm ${CMP_NAM} || exit
 #- At this stage the configuration has beeen chosen
 …
         rm -rf ${NEMO_TDIR}/${NEW_CONF}/BLD
         rm -rf ${NEMO_TDIR}/${NEW_CONF}/EXP00/opa
+        rm -f ${COMPIL_DIR}/*history ${COMPIL_DIR}/*fcm ${COMPIL_DIR}/*txt
         echo "cleaning ${NEW_CONF} WORK, BLD"
     fi

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/EXTERNAL/AGRIF/LIB/SubLoopCreation.c

-                      r2715
+                      r4258
       if ( mark == 1 ) fprintf(fortranout,"!!! aaaaaaaaaaaaaaa \n");
       WriteLocalParamDeclaration();
+      if ( mark == 1 ) fprintf(fortranout,"!!! bbbbbbbbbbbbbbb \n");
+      if ( mark == 1 ) fprintf(fortranout,"!!! bbbbbbbbbbbbbbb \n");
+      WriteArgumentDeclaration_beforecall();
+      if ( mark == 1 ) fprintf(fortranout,"!!! bbbbbbccccccccc \n");
       if ( functiondeclarationisdone == 0 ) WriteFunctionDeclaration(1);
-      if ( mark == 1 ) fprintf(fortranout,"!!! bbbbbbccccccccc \n");
-      WriteArgumentDeclaration_beforecall();
 /*      writesub_loopdeclaration_scalar(List_SubroutineArgument_Var,fortranout);
       writesub_loopdeclaration_tab(List_SubroutineArgument_Var,fortranout);*/
 …
       AddUseAgrifUtilBeforeCall_0(fortranout);
+      WriteArgumentDeclaration_beforecall();
       if ( functiondeclarationisdone == 0 ) WriteFunctionDeclaration(0);
-      WriteArgumentDeclaration_beforecall();
       if ( !strcasecmp(subofagrifinitgrids,subroutinename) )
                      fprintf(oldfortranout,"      Call Agrif_Init_Grids () \n");
 …
                                                        "      IMPLICIT NONE\n");
       WriteLocalParamDeclaration();
+      WriteArgumentDeclaration_beforecall();
       if ( functiondeclarationisdone == 0 ) WriteFunctionDeclaration(0);
-      WriteArgumentDeclaration_beforecall();
       WriteSubroutineDeclaration(0);
       if ( !strcasecmp(subofagrifinitgrids,subroutinename) )

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/LIM_SRC_2/limsbc_2.F90

r4178	r4258
219	219	zemp_snw = rdm_snw(ji,jj) * r1_rdtice ! snow melting = pure water that enters the ocean
220	220	zfmm = rdm_ice(ji,jj) * r1_rdtice ! Freezing minus Melting (F-M)
	221
	222	fmmflx(ji,jj) = zfmm ! F/M mass flux save at least for biogeochemical model
221	223
222	224	! salt flux at the ice/ocean interface (sea ice fraction) [PSU*kg/m2/s]

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/LIM_SRC_3/limsbc.F90

r3625	r4258
226	226	zemp_snw = rdm_snw(ji,jj) * r1_rdtice ! snow melting = pure water that enters the ocean
227	227	zfmm = rdm_ice(ji,jj) * r1_rdtice ! Freezing minus mesting
	228
	229	fmmflx(ji,jj) = zfmm ! F/M mass flux save at least for biogeochemical model
228	230
229	231	emp(ji,jj) = zemp + zemp_snw + zfmm ! mass flux + F/M mass flux (always ice/ocean mass exchange)

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/NST_SRC/agrif_opa_sponge.F90

-                      r3698
+                      r4258
       INTEGER  :: ji,jj,jk
       INTEGER  :: ispongearea, ilci, ilcj
+      REAL(wp) :: z1spongearea
+      REAL(wp), POINTER, DIMENSION(:,:) :: zlocalviscsponge
+      LOGICAL  :: ll_spdone
+      REAL(wp) :: z1spongearea, zramp
+      REAL(wp), POINTER, DIMENSION(:,:) :: ztabramp
 #if defined SPONGE || defined SPONGE_TOP
+      CALL wrk_alloc( jpi, jpj, zlocalviscsponge )
+      ispongearea  = 2 + 2 * Agrif_irhox()
+      ilci = nlci - ispongearea
+      ilcj = nlcj - ispongearea
+      z1spongearea = 1._wp / REAL( ispongearea - 2 )
+      spbtr2(:,:) = 1. / ( e1t(:,:) * e2t(:,:) )
+      ll_spdone=.TRUE.
+      IF (( .NOT. spongedoneT ).OR.( .NOT. spongedoneU )) THEN
+         ! Define ramp from boundaries towards domain interior
+         ! at T-points
+         ! Store it in ztabramp
+         ll_spdone=.FALSE.
+         CALL wrk_alloc( jpi, jpj, ztabramp )
+         ispongearea  = 2 + 2 * Agrif_irhox()
+         ilci = nlci - ispongearea
+         ilcj = nlcj - ispongearea
+         z1spongearea = 1._wp / REAL( ispongearea - 2 )
+         spbtr2(:,:) = 1. / ( e1t(:,:) * e2t(:,:) )
+         ztabramp(:,:) = 0.
+         IF( (nbondi == -1) .OR. (nbondi == 2) ) THEN
+            DO jj = 1, jpj
+               IF ( umask(2,jj,1) == 1._wp ) THEN
+                 DO ji = 2, ispongearea
+                    ztabramp(ji,jj) = ( ispongearea-ji ) * z1spongearea
+                 END DO
+               ENDIF
+            ENDDO
+         ENDIF
+         IF( (nbondi == 1) .OR. (nbondi == 2) ) THEN
+            DO jj = 1, jpj
+               IF ( umask(nlci-2,jj,1) == 1._wp ) THEN
+                  DO ji = ilci+1,nlci-1
+                     zramp = (ji - (ilci+1) ) * z1spongearea
+                     ztabramp(ji,jj) = MAX( ztabramp(ji,jj), zramp )
+                  ENDDO
+               ENDIF
+            ENDDO
+         ENDIF
+         IF( (nbondj == -1) .OR. (nbondj == 2) ) THEN
+            DO ji = 1, jpi
+               IF ( vmask(ji,2,1) == 1._wp ) THEN
+                  DO jj = 2, ispongearea
+                     zramp = ( ispongearea-jj ) * z1spongearea
+                     ztabramp(ji,jj) = MAX( ztabramp(ji,jj), zramp )
+                  END DO
+               ENDIF
+            ENDDO
+         ENDIF
+         IF( (nbondj == 1) .OR. (nbondj == 2) ) THEN
+            DO ji = 1, jpi
+               IF ( vmask(ji,nlcj-2,1) == 1._wp ) THEN
+                  DO jj = ilcj+1,nlcj-1
+                     zramp = (jj - (ilcj+1) ) * z1spongearea
+                     ztabramp(ji,jj) = MAX( ztabramp(ji,jj), zramp )
+                  END DO
+               ENDIF
+            ENDDO
+         ENDIF
+      ENDIF
       ! Tracers
       IF( .NOT. spongedoneT ) THEN
-         zlocalviscsponge(:,:) = 0.
          spe1ur(:,:) = 0.
          spe2vr(:,:) = 0.
          IF( (nbondi == -1) .OR. (nbondi == 2) ) THEN
             DO ji = 2, ispongearea
                zlocalviscsponge(ji,:) = visc_tra * ( ispongearea-ji ) * z1spongearea
             ENDDO
             spe1ur(2:ispongearea-1,:      ) = 0.5 * ( zlocalviscsponge(2:ispongearea-1,:      )   &
+               &                         +            zlocalviscsponge(3:ispongearea  ,:      ) ) &
                &                         * e2u(2:ispongearea-1,:      ) / e1u(2:ispongearea-1,:      )
             spe2vr(2:ispongearea  ,1:jpjm1) = 0.5 * ( zlocalviscsponge(2:ispongearea  ,1:jpjm1)   &
                &                         +            zlocalviscsponge(2:ispongearea,2  :jpj  ) ) &
                &                         * e1v(2:ispongearea  ,1:jpjm1) / e2v(2:ispongearea  ,1:jpjm1)
+            spe1ur(2:ispongearea-1,:       ) = visc_tra                                        &
+               &                             *    0.5 * (  ztabramp(2:ispongearea-1,:      )   &
+               &                                         + ztabramp(3:ispongearea  ,:      ) ) &
+               &                             * e2u(2:ispongearea-1,:) / e1u(2:ispongearea-1,:)
+            spe2vr(2:ispongearea  ,1:jpjm1 ) = visc_tra                                        &
+               &                             *    0.5 * (  ztabramp(2:ispongearea  ,1:jpjm1)   &
+               &                                         + ztabramp(2:ispongearea,2  :jpj  ) ) &
+               &                             * e1v(2:ispongearea,1:jpjm1) / e2v(2:ispongearea,1:jpjm1)
          ENDIF
          IF( (nbondi == 1) .OR. (nbondi == 2) ) THEN
+            DO ji = ilci+1,nlci-1
+               zlocalviscsponge(ji,:) = visc_tra * (ji - (ilci+1) ) * z1spongearea
+            ENDDO
+            spe1ur(ilci+1:nlci-2,:      ) = 0.5 * (  zlocalviscsponge(ilci+1:nlci-2,:)    &
+               &                          +          zlocalviscsponge(ilci+2:nlci-1,:) )  &
+               &                          * e2u(ilci+1:nlci-2,:) / e1u(ilci+1:nlci-2,:)
+            spe2vr(ilci+1:nlci-1,1:jpjm1) = 0.5 * (  zlocalviscsponge(ilci+1:nlci-1,1:jpjm1)    &
+               &                            +        zlocalviscsponge(ilci+1:nlci-1,2:jpj  )  ) &
+               &                                   * e1v(ilci+1:nlci-1,1:jpjm1) / e2v(ilci+1:nlci-1,1:jpjm1)
+            spe1ur(ilci+1:nlci-2,:        ) = visc_tra                                   &
+               &                            * 0.5 * (  ztabramp(ilci+1:nlci-2,:      )   &
+               &                                     + ztabramp(ilci+2:nlci-1,:      ) ) &
+               &                            * e2u(ilci+1:nlci-2,:) / e1u(ilci+1:nlci-2,:)
+            spe2vr(ilci+1:nlci-1,1:jpjm1  )  = visc_tra                                  &
+               &                            * 0.5 * (  ztabramp(ilci+1:nlci-1,1:jpjm1)   &
+               &                                     + ztabramp(ilci+1:nlci-1,2:jpj  ) ) &
+               &                            * e1v(ilci+1:nlci-1,1:jpjm1) / e2v(ilci+1:nlci-1,1:jpjm1)
          ENDIF
          IF( (nbondj == -1) .OR. (nbondj == 2) ) THEN
+            DO jj = 2, ispongearea
+               zlocalviscsponge(:,jj) = visc_tra * ( ispongearea-jj ) * z1spongearea
+            ENDDO
+            spe1ur(1:jpim1,2:ispongearea  ) = 0.5 * ( zlocalviscsponge(1:jpim1,2:ispongearea  ) &
+               &                            +         zlocalviscsponge(2:jpi  ,2:ispongearea) ) &
+            spe1ur(1:jpim1,2:ispongearea  ) = visc_tra                                     &
+               &                            * 0.5 * (  ztabramp(1:jpim1,2:ispongearea  )   &
+               &                                     + ztabramp(2:jpi  ,2:ispongearea  ) ) &
                &                            * e2u(1:jpim1,2:ispongearea) / e1u(1:jpim1,2:ispongearea)
+            spe2vr(:      ,2:ispongearea-1) = 0.5 * ( zlocalviscsponge(:,2:ispongearea-1)       &
+               &                            +         zlocalviscsponge(:,3:ispongearea  )     ) &
+            spe2vr(:      ,2:ispongearea-1) = visc_tra                                     &
+               &                            * 0.5 * (  ztabramp(:      ,2:ispongearea-1)   &
+               &                                     + ztabramp(:      ,3:ispongearea  ) ) &
                &                            * e1v(:,2:ispongearea-1) / e2v(:,2:ispongearea-1)
          ENDIF
          IF( (nbondj == 1) .OR. (nbondj == 2) ) THEN
+            DO jj = ilcj+1,nlcj-1
+               zlocalviscsponge(:,jj) = visc_tra * (jj - (ilcj+1) ) * z1spongearea
+            ENDDO
+            spe1ur(1:jpim1,ilcj+1:nlcj-1) = 0.5 * ( zlocalviscsponge(1:jpim1,ilcj+1:nlcj-1)   &
+               &                          +         zlocalviscsponge(2:jpi  ,ilcj+1:nlcj-1) ) &
+            spe1ur(1:jpim1,ilcj+1:nlcj-1) = visc_tra                                   &
+               &                          * 0.5 * (  ztabramp(1:jpim1,ilcj+1:nlcj-1)   &
+               &                                   + ztabramp(2:jpi  ,ilcj+1:nlcj-1) ) &
                &                                * e2u(1:jpim1,ilcj+1:nlcj-1) / e1u(1:jpim1,ilcj+1:nlcj-1)
+            spe2vr(:      ,ilcj+1:nlcj-2) = 0.5 * ( zlocalviscsponge(:,ilcj+1:nlcj-2      )   &
+               &                          +         zlocalviscsponge(:,ilcj+2:nlcj-1)     )   &
+            spe2vr(:      ,ilcj+1:nlcj-2) = visc_tra                                   &
+               &                          * 0.5 * (  ztabramp(:      ,ilcj+1:nlcj-2)   &
+               &                                   + ztabramp(:      ,ilcj+2:nlcj-1) ) &
                &                                * e1v(:,ilcj+1:nlcj-2) / e2v(:,ilcj+1:nlcj-2)
          ENDIF
 …
       ! Dynamics
       IF( .NOT. spongedoneU ) THEN
-         zlocalviscsponge(:,:) = 0.
          spe1ur2(:,:) = 0.
          spe2vr2(:,:) = 0.
          IF( (nbondi == -1) .OR. (nbondi == 2) ) THEN
+            DO ji = 2, ispongearea
+               zlocalviscsponge(ji,:) = visc_dyn * ( ispongearea-ji ) * z1spongearea
+            ENDDO
+            spe1ur2(2:ispongearea-1,:      ) = 0.5 * ( zlocalviscsponge(2:ispongearea-1,:      ) &
+                                             &     +   zlocalviscsponge(3:ispongearea,:    ) )
+            spe2vr2(2:ispongearea  ,1:jpjm1) = 0.5 * ( zlocalviscsponge(2:ispongearea  ,1:jpjm1) &
+                                             &     +   zlocalviscsponge(2:ispongearea,2:jpj) )
+            spe1ur2(2:ispongearea-1,:      ) = visc_dyn                                   &
+               &                             * 0.5 * (  ztabramp(2:ispongearea-1,:      ) &
+               &                                      + ztabramp(3:ispongearea  ,:      ) )
+            spe2vr2(2:ispongearea  ,1:jpjm1) = visc_dyn                                   &
+               &                             * 0.5 * (  ztabramp(2:ispongearea  ,1:jpjm1) &
+               &                                      + ztabramp(2:ispongearea  ,2:jpj  ) )
          ENDIF
          IF( (nbondi == 1) .OR. (nbondi == 2) ) THEN
+            DO ji = ilci+1,nlci-1
+               zlocalviscsponge(ji,:) = visc_dyn * (ji - (ilci+1) ) * z1spongearea
+            ENDDO
+            spe1ur2(ilci+1:nlci-2,:      ) = 0.5 * (  zlocalviscsponge(ilci+1:nlci-2,:) &
+                                           &        + zlocalviscsponge(ilci+2:nlci-1,:) )
+            spe2vr2(ilci+1:nlci-1,1:jpjm1) = 0.5 * (  zlocalviscsponge(ilci+1:nlci-1,1:jpjm1) &
+                                           &        + zlocalviscsponge(ilci+1:nlci-1,2:jpj  )  )
+            spe1ur2(ilci+1:nlci-2  ,:      ) = visc_dyn                                   &
+               &                             * 0.5 * (  ztabramp(ilci+1:nlci-2, :       ) &
+               &                                      + ztabramp(ilci+2:nlci-1, :       ) )
+            spe2vr2(ilci+1:nlci-1  ,1:jpjm1) = visc_dyn                                   &
+               &                             * 0.5 * (  ztabramp(ilci+1:nlci-1,1:jpjm1  ) &
+               &                                      + ztabramp(ilci+1:nlci-1,2:jpj    ) )
          ENDIF
          IF( (nbondj == -1) .OR. (nbondj == 2) ) THEN
+            DO jj = 2, ispongearea
+               zlocalviscsponge(:,jj) = visc_dyn * ( ispongearea-jj ) * z1spongearea
+            ENDDO
+            spe1ur2(1:jpim1,2:ispongearea  ) = 0.5 * ( zlocalviscsponge(1:jpim1,2:ispongearea) &
+                                             &      + zlocalviscsponge(2:jpi,2:ispongearea) )
+            spe2vr2(:      ,2:ispongearea-1) = 0.5 * ( zlocalviscsponge(:,2:ispongearea-1)     &
+                                             &      + zlocalviscsponge(:,3:ispongearea)     )
+            spe1ur2(1:jpim1,2:ispongearea  ) = visc_dyn                                   &
+               &                             * 0.5 * (  ztabramp(1:jpim1,2:ispongearea  ) &
+               &                                      + ztabramp(2:jpi  ,2:ispongearea  ) )
+            spe2vr2(:      ,2:ispongearea-1) = visc_dyn                                   &
+               &                             * 0.5 * (  ztabramp(:      ,2:ispongearea-1) &
+               &                                      + ztabramp(:      ,3:ispongearea  ) )
          ENDIF
          IF( (nbondj == 1) .OR. (nbondj == 2) ) THEN
+            DO jj = ilcj+1,nlcj-1
+               zlocalviscsponge(:,jj) = visc_dyn * (jj - (ilcj+1) ) * z1spongearea
+            ENDDO
+            spe1ur2(1:jpim1,ilcj+1:nlcj-1) = 0.5 * ( zlocalviscsponge(1:jpim1,ilcj+1:nlcj-1) &
+                                           &         + zlocalviscsponge(2:jpi,ilcj+1:nlcj-1) )
+            spe2vr2(:      ,ilcj+1:nlcj-2) = 0.5 * ( zlocalviscsponge(:,ilcj+1:nlcj-2      ) &
+                                           &         + zlocalviscsponge(:,ilcj+2:nlcj-1)     )
+            spe1ur2(1:jpim1,ilcj+1:nlcj-1  ) = visc_dyn                                   &
+               &                             * 0.5 * (  ztabramp(1:jpim1,ilcj+1:nlcj-1  ) &
+               &                                      + ztabramp(2:jpi  ,ilcj+1:nlcj-1  ) )
+            spe2vr2(:      ,ilcj+1:nlcj-2  ) = visc_dyn                                   &
+               &                             * 0.5 * (  ztabramp(:      ,ilcj+1:nlcj-2  ) &
+               &                                      + ztabramp(:      ,ilcj+2:nlcj-1  ) )
          ENDIF
          spongedoneU = .TRUE.
 …
       ENDIF
+      !
       CALL wrk_dealloc( jpi, jpj, zlocalviscsponge )
+      IF (.NOT.ll_spdone) CALL wrk_dealloc( jpi, jpj, ztabramp )
+      !
 #endif

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OFF_SRC/dtadyn.F90

-                      r3827
+                      r4258
    INTEGER  , SAVE      ::   jf_eiv         ! index of v-eiv
    INTEGER  , SAVE      ::   jf_eiw         ! index of w-eiv
    INTEGER  , SAVE      ::   jf_sfx         ! index of downward salt flux
+   INTEGER  , SAVE      ::   jf_fmf         ! index of downward salt flux
    TYPE(FLD), ALLOCATABLE, DIMENSION(:) :: sf_dyn  ! structure of input fields (file informations, fields read)
 …
       wndm(:,:)        = sf_dyn(jf_wnd)%fnow(:,:,1) * tmask(:,:,1)    ! wind speed - needed for gas exchange
       emp (:,:)        = sf_dyn(jf_emp)%fnow(:,:,1) * tmask(:,:,1)    ! E-P
+      sfx (:,:)        = 0.0_wp      ! enable testing with old inputs ! downward salt flux
+!     sfx (:,:)        = sf_dyn(jf_sfx)%fnow(:,:,1) * tmask(:,:,1)    ! downward salt flux (v3.5+)
+      fmmflx(:,:)      = sf_dyn(jf_fmf)%fnow(:,:,1) * tmask(:,:,1)    ! downward salt flux (v3.5+)
       fr_i(:,:)        = sf_dyn(jf_ice)%fnow(:,:,1) * tmask(:,:,1)    ! Sea-ice fraction
       qsr (:,:)        = sf_dyn(jf_qsr)%fnow(:,:,1) * tmask(:,:,1)    ! solar radiation
 …
          CALL prt_ctl(tab2d_1=fr_i             , clinfo1=' fr_i    - : ', mask1=tmask, ovlap=1 )
          CALL prt_ctl(tab2d_1=hmld             , clinfo1=' hmld    - : ', mask1=tmask, ovlap=1 )
          CALL prt_ctl(tab2d_1=sfx              , clinfo1=' sfx     - : ', mask1=tmask, ovlap=1 )
+         CALL prt_ctl(tab2d_1=fmmflx           , clinfo1=' fmmflx  - : ', mask1=tmask, ovlap=1 )
          CALL prt_ctl(tab2d_1=emp              , clinfo1=' emp     - : ', mask1=tmask, ovlap=1 )
          CALL prt_ctl(tab2d_1=wndm             , clinfo1=' wspd    - : ', mask1=tmask, ovlap=1 )
 …
       TYPE(FLD_N) :: sn_tem, sn_sal, sn_mld, sn_emp, sn_ice, sn_qsr, sn_wnd  ! informations about the fields to be read
       TYPE(FLD_N) :: sn_uwd, sn_vwd, sn_wwd, sn_avt, sn_ubl, sn_vbl          !   "                                 "
       TYPE(FLD_N) :: sn_ahu, sn_ahv, sn_ahw, sn_eiu, sn_eiv, sn_eiw, sn_sfx  !   "                                 "
+      TYPE(FLD_N) :: sn_ahu, sn_ahv, sn_ahw, sn_eiu, sn_eiv, sn_eiw, sn_fmf  !   "                                 "
+      !
       NAMELIST/namdta_dyn/cn_dir, ln_dynwzv, ln_dynbbl, ln_degrad,    &
          &                sn_tem, sn_sal, sn_mld, sn_emp, sn_ice, sn_qsr, sn_wnd,  &
          &                sn_uwd, sn_vwd, sn_wwd, sn_avt, sn_ubl, sn_vbl,          &
          &                sn_ahu, sn_ahv, sn_ahw, sn_eiu, sn_eiv, sn_eiw, sn_sfx
+         &                sn_ahu, sn_ahv, sn_ahw, sn_eiu, sn_eiv, sn_eiw, sn_fmf
       !!----------------------------------------------------------------------
 …
       sn_mld  = FLD_N( 'dyna_grid_T' ,    120    , 'somixght' ,  .true.    , .true. ,   'yearly'  , ''       , ''         )
       sn_emp  = FLD_N( 'dyna_grid_T' ,    120    , 'sowaflup' ,  .true.    , .true. ,   'yearly'  , ''       , ''         )
+      sn_sfx  = FLD_N( 'dyna_grid_T' ,    120    , 'sowaflcd' ,  .true.    , .true. ,   'yearly'  , ''       , ''         )
+!!    sn_sfx  = FLD_N( 'dyna_grid_T' ,    120    , 'sosfldow' ,  .true.    , .true. ,   'yearly'  , ''       , ''         ) ! v3.5+
+      sn_fmf  = FLD_N( 'dyna_grid_T' ,    120    , 'sofmflup' ,  .true.    , .true. ,   'yearly'  , ''       , ''         )
       sn_ice  = FLD_N( 'dyna_grid_T' ,    120    , 'soicecov' ,  .true.    , .true. ,   'yearly'  , ''       , ''         )
       sn_qsr  = FLD_N( 'dyna_grid_T' ,    120    , 'soshfldo' ,  .true.    , .true. ,   'yearly'  , ''       , ''         )
 …
       ENDIF
       jf_tem = 1   ;   jf_sal = 2   ;  jf_mld = 3   ;  jf_emp = 4   ;   jf_sfx  = 5   ;  jf_ice = 6   ;   jf_qsr = 7
+      jf_tem = 1   ;   jf_sal = 2   ;  jf_mld = 3   ;  jf_emp = 4   ;   jf_fmf  = 5   ;  jf_ice = 6   ;   jf_qsr = 7
       jf_wnd = 8   ;   jf_uwd = 9   ;  jf_vwd = 10  ;  jf_wwd = 11  ;   jf_avt  = 12  ;  jfld  = 12
+      !
       slf_d(jf_tem) = sn_tem   ;   slf_d(jf_sal)  = sn_sal   ;   slf_d(jf_mld) = sn_mld
       slf_d(jf_emp) = sn_emp   ;   slf_d(jf_sfx ) = sn_sfx   ;   slf_d(jf_ice) = sn_ice
+      slf_d(jf_emp) = sn_emp   ;   slf_d(jf_fmf ) = sn_fmf   ;   slf_d(jf_ice) = sn_ice
       slf_d(jf_qsr) = sn_qsr   ;   slf_d(jf_wnd)  = sn_wnd   ;   slf_d(jf_avt) = sn_avt
       slf_d(jf_uwd) = sn_uwd   ;   slf_d(jf_vwd)  = sn_vwd   ;   slf_d(jf_wwd) = sn_wwd
 …
         ENDIF
       ENDIF
-      ! Salt flux and concntration/dilution terms (new from v3.5) !! disabled to allow testing with old input files
-!!    jf_sfx = jfld + 1    ;    jfld = jfld + 1
-!!    slf_d(jf_sfx) = sn_sfx
       ALLOCATE( sf_dyn(jfld), STAT=ierr )         ! set sf structure

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/ASM/asminc.F90

-                      r3785
+                      r4258
       ! used to prevent the applied increments taking the temperature below the local freezing point
+#if defined key_cice
+        fzptnz(:,:,:) = -1.8_wp
+#else
+        DO jk = 1, jpk
+           DO jj = 1, jpj
+              DO ji = 1, jpk
+                 fzptnz (ji,jj,jk) = ( -0.0575_wp + 1.710523e-3_wp * SQRT( tsn(ji,jj,jk,jp_sal) )                   &
+                                                  - 2.154996e-4_wp *       tsn(ji,jj,jk,jp_sal)   ) * tsn(ji,jj,jk,jp_sal)  &
+                                                  - 7.53e-4_wp * fsdepw(ji,jj,jk)       ! (pressure in dbar)
+              END DO
+           END DO
+        END DO
+#endif
+      DO jk=1, jpkm1
+         fzptnz (:,:,jk) = tfreez( tsn(:,:,jk,jp_sal), fsdept(:,:,jk) )
+      ENDDO
       IF ( ln_asmiau ) THEN

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/BDY/bdyice_lim2.F90

Property svn:keywords set to Id

r4254	r4258
32	32	!!----------------------------------------------------------------------
33	33	!! NEMO/OPA 3.3 , NEMO Consortium (2010)
34		!! $Id~~: bdyice_lim2.F90 4223 2013-11-15 17:21:46Z cbricaud~~ $
	34	!! $Id$
35	35	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
36	36	!!----------------------------------------------------------------------

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/C1D/step_c1d.F90

-                      r3680
+                      r4258
                              indic = 0                ! reset to no error condition
+      IF( kstp == nit000 )   CALL iom_init            ! iom_put initialization (must be done after nemo_init for AGRIF+XIOS+OASIS)
       IF( kstp /= nit000 )   CALL day( kstp )         ! Calendar (day was already called at nit000 in day_init)
                              CALL iom_setkt( kstp )   ! say to iom that we are at time step kstp
+                             CALL iom_setkt( kstp - nit000 + 1 )   ! say to iom that we are at time step kstp
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
                          CALL dia_wri( kstp )       ! ocean model: outputs
+      IF( lk_diahth  )   CALL dia_hth( kstp )       ! Thermocline depth (20°C)
 #if defined key_top

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/DIA/diadct.F90

-                      r3680
+                      r4258
 #endif
 #if defined key_lim3
+  USE ice_3
+  USE par_ice
+  USE ice
 #endif
   USE domvvl
 …
                  ijglo = secs(jsec)%listPoint(jpt)%J + jpjzoom - 1 + njmpp - 1
                  WRITE(numout,*)'         # I J : ',iiglo,ijglo
+                 CALL FLUSH(numout)
               ENDDO
            ENDIF
 …
      !! * Local variables
      INTEGER             :: jk, jseg, jclass,                    &!loop on level/segment/classes
+     INTEGER             :: jk, jseg, jclass,jl,                 &!loop on level/segment/classes/ice categories
                             isgnu, isgnv                          !
      REAL(wp)            :: zumid, zvmid,                        &!U/V velocity on a cell segment
 …
               zTnorm=zumid_ice*e2u(k%I,k%J)+zvmid_ice*e1v(k%I,k%J)
+#if defined key_lim2
               transports_2d(1,jsec,jseg) = transports_2d(1,jsec,jseg) + (zTnorm)*   &
                                    (1.0 - frld(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J))  &
 …
               transports_2d(2,jsec,jseg) = transports_2d(2,jsec,jseg) + (zTnorm)*   &
                                     (1.0 -  frld(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J))
+#endif
+#if defined key_lim3
+              DO jl=1,jpl
+                 transports_2d(1,jsec,jseg) = transports_2d(1,jsec,jseg) + (zTnorm)*     &
+                                   a_i(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J,jl) * &
+                                  ( ht_i(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J,jl) +  &
+                                    ht_s(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J,jl) )
+                 transports_2d(2,jsec,jseg) = transports_2d(2,jsec,jseg) + (zTnorm)*   &
+                                   a_i(sec%listPoint(jseg)%I,sec%listPoint(jseg)%J,jl)
+              ENDDO
+#endif
            ENDIF !end of ice case

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/DIA/diahsb.F90

-                      r3625
+                      r4258
    USE bdy_par         ! (for lk_bdy)
    USE timing          ! preformance summary
+   USE lib_fortran
+   USE sbcrnf
    IMPLICIT NONE
 …
    REAL(dp)                                ::   surf_tot   , vol_tot             !
    REAL(dp)                                ::   frc_t      , frc_s     , frc_v   ! global forcing trends
+   REAL(dp)                                ::   frc_wn_t      , frc_wn_s ! global forcing trends
    REAL(dp)                                ::   fact1                            ! conversion factors
    REAL(dp)                                ::   fact21    , fact22               !     -         -
 …
    REAL(dp), DIMENSION(:,:)  , ALLOCATABLE ::   surf      , ssh_ini              !
    REAL(dp), DIMENSION(:,:,:), ALLOCATABLE ::   hc_loc_ini, sc_loc_ini, e3t_ini  !
+   REAL(dp), DIMENSION(:,:)  , ALLOCATABLE ::   ssh_hc_loc_ini, ssh_sc_loc_ini
    !! * Substitutions
 …
       INTEGER    ::   jk                          ! dummy loop indice
       REAL(dp)   ::   zdiff_hc    , zdiff_sc      ! heat and salt content variations
+      REAL(dp)   ::   zdiff_hc1   , zdiff_sc1     ! heat and salt content variations of ssh
       REAL(dp)   ::   zdiff_v1    , zdiff_v2      ! volume variation
+      REAL(dp)   ::   zerr_hc1    , zerr_sc1      ! Non conservation due to free surface
       REAL(dp)   ::   z1_rau0                     ! local scalars
       REAL(dp)   ::   zdeltat                     !    -     -
       REAL(dp)   ::   z_frc_trd_t , z_frc_trd_s   !    -     -
       REAL(dp)   ::   z_frc_trd_v                 !    -     -
+      REAL(dp)   ::   z_wn_trd_t , z_wn_trd_s   !    -     -
+      REAL(dp)   ::   z_ssh_hc , z_ssh_sc   !    -     -
       !!---------------------------------------------------------------------------
       IF( nn_timing == 1 )   CALL timing_start('dia_hsb')
 …
       ! ------------------------- !
       z1_rau0 = 1.e0 / rau0
+      z_frc_trd_v = z1_rau0 * SUM( - ( emp(:,:) - rnf(:,:) ) * surf(:,:) )     ! volume fluxes
+      z_frc_trd_t =           SUM( sbc_tsc(:,:,jp_tem) * surf(:,:) )     ! heat fluxes
+      z_frc_trd_s =           SUM( sbc_tsc(:,:,jp_sal) * surf(:,:) )     ! salt fluxes
+      z_frc_trd_v = z1_rau0 * glob_sum( - ( emp(:,:) - rnf(:,:) ) * surf(:,:) )     ! volume fluxes
+      z_frc_trd_t =           glob_sum( sbc_tsc(:,:,jp_tem) * surf(:,:) )     ! heat fluxes
+      z_frc_trd_s =           glob_sum( sbc_tsc(:,:,jp_sal) * surf(:,:) )     ! salt fluxes
+      ! Add runoff heat & salt input
+      IF( ln_rnf    )   z_frc_trd_t = z_frc_trd_t + glob_sum( rnf_tsc(:,:,jp_tem) * surf(:,:) )
+      IF( ln_rnf_sal)   z_frc_trd_s = z_frc_trd_s + glob_sum( rnf_tsc(:,:,jp_sal) * surf(:,:) )
       ! Add penetrative solar radiation
       IF( ln_traqsr )   z_frc_trd_t = z_frc_trd_t + r1_rau0_rcp * SUM( qsr     (:,:) * surf(:,:) )
+      IF( ln_traqsr )   z_frc_trd_t = z_frc_trd_t + r1_rau0_rcp * glob_sum( qsr     (:,:) * surf(:,:) )
       ! Add geothermal heat flux
+      IF( ln_trabbc )   z_frc_trd_t = z_frc_trd_t + r1_rau0_rcp * SUM( qgh_trd0(:,:) * surf(:,:) )
+      IF( lk_mpp ) THEN
+         CALL mpp_sum( z_frc_trd_v )
+         CALL mpp_sum( z_frc_trd_t )
+      ENDIF
+      IF( ln_trabbc )   z_frc_trd_t = z_frc_trd_t +  glob_sum( qgh_trd0(:,:) * surf(:,:) )
+      IF( .NOT. lk_vvl ) THEN
+         z_wn_trd_t = - glob_sum( surf(:,:) * wn(:,:,1) * tsb(:,:,1,jp_tem) )
+         z_wn_trd_s = - glob_sum( surf(:,:) * wn(:,:,1) * tsb(:,:,1,jp_sal) )
+      ENDIF
       frc_v = frc_v + z_frc_trd_v * rdt
       frc_t = frc_t + z_frc_trd_t * rdt
       frc_s = frc_s + z_frc_trd_s * rdt
+      !                                          ! Advection flux through fixed surface (z=0)
+      IF( .NOT. lk_vvl ) THEN
+         frc_wn_t = frc_wn_t + z_wn_trd_t * rdt
+         frc_wn_s = frc_wn_s + z_wn_trd_s * rdt
+      ENDIF
       ! ----------------------- !
 …
       zdiff_hc = 0.d0
       zdiff_sc = 0.d0
       ! volume variation (calculated with ssh)
+      zdiff_v1 = SUM( surf(:,:) * tmask(:,:,1) * ( sshn(:,:) - ssh_ini(:,:) ) )
+      zdiff_v1 = glob_sum( surf(:,:) * ( sshn(:,:) - ssh_ini(:,:) ) )
+      ! heat & salt content variation (associated with ssh)
+      IF( .NOT. lk_vvl ) THEN
+         z_ssh_hc = glob_sum( surf(:,:) * ( tsn(:,:,1,jp_tem) * sshn(:,:) - ssh_hc_loc_ini(:,:) ) )
+         z_ssh_sc = glob_sum( surf(:,:) * ( tsn(:,:,1,jp_sal) * sshn(:,:) - ssh_sc_loc_ini(:,:) ) )
+      ENDIF
       DO jk = 1, jpkm1
          ! volume variation (calculated with scale factors)
          zdiff_v2 = zdiff_v2 + SUM( surf(:,:) * tmask(:,:,jk)   &
+        ! volume variation (calculated with scale factors)
+         zdiff_v2 = zdiff_v2 + glob_sum( surf(:,:) * tmask(:,:,jk)   &
             &                       * ( fse3t_n(:,:,jk)         &
             &                           - e3t_ini(:,:,jk) ) )
          ! heat content variation
          zdiff_hc = zdiff_hc + SUM( surf(:,:) * tmask(:,:,jk)          &
+         zdiff_hc = zdiff_hc + glob_sum( surf(:,:) * tmask(:,:,jk)          &
             &                       * ( fse3t_n(:,:,jk) * tsn(:,:,jk,jp_tem)   &
             &                           - hc_loc_ini(:,:,jk) ) )
          ! salt content variation
          zdiff_sc = zdiff_sc + SUM( surf(:,:) * tmask(:,:,jk)          &
+         zdiff_sc = zdiff_sc + glob_sum( surf(:,:) * tmask(:,:,jk)          &
             &                       * ( fse3t_n(:,:,jk) * tsn(:,:,jk,jp_sal)   &
             &                           - sc_loc_ini(:,:,jk) ) )
       ENDDO
-      IF( lk_mpp ) THEN
-         CALL mpp_sum( zdiff_hc )
-         CALL mpp_sum( zdiff_sc )
-         CALL mpp_sum( zdiff_v1 )
-         CALL mpp_sum( zdiff_v2 )
-      ENDIF
       ! Substract forcing from heat content, salt content and volume variations
       zdiff_v1 = zdiff_v1 - frc_v
       zdiff_v2 = zdiff_v2 - frc_v
+      IF( lk_vvl )   zdiff_v2 = zdiff_v2 - frc_v
       zdiff_hc = zdiff_hc - frc_t
       zdiff_sc = zdiff_sc - frc_s
+      IF( .NOT. lk_vvl ) THEN
+         zdiff_hc1 = zdiff_hc + z_ssh_hc
+         zdiff_sc1 = zdiff_sc + z_ssh_sc
+         zerr_hc1  = z_ssh_hc - frc_wn_t
+         zerr_sc1  = z_ssh_sc - frc_wn_s
+      ENDIF
       ! ----------------------- !
 …
       ! ----------------------- !
       zdeltat  = 1.e0 / ( ( kt - nit000 + 1 ) * rdt )
+      WRITE(numhsb , 9020) kt , zdiff_hc / vol_tot , zdiff_hc * fact1  * zdeltat,                                &
+         &                      zdiff_sc / vol_tot , zdiff_sc * fact21 * zdeltat, zdiff_sc * fact22 * zdeltat,   &
+         &                      zdiff_v1           , zdiff_v1 * fact31 * zdeltat, zdiff_v1 * fact32 * zdeltat,   &
+         &                      zdiff_v2           , zdiff_v2 * fact31 * zdeltat, zdiff_v2 * fact32 * zdeltat
+      IF( lk_vvl ) THEN
+         WRITE(numhsb , 9020) kt , zdiff_hc / vol_tot , zdiff_hc * fact1  * zdeltat,                                &
+            &                      zdiff_sc / vol_tot , zdiff_sc * fact21 * zdeltat, zdiff_sc * fact22 * zdeltat,   &
+            &                      zdiff_v1           , zdiff_v1 * fact31 * zdeltat, zdiff_v1 * fact32 * zdeltat,   &
+            &                      zdiff_v2           , zdiff_v2 * fact31 * zdeltat, zdiff_v2 * fact32 * zdeltat
+      ELSE
+         WRITE(numhsb , 9030) kt , zdiff_hc1 / vol_tot , zdiff_hc1 * fact1  * zdeltat,                                &
+            &                      zdiff_sc1 / vol_tot , zdiff_sc1 * fact21 * zdeltat, zdiff_sc1 * fact22 * zdeltat,   &
+            &                      zdiff_v1            , zdiff_v1  * fact31 * zdeltat, zdiff_v1  * fact32 * zdeltat,   &
+            &                      zerr_hc1 / vol_tot  , zerr_sc1 / vol_tot
+      ENDIF
       IF ( kt == nitend ) CLOSE( numhsb )
 …
   FORMAT(I5,11D15.7)
+  FORMAT(I5,10D15.7)
+      !
    END SUBROUTINE dia_hsb
 …
       IF( .NOT. ln_diahsb )   RETURN
+      IF( .NOT. lk_mpp_rep ) &
+        CALL ctl_stop (' Your global mpp_sum if performed in single precision - 64 bits -', &
+             &         ' whereas the global sum to be precise must be done in double precision ',&
+             &         ' please add key_mpp_rep')
       ! ------------------- !
       ! 1 - Allocate memory !
       ! ------------------- !
+      ALLOCATE( hc_loc_ini(jpi,jpj,jpk), STAT=ierror )
+      ALLOCATE( hc_loc_ini(jpi,jpj,jpk), sc_loc_ini(jpi,jpj,jpk), &
+         &      ssh_hc_loc_ini(jpi,jpj), ssh_sc_loc_ini(jpi,jpj), &
+         &      e3t_ini(jpi,jpj,jpk)                            , &
+         &      surf(jpi,jpj),  ssh_ini(jpi,jpj), STAT=ierror )
       IF( ierror > 0 ) THEN
          CALL ctl_stop( 'dia_hsb: unable to allocate hc_loc_ini' )   ;   RETURN
-      ENDIF
-      ALLOCATE( sc_loc_ini(jpi,jpj,jpk), STAT=ierror )
-      IF( ierror > 0 ) THEN
-         CALL ctl_stop( 'dia_hsb: unable to allocate sc_loc_ini' )   ;   RETURN
-      ENDIF
-      ALLOCATE( e3t_ini(jpi,jpj,jpk)   , STAT=ierror )
-      IF( ierror > 0 ) THEN
-         CALL ctl_stop( 'dia_hsb: unable to allocate e3t_ini' )      ;   RETURN
-      ENDIF
-      ALLOCATE( surf(jpi,jpj)          , STAT=ierror )
-      IF( ierror > 0 ) THEN
-         CALL ctl_stop( 'dia_hsb: unable to allocate surf' )         ;   RETURN
-      ENDIF
-      ALLOCATE( ssh_ini(jpi,jpj)       , STAT=ierror )
-      IF( ierror > 0 ) THEN
-         CALL ctl_stop( 'dia_hsb: unable to allocate ssh_ini' )      ;   RETURN
       ENDIF
 …
       cl_name    = 'heat_salt_volume_budgets.txt'                         ! name of output file
       surf(:,:) = e1t(:,:) * e2t(:,:) * tmask(:,:,1) * tmask_i(:,:)      ! masked surface grid cell area
       surf_tot  = SUM( surf(:,:) )                                       ! total ocean surface area
+      surf_tot  = glob_sum( surf(:,:) )                                       ! total ocean surface area
       vol_tot   = 0.d0                                                   ! total ocean volume
       DO jk = 1, jpkm1
          vol_tot  = vol_tot + SUM( surf(:,:) * tmask(:,:,jk)     &
             &                      * fse3t_n(:,:,jk)         )
+         vol_tot  = vol_tot + glob_sum( surf(:,:) * tmask(:,:,jk)     &
+            &                         * fse3t_n(:,:,jk)         )
       END DO
-      IF( lk_mpp ) THEN
-         CALL mpp_sum( vol_tot )
-         CALL mpp_sum( surf_tot )
-      ENDIF
       CALL ctl_opn( numhsb , cl_name , 'UNKNOWN' , 'FORMATTED' , 'SEQUENTIAL' , 1 , numout , lwp , 1 )
+      !                   12345678901234567890123456789012345678901234567890123456789012345678901234567890 -> 80
+      WRITE( numhsb, 9010 ) "kt   |     heat content budget     |            salt content budget             ",   &
+         !                                                   123456789012345678901234567890123456789012345 -> 45
+         &                                                  "|            volume budget (ssh)             ",   &
+         !                                                   678901234567890123456789012345678901234567890 -> 45
+         &                                                  "|            volume budget (e3t)             "
+      WRITE( numhsb, 9010 ) "     |      [C]         [W/m2]     |     [psu]        [mmm/s]          [SV]     ",   &
+         &                                                  "|     [m3]         [mmm/s]          [SV]     ",   &
+         &                                                  "|     [m3]         [mmm/s]          [SV]     "
+      IF( lk_vvl ) THEN
+         !                   12345678901234567890123456789012345678901234567890123456789012345678901234567890 -> 80
+         WRITE( numhsb, 9010 ) "kt   |     heat content budget     |            salt content budget             ",   &
+            !                                                   123456789012345678901234567890123456789012345 -> 45
+            &                                                  "|            volume budget (ssh)             ",   &
+            !                                                   678901234567890123456789012345678901234567890 -> 45
+            &                                                  "|            volume budget (e3t)             "
+         WRITE( numhsb, 9010 ) "     |      [C]         [W/m2]     |     [psu]        [mmm/s]          [SV]     ",   &
+            &                                                  "|     [m3]         [mmm/s]          [SV]     ",   &
+            &                                                  "|     [m3]         [mmm/s]          [SV]     "
+      ELSE
+         !                   12345678901234567890123456789012345678901234567890123456789012345678901234567890 -> 80
+         WRITE( numhsb, 9011 ) "kt   |     heat content budget     |            salt content budget             ",   &
+            !                                                   123456789012345678901234567890123456789012345 -> 45
+            &                                                  "|            volume budget (ssh)             ",   &
+            !                                                   678901234567890123456789012345678901234567890 -> 45
+            &                                                  "|  Non conservation due to free surface      "
+         WRITE( numhsb, 9011 ) "     |      [C]         [W/m2]     |     [psu]        [mmm/s]          [SV]     ",   &
+            &                                                  "|     [m3]         [mmm/s]          [SV]     ",   &
+            &                                                  "|  [heat - C]     [salt - psu]                "
+      ENDIF
       ! --------------- !
       ! 3 - Conversions ! (factors will be multiplied by duration afterwards)
 …
       frc_t = 0.d0                                           ! heat content   -    -   -    -
       frc_s = 0.d0                                           ! salt content   -    -   -    -
+      IF( .NOT. lk_vvl ) THEN
+         ssh_hc_loc_ini(:,:) = tsn(:,:,1,jp_tem) * ssh_ini(:,:)   ! initial heat content associated with ssh
+         ssh_sc_loc_ini(:,:) = tsn(:,:,1,jp_sal) * ssh_ini(:,:)   ! initial salt content associated with ssh
+         frc_wn_t = 0.d0
+         frc_wn_s = 0.d0
+      ENDIF
+      !
   FORMAT(A80,A45,A45)
+  FORMAT(A80,A45,A45)
+      !
    END SUBROUTINE dia_hsb_init

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/DIA/diaptr.F90

-                      r3865
+                      r4258
                DO jn = 1, nptr
                   tn_jk(:,:,jn) = ptr_tjk( tsn(:,:,:,jp_tem), btmsk(:,:,jn) ) * r1_sjk(:,:,jn)
+                  sn_jk(:,:,jn) = ptr_tjk( tsn(:,:,:,jp_sal), btmsk(:,:,jn) ) * r1_sjk(:,:,jn)
                END DO
             ENDIF
 …
       !!--------------------------------------------------------------------
+      !
       CALL wrk_alloc( jpi      , zphi , zfoo )
       CALL wrk_alloc( jpi , jpk, z_1 )
+      CALL wrk_alloc( jpj      , zphi , zfoo )
+      CALL wrk_alloc( jpj , jpk, z_1 )
       ! define time axis
 …
       ENDIF
+      !
       CALL wrk_dealloc( jpi      , zphi , zfoo )
       CALL wrk_dealloc( jpi , jpk, z_1 )
+      CALL wrk_dealloc( jpj      , zphi , zfoo )
+      CALL wrk_dealloc( jpj , jpk, z_1 )
+      !
   END SUBROUTINE dia_ptr_wri

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/DOM/closea.F90

-                      r3632
+                      r4258
             ncsi1(2)   =  97  ;  ncsj1(2)   = 107
             ncsi2(2)   = 103  ;  ncsj2(2)   = 111
+            ncsir(2,1) = 110  ;  ncsjr(2,1) = 111
+            !                                            ! Black Sea 1 : west part of the Black Sea
+            ncsnr(3)   = 1    ; ncstt(3)   =   2            !            (ie west of the cyclic b.c.)
+            ncsi1(3)   = 174  ; ncsj1(3)   = 107            ! put in Med Sea
+            ncsi2(3)   = 181  ; ncsj2(3)   = 112
+            ncsir(3,1) = 171  ; ncsjr(3,1) = 106
+            !                                            ! Black Sea 2 : est part of the Black Sea
+            ncsnr(4)   =   1  ;  ncstt(4)   =   2           !               (ie est of the cyclic b.c.)
+            ncsi1(4)   =   2  ;  ncsj1(4)   = 107           ! put in Med Sea
+            ncsi2(4)   =   6  ;  ncsj2(4)   = 112
+            ncsir(4,1) = 171  ;  ncsjr(4,1) = 106
+            ncsir(2,1) = 110  ;  ncsjr(2,1) = 111
+            !                                            ! Black Sea (crossed by the cyclic boundary condition)
+            ncsnr(3:4) =   4  ;  ncstt(3:4) =   2           ! put in Med Sea (north of Aegean Sea)
+            ncsir(3:4,1) = 171;  ncsjr(3:4,1) = 106         !
+            ncsir(3:4,2) = 170;  ncsjr(3:4,2) = 106
+            ncsir(3:4,3) = 171;  ncsjr(3:4,3) = 105
+            ncsir(3:4,4) = 170;  ncsjr(3:4,4) = 105
+            ncsi1(3)   = 174  ;  ncsj1(3)   = 107           ! 1 : west part of the Black Sea
+            ncsi2(3)   = 181  ;  ncsj2(3)   = 112           !            (ie west of the cyclic b.c.)
+            ncsi1(4)   =   2  ;  ncsj1(4)   = 107           ! 2 : east part of the Black Sea
+            ncsi2(4)   =   6  ;  ncsj2(4)   = 112           !           (ie east of the cyclic b.c.)
             !                                        ! =======================
          CASE ( 4 )                                  !  ORCA_R4 configuration
 …
       REAL(wp), DIMENSION(jpi,jpj), INTENT(inout) ::   p_rnfmsk   ! river runoff mask (rnfmsk array)
+      !
+      INTEGER  ::   jc, jn      ! dummy loop indices
+      INTEGER  ::   ii, ij      ! temporary integer
+      INTEGER  ::   jc, jn, ji, jj      ! dummy loop indices
       !!----------------------------------------------------------------------
+      !
 …
          IF( ncstt(jc) >= 1 ) THEN            ! runoff mask set to 1 at closed sea outflows
              DO jn = 1, 4
+               ii = mi0( ncsir(jc,jn) )
+               ij = mj0( ncsjr(jc,jn) )
+               p_rnfmsk(ii,ij) = MAX( p_rnfmsk(ii,ij), 1.0_wp )
+                DO jj =    mj0( ncsjr(jc,jn) ), mj1( ncsjr(jc,jn) )
+                   DO ji = mi0( ncsir(jc,jn) ), mi1( ncsir(jc,jn) )
+                      p_rnfmsk(ji,jj) = MAX( p_rnfmsk(ji,jj), 1.0_wp )
+                   END DO
+                END DO
             END DO
          ENDIF

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/DOM/daymod.F90

-                      r3851
+                      r4258
                nday_year = 1
                nsec_year = ndt05
+               IF( nsec1jan000 >= 2 * (2**30 - nsecd * nyear_len(1) / 2 ) ) THEN   ! test integer 4 max value
+                  CALL ctl_stop( 'The number of seconds between Jan. 1st 00h of nit000 year and Jan. 1st 00h ',   &
+                     &           'of the current year is exceeding the INTEGER 4 max VALUE: 2^31-1 -> 68.09 years in seconds', &
+                     & 'You must do a restart at higher frequency (or remove this STOP and recompile everything in I8)' )
+               ENDIF
                nsec1jan000 = nsec1jan000 + nsecd * nyear_len(1)
                IF( nleapy == 1 )   CALL day_mth

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/DOM/domzgr.F90

-                      r3865
+                      r4258
          END DO
       END DO
+      IF( lk_mpp )   CALL mpp_sum( icompt )
       IF( icompt == 0 ) THEN
          IF(lwp) WRITE(numout,*)'     no isolated ocean grid points'
 …
          DO jj = 1, jpj
             DO ji = 1, jpi
                ztaper = EXP( -(gphit(ji,jj)/8._wp)**2 )
+               ztaper = EXP( -(gphit(ji,jj)/8._wp)**2._wp )
                hbatt(ji,jj) = rn_sbot_max * ztaper + hbatt(ji,jj) * ( 1._wp - ztaper )
             END DO
 …
       where (e3vw_0  (:,:,:).eq.0.0)  e3vw_0(:,:,:) = 1.0
+#if defined key_agrif
+      ! Ensure meaningful vertical scale factors in ghost lines/columns
+      IF( .NOT. Agrif_Root() ) THEN
+         !
+         IF((nbondi == -1).OR.(nbondi == 2)) THEN
+            e3u_0(1,:,:) = e3u_0(2,:,:)
+         ENDIF
+         !
+         IF((nbondi ==  1).OR.(nbondi == 2)) THEN
+            e3u_0(nlci-1,:,:) = e3u_0(nlci-2,:,:)
+         ENDIF
+         !
+         IF((nbondj == -1).OR.(nbondj == 2)) THEN
+            e3v_0(:,1,:) = e3v_0(:,2,:)
+         ENDIF
+         !
+         IF((nbondj ==  1).OR.(nbondj == 2)) THEN
+            e3v_0(:,nlcj-1,:) = e3v_0(:,nlcj-2,:)
+         ENDIF
+         !
+      ENDIF
+#endif
       fsdept(:,:,:) = gdept_0 (:,:,:)

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/DYN/dynspg_flt.F90

-                      r3765
+                      r4258
       INTEGER  ::   ji, jj, jk   ! dummy loop indices
       REAL(wp) ::   z2dt, z2dtg, zgcb, zbtd, ztdgu, ztdgv   ! local scalars
-      REAL(wp), POINTER, DIMENSION(:,:,:) ::  zub, zvb
       !!----------------------------------------------------------------------
+      !
       IF( nn_timing == 1 )  CALL timing_start('dyn_spg_flt')
+      !
-      CALL wrk_alloc( jpi,jpj,jpk, zub, zvb )
+      !
       IF( kt == nit000 ) THEN
 …
          DO jk = 1, jpkm1
             DO ji = 1, jpij
                spgu(ji,1) = spgu(ji,1) + fse3u(ji,1,jk) * ua(ji,1,jk)
                spgv(ji,1) = spgv(ji,1) + fse3v(ji,1,jk) * va(ji,1,jk)
+               spgu(ji,1) = spgu(ji,1) + fse3u_a(ji,1,jk) * ua(ji,1,jk)
+               spgv(ji,1) = spgv(ji,1) + fse3v_a(ji,1,jk) * va(ji,1,jk)
             END DO
          END DO
 …
             DO jj = 2, jpjm1
                DO ji = 2, jpim1
                   spgu(ji,jj) = spgu(ji,jj) + fse3u(ji,jj,jk) * ua(ji,jj,jk)
                   spgv(ji,jj) = spgv(ji,jj) + fse3v(ji,jj,jk) * va(ji,jj,jk)
+                  spgu(ji,jj) = spgu(ji,jj) + fse3u_a(ji,jj,jk) * ua(ji,jj,jk)
+                  spgv(ji,jj) = spgv(ji,jj) + fse3v_a(ji,jj,jk) * va(ji,jj,jk)
                END DO
             END DO
 …
       IF( lrst_oce ) CALL flt_rst( kt, 'WRITE' )
+      !
-      CALL wrk_dealloc( jpi,jpj,jpk, zub, zvb )
+      !
       IF( nn_timing == 1 )  CALL timing_stop('dyn_spg_flt')

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/ICB/icb_oce.F90

-                      r3614
+                      r4258
    USE par_oce   ! ocean parameters
    USE lib_mpp   ! MPP library
-   USE fldread   ! read input fields (FLD type)
    IMPLICIT NONE
 …
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:)   :: griddata                           !: work array for icbrst
-   TYPE(FLD), PUBLIC, ALLOCATABLE     , DIMENSION(:)       ::   sf_icb   !: structure: file information, fields read
    !!----------------------------------------------------------------------
    !! NEMO/OPA 3.3 , NEMO Consortium (2011)
 …
+      !
       icb_alloc = 0
+      ALLOCATE( berg_grid                      ,                                               &
+         &      berg_grid%calving    (jpi,jpj) , berg_grid%calving_hflx (jpi,jpj)          ,   &
+      ALLOCATE( berg_grid%calving    (jpi,jpj) , berg_grid%calving_hflx (jpi,jpj)          ,   &
          &      berg_grid%stored_heat(jpi,jpj) , berg_grid%floating_melt(jpi,jpj)          ,   &
          &      berg_grid%maxclass   (jpi,jpj) , berg_grid%stored_ice   (jpi,jpj,nclasses) ,   &

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/ICB/icbini.F90

-                      r3785
+                      r4258
    PUBLIC   icb_init  ! routine called in nemogcm.F90 module
+   CHARACTER(len=100) ::   cn_dir = './'   ! Root directory for location of icb files
+   TYPE(FLD_N)        ::   sn_icb          ! information about the calving file to be read
+   CHARACTER(len=100)                                 ::   cn_dir = './'   !: Root directory for location of icb files
+   TYPE(FLD_N)                                        ::   sn_icb          !: information about the calving file to be read
+   TYPE(FLD), PUBLIC, ALLOCATABLE     , DIMENSION(:)  ::   sf_icb          !: structure: file information, fields read
+                                                                           !: used in icbini and icbstp
    !!----------------------------------------------------------------------

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/ICB/icbstp.F90

r3614	r4258
24	24	USE lib_mpp
25	25	USE iom
	26	USE fldread
26	27	USE timing ! timing
27	28

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/IOM/iom.F90

-                      r3862
+                      r4258
    USE sbc_oce, ONLY :   nn_fsbc         ! ocean space and time domain
    USE trc_oce, ONLY :   nn_dttrc        !  !: frequency of step on passive tracers
+   USE icb_oce, ONLY :   class_num       !  !: iceberg classes
    USE domngb          ! ocean space and time domain
    USE phycst          ! physical constants
 …
    USE xios
 # endif
+   USE ioipsl, ONLY :  ju2ymds    ! for calendar
    IMPLICIT NONE
 …
    PRIVATE iom_p1d, iom_p2d, iom_p3d
 #if defined key_iomput
    PRIVATE iom_set_domain_attr, iom_set_axis_attr, iom_set_field_attr, iom_set_file_attr, iom_set_grid_attr
    PRIVATE set_grid, set_scalar, set_xmlatt, set_mooring
+   PRIVATE iom_set_domain_attr, iom_set_axis_attr, iom_set_field_attr, iom_set_file_attr, iom_get_file_attr, iom_set_grid_attr
+   PRIVATE set_grid, set_scalar, set_xmlatt, set_mooring, iom_update_file_name, iom_sdate
 # endif
 …
       clname = "nemo"
       IF( TRIM(Agrif_CFixed()) /= '0' )   clname = TRIM(Agrif_CFixed())//"_"//TRIM(clname)
+# if defined key_mpp_mpi
       CALL xios_context_initialize(TRIM(clname), mpi_comm_opa)
+# else
+      CALL xios_context_initialize(TRIM(clname), 0)
+# endif
       CALL iom_swap
 …
       CALL iom_set_axis_attr( "depthw", gdepw_1d )
 # if defined key_floats
       CALL iom_set_axis_attr( "nfloat", (ji, ji=1,nfloat) )
+      CALL iom_set_axis_attr( "nfloat", (/ (REAL(ji,wp), ji=1,nfloat) /) )
 # endif
+      CALL iom_set_axis_attr( "icbcla", class_num )
       ! automatic definitions of some of the xml attributs
 …
       ! end file definition
        dtime%second=rdt
        CALL xios_set_timestep(dtime)
        CALL xios_close_context_definition()
        CALL xios_update_calendar(0)
+      dtime%second = rdt
+      CALL xios_set_timestep(dtime)
+      CALL xios_close_context_definition()
+      CALL xios_update_calendar(0)
 #endif
    END SUBROUTINE iom_init
 …
       LOGICAL         , INTENT(in   ), OPTIONAL ::   ldiof    ! Interp On the Fly, needed for AGRIF (default = .FALSE.)
       CHARACTER(LEN=100)    ::   clname    ! the name of the file based on cdname [[+clcpu]+clcpu]
       CHARACTER(LEN=100)    ::   cltmpn    ! tempory name to store clname (in writting mode)
+      CHARACTER(LEN=256)    ::   clname    ! the name of the file based on cdname [[+clcpu]+clcpu]
+      CHARACTER(LEN=256)    ::   cltmpn    ! tempory name to store clname (in writting mode)
       CHARACTER(LEN=10)     ::   clsuffix  ! ".nc" or ".dimg"
       CHARACTER(LEN=15)     ::   clcpu     ! the cpu number (max jpmax_digits digits)
       CHARACTER(LEN=100)    ::   clinfo    ! info character
+      CHARACTER(LEN=256)    ::   clinfo    ! info character
       LOGICAL               ::   llok      ! check the existence
       LOGICAL               ::   llwrt     ! local definition of ldwrt
 …
       REAL(wp)                       ::   zscf, zofs  ! sacle_factor and add_offset
       INTEGER                        ::   itmp        ! temporary integer
       CHARACTER(LEN=100)             ::   clinfo      ! info character
       CHARACTER(LEN=100)             ::   clname      ! file name
+      CHARACTER(LEN=256)             ::   clinfo      ! info character
+      CHARACTER(LEN=256)             ::   clname      ! file name
       CHARACTER(LEN=1)               ::   clrankpv, cldmspc      !
       !---------------------------------------------------------------------
 …
    !!----------------------------------------------------------------------
 #if defined key_iomput
    SUBROUTINE iom_set_domain_attr( cdname, ni_glo, nj_glo, ibegin, jbegin, ni, nj, zoom_ibegin, zoom_jbegin, zoom_ni, zoom_nj,   &
+   SUBROUTINE iom_set_domain_attr( cdid, ni_glo, nj_glo, ibegin, jbegin, ni, nj, zoom_ibegin, zoom_jbegin, zoom_ni, zoom_nj,   &
       &                                    data_dim, data_ibegin, data_ni, data_jbegin, data_nj, lonvalue, latvalue, mask )
       CHARACTER(LEN=*)                 , INTENT(in) ::   cdname
+      CHARACTER(LEN=*)                 , INTENT(in) ::   cdid
       INTEGER                , OPTIONAL, INTENT(in) ::   ni_glo, nj_glo, ibegin, jbegin, ni, nj
       INTEGER                , OPTIONAL, INTENT(in) ::   data_dim, data_ibegin, data_ni, data_jbegin, data_nj
 …
       LOGICAL, DIMENSION(:,:), OPTIONAL, INTENT(in) ::   mask
       IF ( xios_is_valid_domain     (cdname) ) THEN
          CALL xios_set_domain_attr     ( cdname, ni_glo=ni_glo, nj_glo=nj_glo, ibegin=ibegin, jbegin=jbegin, ni=ni, nj=nj,   &
             &    data_dim=data_dim, data_ibegin=data_ibegin, data_ni=data_ni, data_jbegin=data_jbegin, data_nj=data_nj   ,   &
             &    zoom_ibegin=zoom_ibegin, zoom_jbegin=zoom_jbegin, zoom_ni=zoom_ni, zoom_nj=zoom_nj,                         &
+      IF ( xios_is_valid_domain     (cdid) ) THEN
+         CALL xios_set_domain_attr     ( cdid, ni_glo=ni_glo, nj_glo=nj_glo, ibegin=ibegin, jbegin=jbegin, ni=ni, nj=nj,   &
+            &    data_dim=data_dim, data_ibegin=data_ibegin, data_ni=data_ni, data_jbegin=data_jbegin, data_nj=data_nj ,   &
+            &    zoom_ibegin=zoom_ibegin, zoom_jbegin=zoom_jbegin, zoom_ni=zoom_ni, zoom_nj=zoom_nj,                       &
             &    lonvalue=lonvalue, latvalue=latvalue,mask=mask )
       ENDIF
       IF ( xios_is_valid_domaingroup(cdname) ) THEN
          CALL xios_set_domaingroup_attr( cdname, ni_glo=ni_glo, nj_glo=nj_glo, ibegin=ibegin, jbegin=jbegin, ni=ni, nj=nj,   &
             &    data_dim=data_dim, data_ibegin=data_ibegin, data_ni=data_ni, data_jbegin=data_jbegin, data_nj=data_nj   ,   &
             &    zoom_ibegin=zoom_ibegin, zoom_jbegin=zoom_jbegin, zoom_ni=zoom_ni, zoom_nj=zoom_nj,                         &
+      IF ( xios_is_valid_domaingroup(cdid) ) THEN
+         CALL xios_set_domaingroup_attr( cdid, ni_glo=ni_glo, nj_glo=nj_glo, ibegin=ibegin, jbegin=jbegin, ni=ni, nj=nj,   &
+            &    data_dim=data_dim, data_ibegin=data_ibegin, data_ni=data_ni, data_jbegin=data_jbegin, data_nj=data_nj ,   &
+            &    zoom_ibegin=zoom_ibegin, zoom_jbegin=zoom_jbegin, zoom_ni=zoom_ni, zoom_nj=zoom_nj,                       &
             &    lonvalue=lonvalue, latvalue=latvalue,mask=mask )
       ENDIF
+      CALL xios_solve_inheritance()
    END SUBROUTINE iom_set_domain_attr
    SUBROUTINE iom_set_axis_attr( cdname, paxis )
       CHARACTER(LEN=*)      , INTENT(in) ::   cdname
+   SUBROUTINE iom_set_axis_attr( cdid, paxis )
+      CHARACTER(LEN=*)      , INTENT(in) ::   cdid
       REAL(wp), DIMENSION(:), INTENT(in) ::   paxis
+      IF ( xios_is_valid_axis     (cdname) )   CALL xios_set_axis_attr     ( cdname, size=size(paxis),value=paxis )
+      IF ( xios_is_valid_axisgroup(cdname) )   CALL xios_set_axisgroup_attr( cdname, size=size(paxis),value=paxis )
+      IF ( xios_is_valid_axis     (cdid) )   CALL xios_set_axis_attr     ( cdid, size=size(paxis),value=paxis )
+      IF ( xios_is_valid_axisgroup(cdid) )   CALL xios_set_axisgroup_attr( cdid, size=size(paxis),value=paxis )
+      CALL xios_solve_inheritance()
    END SUBROUTINE iom_set_axis_attr
    SUBROUTINE iom_set_field_attr( cdname, freq_op)
       CHARACTER(LEN=*)          , INTENT(in) ::   cdname
+   SUBROUTINE iom_set_field_attr( cdid, freq_op, freq_offset )
+      CHARACTER(LEN=*)          , INTENT(in) ::   cdid
       CHARACTER(LEN=*),OPTIONAL , INTENT(in) ::   freq_op
+      IF ( xios_is_valid_field     (cdname) )   CALL xios_set_field_attr     ( cdname, freq_op=freq_op )
+      IF ( xios_is_valid_fieldgroup(cdname) )   CALL xios_set_fieldgroup_attr( cdname, freq_op=freq_op )
+      CHARACTER(LEN=*),OPTIONAL , INTENT(in) ::   freq_offset
+      IF ( xios_is_valid_field     (cdid) )   CALL xios_set_field_attr     ( cdid, freq_op=freq_op, freq_offset=freq_offset )
+      IF ( xios_is_valid_fieldgroup(cdid) )   CALL xios_set_fieldgroup_attr( cdid, freq_op=freq_op, freq_offset=freq_offset )
+      CALL xios_solve_inheritance()
    END SUBROUTINE iom_set_field_attr
    SUBROUTINE iom_set_file_attr( cdname, name, name_suffix )
       CHARACTER(LEN=*)          , INTENT(in) ::   cdname
+   SUBROUTINE iom_set_file_attr( cdid, name, name_suffix )
+      CHARACTER(LEN=*)          , INTENT(in) ::   cdid
       CHARACTER(LEN=*),OPTIONAL , INTENT(in) ::   name, name_suffix
+      IF ( xios_is_valid_file     (cdname) )   CALL xios_set_file_attr     ( cdname, name=name, name_suffix=name_suffix )
+      IF ( xios_is_valid_filegroup(cdname) )   CALL xios_set_filegroup_attr( cdname, name=name, name_suffix=name_suffix )
+      IF ( xios_is_valid_file     (cdid) )   CALL xios_set_file_attr     ( cdid, name=name, name_suffix=name_suffix )
+      IF ( xios_is_valid_filegroup(cdid) )   CALL xios_set_filegroup_attr( cdid, name=name, name_suffix=name_suffix )
+      CALL xios_solve_inheritance()
    END SUBROUTINE iom_set_file_attr
+   SUBROUTINE iom_set_grid_attr( cdname, mask )
+      CHARACTER(LEN=*)                   , INTENT(in) ::   cdname
+   SUBROUTINE iom_get_file_attr( cdid, name, name_suffix, output_freq )
+      CHARACTER(LEN=*)          , INTENT(in ) ::   cdid
+      CHARACTER(LEN=*),OPTIONAL , INTENT(out) ::   name, name_suffix, output_freq
+      LOGICAL                                 ::   llexist1,llexist2,llexist3
+      !---------------------------------------------------------------------
+      IF( PRESENT( name        ) )   name = ''          ! default values
+      IF( PRESENT( name_suffix ) )   name_suffix = ''
+      IF( PRESENT( output_freq ) )   output_freq = ''
+      IF ( xios_is_valid_file     (cdid) ) THEN
+         CALL xios_solve_inheritance()
+         CALL xios_is_defined_file_attr     ( cdid, name = llexist1, name_suffix = llexist2, output_freq = llexist3)
+         IF(llexist1)   CALL xios_get_file_attr     ( cdid, name = name )
+         IF(llexist2)   CALL xios_get_file_attr     ( cdid, name_suffix = name_suffix )
+         IF(llexist3)   CALL xios_get_file_attr     ( cdid, output_freq = output_freq )
+      ENDIF
+      IF ( xios_is_valid_filegroup(cdid) ) THEN
+         CALL xios_solve_inheritance()
+         CALL xios_is_defined_filegroup_attr( cdid, name = llexist1, name_suffix = llexist2, output_freq = llexist3)
+         IF(llexist1)   CALL xios_get_filegroup_attr( cdid, name = name )
+         IF(llexist2)   CALL xios_get_filegroup_attr( cdid, name_suffix = name_suffix )
+         IF(llexist3)   CALL xios_get_filegroup_attr( cdid, output_freq = output_freq )
+      ENDIF
+   END SUBROUTINE iom_get_file_attr
+   SUBROUTINE iom_set_grid_attr( cdid, mask )
+      CHARACTER(LEN=*)                   , INTENT(in) ::   cdid
       LOGICAL, DIMENSION(:,:,:), OPTIONAL, INTENT(in) ::   mask
+      IF ( xios_is_valid_grid     (cdname) )   CALL xios_set_grid_attr     ( cdname, mask=mask )
+      IF ( xios_is_valid_gridgroup(cdname) )   CALL xios_set_gridgroup_attr( cdname, mask=mask )
+      IF ( xios_is_valid_grid     (cdid) )   CALL xios_set_grid_attr     ( cdid, mask=mask )
+      IF ( xios_is_valid_gridgroup(cdid) )   CALL xios_set_gridgroup_attr( cdid, mask=mask )
+      CALL xios_solve_inheritance()
    END SUBROUTINE iom_set_grid_attr
 …
    SUBROUTINE set_grid( cdgrd, plon, plat )
       !!----------------------------------------------------------------------
       !!                     ***  ROUTINE   ***
+      !!                     ***  ROUTINE set_grid  ***
       !!
       !! ** Purpose :   define horizontal grids
 …
          END SELECT
+         !
          CALL iom_set_domain_attr( "grid_"//cdgrd       , mask = zmask(:,:,1) /= 0. )
          CALL iom_set_grid_attr  ( "grid_"//cdgrd//"_3D", mask = zmask(:,:,:) /= 0. )
+         CALL iom_set_domain_attr( "grid_"//cdgrd       , mask = RESHAPE(zmask(nldi:nlei,nldj:nlej,1),(/ni,nj    /)) /= 0. )
+         CALL iom_set_grid_attr  ( "grid_"//cdgrd//"_3D", mask = RESHAPE(zmask(nldi:nlei,nldj:nlej,:),(/ni,nj,jpk/)) /= 0. )
       ENDIF
 …
    SUBROUTINE set_scalar
       !!----------------------------------------------------------------------
       !!                     ***  ROUTINE   ***
+      !!                     ***  ROUTINE set_scalar  ***
       !!
       !! ** Purpose :   define fake grids for scalar point
 …
    SUBROUTINE set_xmlatt
       !!----------------------------------------------------------------------
       !!                     ***  ROUTINE   ***
+      !!                     ***  ROUTINE set_xmlatt  ***
       !!
       !! ** Purpose :   automatic definitions of some of the xml attributs...
       !!
       !!----------------------------------------------------------------------
-      CHARACTER(len=6),DIMENSION( 8) ::   clsuff                   ! suffix name
       CHARACTER(len=1),DIMENSION( 3) ::   clgrd                    ! suffix name
       CHARACTER(len=50)              ::   clname                   ! file name
+      CHARACTER(len=256)             ::   clsuff                   ! suffix name
       CHARACTER(len=1)               ::   cl1                      ! 1 character
       CHARACTER(len=2)               ::   cl2                      ! 1 character
+      CHARACTER(len=255)             ::   tfo
+      INTEGER                        ::   idt                      ! time-step in seconds
+      INTEGER                        ::   iddss, ihhss             ! number of seconds in 1 day, 1 hour and 1 year
+      INTEGER                        ::   iyymo                    ! number of months in 1 year
+      INTEGER                        ::   jg, jh, jd, jm, jy       ! loop counters
+      INTEGER                        ::   ji, jg                   ! loop counters
       INTEGER                        ::   ix, iy                   ! i-,j- index
       REAL(wp)        ,DIMENSION(11) ::   zlontao                  ! longitudes of tao    moorings
 …
       !!----------------------------------------------------------------------
+      !
-      idt   = NINT( rdttra(1)     )
-      iddss = NINT( rday          )                                         ! number of seconds in 1 day
-      ihhss = NINT( rmmss * rhhmm )                                         ! number of seconds in 1 hour
-      iyymo = NINT( raamo         )                                         ! number of months in 1 year
       ! frequency of the call of iom_put (attribut: freq_op)
+      tfo = TRIM(i2str(idt))//'s'
+      CALL iom_set_field_attr('field_definition', freq_op=tfo)
+      CALL iom_set_field_attr('SBC'   , freq_op=TRIM(i2str(idt* nn_fsbc ))//'s')
+      CALL iom_set_field_attr('ptrc_T', freq_op=TRIM(i2str(idt* nn_dttrc))//'s')
+      CALL iom_set_field_attr('diad_T', freq_op=TRIM(i2str(idt* nn_dttrc))//'s')
+      WRITE(cl1,'(i1)')        1   ;   CALL iom_set_field_attr('field_definition', freq_op = cl1//'ts', freq_offset='0ts')
+      WRITE(cl1,'(i1)')  nn_fsbc   ;   CALL iom_set_field_attr('SBC'             , freq_op = cl1//'ts', freq_offset='0ts')
+      WRITE(cl1,'(i1)') nn_dttrc   ;   CALL iom_set_field_attr('ptrc_T'          , freq_op = cl1//'ts', freq_offset='0ts')
+      WRITE(cl1,'(i1)') nn_dttrc   ;   CALL iom_set_field_attr('diad_T'          , freq_op = cl1//'ts', freq_offset='0ts')
       ! output file names (attribut: name)
+      clsuff(:) = (/ 'grid_T', 'grid_U', 'grid_V', 'grid_W', 'icemod', 'ptrc_T', 'diad_T', 'scalar' /)
+      DO jg = 1, SIZE(clsuff)                                                                  ! grid type
+         DO jh = 1, 24                                                                         ! 1-24 hours
+            WRITE(cl2,'(i2)') jh
+            CALL dia_nam( clname, jh * ihhss, clsuff(jg), ldfsec = .TRUE. )
+            CALL iom_set_file_attr(TRIM(ADJUSTL(cl2))//'h_'//clsuff(jg), name=TRIM(clname))
+         END DO
+         DO jd = 1, 30                                                                         ! 1-30 days
+            WRITE(cl1,'(i1)') jd
+            CALL dia_nam( clname, jd * iddss, clsuff(jg), ldfsec = .TRUE. )
+            CALL iom_set_file_attr(cl1//'d_'//clsuff(jg), name=TRIM(clname))
+         END DO
+         DO jm = 1, 11                                                                         ! 1-11 months
+            WRITE(cl1,'(i1)') jm
+            CALL dia_nam( clname, -jm, clsuff(jg) )
+            CALL iom_set_file_attr(cl1//'m_'//clsuff(jg), name=TRIM(clname))
+         END DO
+         DO jy = 1, 50                                                                         ! 1-50 years
+            WRITE(cl2,'(i2)') jy
+            CALL dia_nam( clname, -jy * iyymo, clsuff(jg) )
+            CALL iom_set_file_attr(TRIM(ADJUSTL(cl2))//'y_'//clsuff(jg), name=TRIM(clname))
+         END DO
+      DO ji = 1, 9
+         WRITE(cl1,'(i1)') ji
+         CALL iom_update_file_name('file'//cl1)
+      END DO
+      DO ji = 1, 99
+         WRITE(cl2,'(i2.2)') ji
+         CALL iom_update_file_name('file'//cl2)
       END DO
 …
          ! Equatorial section (attributs: jbegin, ni, name_suffix)
          CALL dom_ngb( 0., 0., ix, iy, cl1 )
+         CALL iom_set_domain_attr('Eq'//cl1, zoom_jbegin=iy, zoom_ni=jpiglo)
+         CALL iom_set_file_attr('Eq'//cl1, name_suffix= '_Eq')
+         CALL iom_set_domain_attr ('Eq'//cl1, zoom_jbegin=iy, zoom_ni=jpiglo)
+         CALL iom_get_file_attr   ('Eq'//cl1, name_suffix = clsuff             )
+         CALL iom_set_file_attr   ('Eq'//cl1, name_suffix = TRIM(clsuff)//'_Eq')
+         CALL iom_update_file_name('Eq'//cl1)
       END DO
       ! TAO moorings (attributs: ibegin, jbegin, name_suffix)
 …
    SUBROUTINE set_mooring( plon, plat)
       !!----------------------------------------------------------------------
       !!                     ***  ROUTINE   ***
+      !!                     ***  ROUTINE set_mooring  ***
       !!
       !! ** Purpose :   automatic definitions of moorings xml attributs...
 …
 !!$      CHARACTER(len=1),DIMENSION(4) ::   clgrd = (/ 'T', 'U', 'V', 'W' /)   ! suffix name
       CHARACTER(len=1),DIMENSION(1) ::   clgrd = (/ 'T' /)        ! suffix name
+      CHARACTER(len=50)             ::   clname                   ! file name
+      CHARACTER(len=256)            ::   clname                   ! file name
+      CHARACTER(len=256)            ::   clsuff                   ! suffix name
       CHARACTER(len=1)              ::   cl1                      ! 1 character
       CHARACTER(len=6)              ::   clon,clat                ! name of longitude, latitude
 …
                ENDIF
                clname = TRIM(ADJUSTL(clat))//TRIM(ADJUSTL(clon))
+               CALL iom_set_domain_attr(TRIM(clname)//cl1, zoom_ibegin= ix, zoom_jbegin= iy)
+               CALL iom_set_file_attr(TRIM(clname)//cl1, name_suffix= '_'//TRIM(clname))
+               CALL iom_set_domain_attr (TRIM(clname)//cl1, zoom_ibegin= ix, zoom_jbegin= iy)
+               CALL iom_get_file_attr   (TRIM(clname)//cl1, name_suffix = clsuff                         )
+               CALL iom_set_file_attr   (TRIM(clname)//cl1, name_suffix = TRIM(clsuff)//'_'//TRIM(clname))
+               CALL iom_update_file_name(TRIM(clname)//cl1)
             END DO
          END DO
 …
    END SUBROUTINE set_mooring
+   SUBROUTINE iom_update_file_name( cdid )
+      !!----------------------------------------------------------------------
+      !!                     ***  ROUTINE iom_update_file_name  ***
+      !!
+      !! ** Purpose :
+      !!
+      !!----------------------------------------------------------------------
+      CHARACTER(LEN=*)          , INTENT(in) ::   cdid
+      !
+      CHARACTER(LEN=256) ::   clname
+      CHARACTER(LEN=20)  ::   clfreq
+      CHARACTER(LEN=20)  ::   cldate
+      INTEGER            ::   idx
+      INTEGER            ::   jn
+      INTEGER            ::   itrlen
+      INTEGER            ::   iyear, imonth, iday, isec
+      REAL(wp)           ::   zsec
+      LOGICAL            ::   llexist
+      !!----------------------------------------------------------------------
+      DO jn = 1,2
+         IF( jn == 1 )   CALL iom_get_file_attr( cdid, name        = clname, output_freq = clfreq )
+         IF( jn == 2 )   CALL iom_get_file_attr( cdid, name_suffix = clname )
+         IF ( TRIM(clname) /= '' ) THEN
+            idx = INDEX(clname,'@expname@') + INDEX(clname,'@EXPNAME@')
+            DO WHILE ( idx /= 0 )
+               clname = clname(1:idx-1)//TRIM(cexper)//clname(idx+9:LEN_TRIM(clname))
+               idx = INDEX(clname,'@expname@') + INDEX(clname,'@EXPNAME@')
+            END DO
+            idx = INDEX(clname,'@freq@') + INDEX(clname,'@FREQ@')
+            DO WHILE ( idx /= 0 )
+               IF ( TRIM(clfreq) /= '' ) THEN
+                  itrlen = LEN_TRIM(clfreq)
+                  IF ( clfreq(itrlen-1:itrlen) == 'mo' ) clfreq = clfreq(1:itrlen-1)
+                  clname = clname(1:idx-1)//TRIM(clfreq)//clname(idx+6:LEN_TRIM(clname))
+               ELSE
+                  CALL ctl_stop('error in the name of file id '//TRIM(cdid),   &
+                     & ' attribute output_freq is undefined -> cannot replace @freq@ in '//TRIM(clname) )
+               ENDIF
+               idx = INDEX(clname,'@freq@') + INDEX(clname,'@FREQ@')
+            END DO
+            idx = INDEX(clname,'@startdate@') + INDEX(clname,'@STARTDATE@')
+            DO WHILE ( idx /= 0 )
+               cldate = iom_sdate( fjulday - rdttra(1) / rday )
+               clname = clname(1:idx-1)//TRIM(cldate)//clname(idx+11:LEN_TRIM(clname))
+               idx = INDEX(clname,'@startdate@') + INDEX(clname,'@STARTDATE@')
+            END DO
+            idx = INDEX(clname,'@startdatefull@') + INDEX(clname,'@STARTDATEFULL@')
+            DO WHILE ( idx /= 0 )
+               cldate = iom_sdate( fjulday - rdttra(1) / rday, ldfull = .TRUE. )
+               clname = clname(1:idx-1)//TRIM(cldate)//clname(idx+15:LEN_TRIM(clname))
+               idx = INDEX(clname,'@startdatefull@') + INDEX(clname,'@STARTDATEFULL@')
+            END DO
+            idx = INDEX(clname,'@enddate@') + INDEX(clname,'@ENDDATE@')
+            DO WHILE ( idx /= 0 )
+               cldate = iom_sdate( fjulday + rdttra(1) / rday * REAL( nitend - nit000, wp ), ld24 = .TRUE. )
+               clname = clname(1:idx-1)//TRIM(cldate)//clname(idx+9:LEN_TRIM(clname))
+               idx = INDEX(clname,'@enddate@') + INDEX(clname,'@ENDDATE@')
+            END DO
+            idx = INDEX(clname,'@enddatefull@') + INDEX(clname,'@ENDDATEFULL@')
+            DO WHILE ( idx /= 0 )
+               cldate = iom_sdate( fjulday + rdttra(1) / rday * REAL( nitend - nit000, wp ), ld24 = .TRUE., ldfull = .TRUE. )
+               clname = clname(1:idx-1)//TRIM(cldate)//clname(idx+13:LEN_TRIM(clname))
+               idx = INDEX(clname,'@enddatefull@') + INDEX(clname,'@ENDDATEFULL@')
+            END DO
+            IF( jn == 1 )   CALL iom_set_file_attr( cdid, name        = clname )
+            IF( jn == 2 )   CALL iom_set_file_attr( cdid, name_suffix = clname )
+         ENDIF
+      END DO
+   END SUBROUTINE iom_update_file_name
+   FUNCTION iom_sdate( pjday, ld24, ldfull )
+      !!----------------------------------------------------------------------
+      !!                     ***  ROUTINE iom_sdate  ***
+      !!
+      !! ** Purpose :   send back the date corresponding to the given julian day
+      !!
+      !!----------------------------------------------------------------------
+      REAL(wp), INTENT(in   )           ::   pjday         ! julian day
+      LOGICAL , INTENT(in   ), OPTIONAL ::   ld24          ! true to force 24:00 instead of 00:00
+      LOGICAL , INTENT(in   ), OPTIONAL ::   ldfull        ! true to get the compleate date: yyyymmdd_hh:mm:ss
+      !
+      CHARACTER(LEN=20) ::   iom_sdate
+      CHARACTER(LEN=50) ::   clfmt                         !  format used to write the date
+      INTEGER           ::   iyear, imonth, iday, ihour, iminute, isec
+      REAL(wp)          ::   zsec
+      LOGICAL           ::   ll24, llfull
+      !
+      IF( PRESENT(ld24) ) THEN   ;   ll24 = ld24
+      ELSE                       ;   ll24 = .FALSE.
+      ENDIF
+      IF( PRESENT(ldfull) ) THEN   ;   llfull = ldfull
+      ELSE                         ;   llfull = .FALSE.
+      ENDIF
+      CALL ju2ymds( pjday, iyear, imonth, iday, zsec )
+      isec = NINT(zsec)
+      IF ( ll24 .AND. isec == 0 ) THEN   ! 00:00 of the next day -> move to 24:00 of the current day
+         CALL ju2ymds( pjday - 1., iyear, imonth, iday, zsec )
+         isec = 86400
+      ENDIF
+      IF( iyear < 10000 ) THEN   ;   clfmt = "i4.4,2i2.2"                ! format used to write the date
+      ELSE                       ;   WRITE(clfmt, "('i',i1,',2i2.2')") INT(LOG10(REAL(iyear,wp))) + 1
+      ENDIF
+      IF( llfull ) THEN
+         clfmt = TRIM(clfmt)//",'_',i2.2,':',i2.2,':',i2.2"
+         ihour   = isec / 3600
+         isec    = MOD(isec, 3600)
+         iminute = isec / 60
+         isec    = MOD(isec, 60)
+         WRITE(iom_sdate, '('//TRIM(clfmt)//')') iyear, imonth, iday, ihour, iminute, isec    ! date of the end of run
+      ELSE
+         WRITE(iom_sdate, '('//TRIM(clfmt)//')') iyear, imonth, iday                          ! date of the end of run
+      ENDIF
+   END FUNCTION iom_sdate
 #else
 …
 #endif
-   FUNCTION i2str(int)
-   IMPLICIT NONE
-      INTEGER, INTENT(IN) :: int
-      CHARACTER(LEN=255) :: i2str
-      WRITE(i2str,*) int
-   END FUNCTION i2str
    !!======================================================================

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/LBC/lbclnk.F90

-                      r3768
+                      r4258
    END SUBROUTINE lbc_lnk_3d
-   SUBROUTINE lbc_bdy_lnk_3d( pt3d, cd_type, psgn, ib_bdy )
-      !!---------------------------------------------------------------------
-      !!                  ***  ROUTINE lbc_bdy_lnk  ***
-      !!
-      !! ** Purpose :   wrapper rountine to 'lbc_lnk_3d'. This wrapper is used
-      !!                to maintain the same interface with regards to the mpp case
-      !!
-      !!----------------------------------------------------------------------
-      CHARACTER(len=1)                , INTENT(in   )           ::   cd_type   ! nature of pt3d grid-points
-      REAL(wp), DIMENSION(jpi,jpj,jpk), INTENT(inout)           ::   pt3d      ! 3D array on which the lbc is applied
-      REAL(wp)                        , INTENT(in   )           ::   psgn      ! control of the sign
-      INTEGER                                                   ::   ib_bdy    ! BDY boundary set
-      !!
-      CALL lbc_lnk_3d( pt3d, cd_type, psgn)
-   END SUBROUTINE lbc_bdy_lnk_3d
-   SUBROUTINE lbc_bdy_lnk_2d( pt2d, cd_type, psgn, ib_bdy )
-      !!---------------------------------------------------------------------
-      !!                  ***  ROUTINE lbc_bdy_lnk  ***
-      !!
-      !! ** Purpose :   wrapper rountine to 'lbc_lnk_3d'. This wrapper is used
-      !!                to maintain the same interface with regards to the mpp case
-      !!
-      !!----------------------------------------------------------------------
-      CHARACTER(len=1)                , INTENT(in   )           ::   cd_type   ! nature of pt3d grid-points
-      REAL(wp), DIMENSION(jpi,jpj),     INTENT(inout)           ::   pt2d      ! 3D array on which the lbc is applied
-      REAL(wp)                        , INTENT(in   )           ::   psgn      ! control of the sign
-      INTEGER                                                   ::   ib_bdy    ! BDY boundary set
-      !!
-      CALL lbc_lnk_2d( pt2d, cd_type, psgn)
-   END SUBROUTINE lbc_bdy_lnk_2d
    SUBROUTINE lbc_lnk_2d( pt2d, cd_type, psgn, cd_mpp, pval )
       !!---------------------------------------------------------------------
 …
    END SUBROUTINE lbc_lnk_2d
+#endif
+   SUBROUTINE lbc_bdy_lnk_3d( pt3d, cd_type, psgn, ib_bdy )
+      !!---------------------------------------------------------------------
+      !!                  ***  ROUTINE lbc_bdy_lnk  ***
+      !!
+      !! ** Purpose :   wrapper rountine to 'lbc_lnk_3d'. This wrapper is used
+      !!                to maintain the same interface with regards to the mpp
+      !case
+      !!
+      !!----------------------------------------------------------------------
+      CHARACTER(len=1)                , INTENT(in   )           ::   cd_type   ! nature of pt3d grid-points
+      REAL(wp), DIMENSION(jpi,jpj,jpk), INTENT(inout)           ::   pt3d      ! 3D array on which the lbc is applied
+      REAL(wp)                        , INTENT(in   )           ::   psgn      ! control of the sign
+      INTEGER                                                   ::   ib_bdy    ! BDY boundary set
+      !!
+      CALL lbc_lnk_3d( pt3d, cd_type, psgn)
+   END SUBROUTINE lbc_bdy_lnk_3d
+   SUBROUTINE lbc_bdy_lnk_2d( pt2d, cd_type, psgn, ib_bdy )
+      !!---------------------------------------------------------------------
+      !!                  ***  ROUTINE lbc_bdy_lnk  ***
+      !!
+      !! ** Purpose :   wrapper rountine to 'lbc_lnk_3d'. This wrapper is used
+      !!                to maintain the same interface with regards to the mpp
+      !case
+      !!
+      !!----------------------------------------------------------------------
+      CHARACTER(len=1)                , INTENT(in   )           ::   cd_type   ! nature of pt3d grid-points
+      REAL(wp), DIMENSION(jpi,jpj),     INTENT(inout)           ::   pt2d      ! 3D array on which the lbc is applied
+      REAL(wp)                        , INTENT(in   )           ::   psgn      ! control of the sign
+      INTEGER                                                   ::   ib_bdy    ! BDY boundary set
+      !!
+      CALL lbc_lnk_2d( pt2d, cd_type, psgn)
+   END SUBROUTINE lbc_bdy_lnk_2d
    SUBROUTINE lbc_lnk_2d_e( pt2d, cd_type, psgn, jpri, jprj )
       !!---------------------------------------------------------------------
 …
    END SUBROUTINE lbc_lnk_2d_e
-# endif
 #endif

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/LBC/lib_mpp.F90

-                      r3799
+                      r4258
    ! Arrays used in mpp_lbc_north_3d()
    REAL(wp), DIMENSION(:,:,:)  , ALLOCATABLE, SAVE   ::   ztab, znorthloc
    REAL(wp), DIMENSION(:,:,:,:), ALLOCATABLE, SAVE   ::   znorthgloio
    REAL(wp), DIMENSION(:,:,:)  , ALLOCATABLE, SAVE   ::   zfoldwk      ! Workspace for message transfers avoiding mpi_allgather
+   REAL(wp), DIMENSION(:,:,:)  , ALLOCATABLE, SAVE   ::   tab_3d, xnorthloc
+   REAL(wp), DIMENSION(:,:,:,:), ALLOCATABLE, SAVE   ::   xnorthgloio
+   REAL(wp), DIMENSION(:,:,:)  , ALLOCATABLE, SAVE   ::   foldwk      ! Workspace for message transfers avoiding mpi_allgather
    ! Arrays used in mpp_lbc_north_2d()
    REAL(wp), DIMENSION(:,:)  , ALLOCATABLE, SAVE    ::   ztab_2d, znorthloc_2d
    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE, SAVE    ::   znorthgloio_2d
    REAL(wp), DIMENSION(:,:)  , ALLOCATABLE, SAVE    ::   zfoldwk_2d    ! Workspace for message transfers avoiding mpi_allgather
+   REAL(wp), DIMENSION(:,:)  , ALLOCATABLE, SAVE    ::   tab_2d, xnorthloc_2d
+   REAL(wp), DIMENSION(:,:,:), ALLOCATABLE, SAVE    ::   xnorthgloio_2d
+   REAL(wp), DIMENSION(:,:)  , ALLOCATABLE, SAVE    ::   foldwk_2d    ! Workspace for message transfers avoiding mpi_allgather
    ! Arrays used in mpp_lbc_north_e()
    REAL(wp), DIMENSION(:,:)  , ALLOCATABLE, SAVE    ::   ztab_e, znorthloc_e
    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE, SAVE    ::   znorthgloio_e
+   REAL(wp), DIMENSION(:,:)  , ALLOCATABLE, SAVE    ::   tab_e, xnorthloc_e
+   REAL(wp), DIMENSION(:,:,:), ALLOCATABLE, SAVE    ::   xnorthgloio_e
    ! North fold arrays used to minimise the use of allgather operations. Set in nemo_northcomms (nemogcm) so need to be public
 …
          &      t2p1(jpi,jprecj    ,2)   , t2p2(jpi,jprecj    ,2)   ,                                            &
+         !
          &      ztab(jpiglo,4,jpk) , znorthloc(jpi,4,jpk) , znorthgloio(jpi,4,jpk,jpni) ,                        &
          &      zfoldwk(jpi,4,jpk) ,                                                                             &
+         !
          &      ztab_2d(jpiglo,4)  , znorthloc_2d(jpi,4)  , znorthgloio_2d(jpi,4,jpni)  ,                        &
          &      zfoldwk_2d(jpi,4)  ,                                                                             &
+         !
          &      ztab_e(jpiglo,4+2*jpr2dj) , znorthloc_e(jpi,4+2*jpr2dj) , znorthgloio_e(jpi,4+2*jpr2dj,jpni) ,   &
+         &      tab_3d(jpiglo,4,jpk) , xnorthloc(jpi,4,jpk) , xnorthgloio(jpi,4,jpk,jpni) ,                        &
+         &      foldwk(jpi,4,jpk) ,                                                                             &
+         !
+         &      tab_2d(jpiglo,4)  , xnorthloc_2d(jpi,4)  , xnorthgloio_2d(jpi,4,jpni)  ,                        &
+         &      foldwk_2d(jpi,4)  ,                                                                             &
+         !
+         &      tab_e(jpiglo,4+2*jpr2dj) , xnorthloc_e(jpi,4+2*jpr2dj) , xnorthgloio_e(jpi,4+2*jpr2dj,jpni) ,   &
+         !
          &      STAT=lib_mpp_alloc )
 …
 !!gm Remark : this is very time consumming!!!
       !                                         ! ------------------------ !
             IF( ijpt0 > ijpt1 .OR. iipt0 > iipt1 ) THEN
+        IF(((nbondi .ne. 0) .AND. (ktype .eq. 2)) .OR. ((nbondj .ne. 0) .AND. (ktype .eq. 1))) THEN
             ! there is nothing to be migrated
                lmigr = .FALSE.
+              lmigr = .TRUE.
             ELSE
               lmigr = .TRUE.
+              lmigr = .FALSE.
             ENDIF
 …
       ityp = -1
       ijpjm1 = 3
       ztab(:,:,:) = 0.e0
+      !
       DO jj = nlcj - ijpj +1, nlcj          ! put in znorthloc the last 4 jlines of pt3d
+      tab_3d(:,:,:) = 0.e0
+      !
+      DO jj = nlcj - ijpj +1, nlcj          ! put in xnorthloc the last 4 jlines of pt3d
          ij = jj - nlcj + ijpj
          znorthloc(:,ij,:) = pt3d(:,jj,:)
+         xnorthloc(:,ij,:) = pt3d(:,jj,:)
       END DO
+      !
       !                                     ! Build in procs of ncomm_north the znorthgloio
+      !                                     ! Build in procs of ncomm_north the xnorthgloio
       itaille = jpi * jpk * ijpj
       IF ( l_north_nogather ) THEN
 …
             ij = jj - nlcj + ijpj
             DO ji = 1, nlci
                ztab(ji+nimpp-1,ij,:) = pt3d(ji,jj,:)
+               tab_3d(ji+nimpp-1,ij,:) = pt3d(ji,jj,:)
             END DO
          END DO
 …
             DO jr = 1,nsndto(ityp)
                CALL mppsend(5, znorthloc, itaille, isendto(jr,ityp), ml_req_nf(jr) )
+               CALL mppsend(5, xnorthloc, itaille, isendto(jr,ityp), ml_req_nf(jr) )
             END DO
             DO jr = 1,nsndto(ityp)
                CALL mpprecv(5, zfoldwk, itaille, isendto(jr,ityp))
+               CALL mpprecv(5, foldwk, itaille, isendto(jr,ityp))
                iproc = isendto(jr,ityp) + 1
                ildi = nldit (iproc)
 …
                DO jj = 1, ijpj
                   DO ji = ildi, ilei
                      ztab(ji+iilb-1,jj,:) = zfoldwk(ji,jj,:)
+                     tab_3d(ji+iilb-1,jj,:) = foldwk(ji,jj,:)
                   END DO
                END DO
 …
       IF ( ityp .lt. 0 ) THEN
          CALL MPI_ALLGATHER( znorthloc  , itaille, MPI_DOUBLE_PRECISION,                &
             &                znorthgloio, itaille, MPI_DOUBLE_PRECISION, ncomm_north, ierr )
+         CALL MPI_ALLGATHER( xnorthloc  , itaille, MPI_DOUBLE_PRECISION,                &
+            &                xnorthgloio, itaille, MPI_DOUBLE_PRECISION, ncomm_north, ierr )
+         !
          DO jr = 1, ndim_rank_north         ! recover the global north array
 …
             DO jj = 1, ijpj
                DO ji = ildi, ilei
                   ztab(ji+iilb-1,jj,:) = znorthgloio(ji,jj,:,jr)
+                  tab_3d(ji+iilb-1,jj,:) = xnorthgloio(ji,jj,:,jr)
                END DO
             END DO
 …
       ENDIF
+      !
       ! The ztab array has been either:
+      ! The tab_3d array has been either:
       !  a. Fully populated by the mpi_allgather operation or
       !  b. Had the active points for this domain and northern neighbours populated
 …
       ! this domain will be identical.
+      !
       CALL lbc_nfd( ztab, cd_type, psgn )   ! North fold boundary condition
+      CALL lbc_nfd( tab_3d, cd_type, psgn )   ! North fold boundary condition
+      !
       DO jj = nlcj-ijpj+1, nlcj             ! Scatter back to pt3d
          ij = jj - nlcj + ijpj
          DO ji= 1, nlci
             pt3d(ji,jj,:) = ztab(ji+nimpp-1,ij,:)
+            pt3d(ji,jj,:) = tab_3d(ji+nimpp-1,ij,:)
          END DO
       END DO
 …
       ityp = -1
       ijpjm1 = 3
       ztab_2d(:,:) = 0.e0
+      !
       DO jj = nlcj-ijpj+1, nlcj             ! put in znorthloc_2d the last 4 jlines of pt2d
+      tab_2d(:,:) = 0.e0
+      !
+      DO jj = nlcj-ijpj+1, nlcj             ! put in xnorthloc_2d the last 4 jlines of pt2d
          ij = jj - nlcj + ijpj
          znorthloc_2d(:,ij) = pt2d(:,jj)
+         xnorthloc_2d(:,ij) = pt2d(:,jj)
       END DO
       !                                     ! Build in procs of ncomm_north the znorthgloio_2d
+      !                                     ! Build in procs of ncomm_north the xnorthgloio_2d
       itaille = jpi * ijpj
       IF ( l_north_nogather ) THEN
 …
             ij = jj - nlcj + ijpj
             DO ji = 1, nlci
                ztab_2d(ji+nimpp-1,ij) = pt2d(ji,jj)
+               tab_2d(ji+nimpp-1,ij) = pt2d(ji,jj)
             END DO
          END DO
 …
             DO jr = 1,nsndto(ityp)
                CALL mppsend(5, znorthloc_2d, itaille, isendto(jr,ityp), ml_req_nf(jr) )
+               CALL mppsend(5, xnorthloc_2d, itaille, isendto(jr,ityp), ml_req_nf(jr) )
             END DO
             DO jr = 1,nsndto(ityp)
                CALL mpprecv(5, zfoldwk_2d, itaille, isendto(jr,ityp))
+               CALL mpprecv(5, foldwk_2d, itaille, isendto(jr,ityp))
                iproc = isendto(jr,ityp) + 1
                ildi = nldit (iproc)
 …
                DO jj = 1, ijpj
                   DO ji = ildi, ilei
                      ztab_2d(ji+iilb-1,jj) = zfoldwk_2d(ji,jj)
+                     tab_2d(ji+iilb-1,jj) = foldwk_2d(ji,jj)
                   END DO
                END DO
 …
       IF ( ityp .lt. 0 ) THEN
          CALL MPI_ALLGATHER( znorthloc_2d  , itaille, MPI_DOUBLE_PRECISION,        &
             &                znorthgloio_2d, itaille, MPI_DOUBLE_PRECISION, ncomm_north, ierr )
+         CALL MPI_ALLGATHER( xnorthloc_2d  , itaille, MPI_DOUBLE_PRECISION,        &
+            &                xnorthgloio_2d, itaille, MPI_DOUBLE_PRECISION, ncomm_north, ierr )
+         !
          DO jr = 1, ndim_rank_north            ! recover the global north array
 …
             DO jj = 1, ijpj
                DO ji = ildi, ilei
                   ztab_2d(ji+iilb-1,jj) = znorthgloio_2d(ji,jj,jr)
+                  tab_2d(ji+iilb-1,jj) = xnorthgloio_2d(ji,jj,jr)
                END DO
             END DO
 …
       ENDIF
+      !
       ! The ztab array has been either:
+      ! The tab array has been either:
       !  a. Fully populated by the mpi_allgather operation or
       !  b. Had the active points for this domain and northern neighbours populated
 …
       ! this domain will be identical.
+      !
       CALL lbc_nfd( ztab_2d, cd_type, psgn )   ! North fold boundary condition
+      CALL lbc_nfd( tab_2d, cd_type, psgn )   ! North fold boundary condition
+      !
+      !
 …
          ij = jj - nlcj + ijpj
          DO ji = 1, nlci
             pt2d(ji,jj) = ztab_2d(ji+nimpp-1,ij)
+            pt2d(ji,jj) = tab_2d(ji+nimpp-1,ij)
          END DO
       END DO
 …
+      !
       ijpj=4
       ztab_e(:,:) = 0.e0
+      tab_e(:,:) = 0.e0
       ij=0
       ! put in znorthloc_e the last 4 jlines of pt2d
+      ! put in xnorthloc_e the last 4 jlines of pt2d
       DO jj = nlcj - ijpj + 1 - jpr2dj, nlcj +jpr2dj
          ij = ij + 1
          DO ji = 1, jpi
             znorthloc_e(ji,ij)=pt2d(ji,jj)
+            xnorthloc_e(ji,ij)=pt2d(ji,jj)
          END DO
       END DO
+      !
       itaille = jpi * ( ijpj + 2 * jpr2dj )
       CALL MPI_ALLGATHER( znorthloc_e(1,1)  , itaille, MPI_DOUBLE_PRECISION,    &
          &                znorthgloio_e(1,1,1), itaille, MPI_DOUBLE_PRECISION, ncomm_north, ierr )
+      CALL MPI_ALLGATHER( xnorthloc_e(1,1)  , itaille, MPI_DOUBLE_PRECISION,    &
+         &                xnorthgloio_e(1,1,1), itaille, MPI_DOUBLE_PRECISION, ncomm_north, ierr )
+      !
       DO jr = 1, ndim_rank_north            ! recover the global north array
 …
          DO jj = 1, ijpj+2*jpr2dj
             DO ji = ildi, ilei
                ztab_e(ji+iilb-1,jj) = znorthgloio_e(ji,jj,jr)
+               tab_e(ji+iilb-1,jj) = xnorthgloio_e(ji,jj,jr)
             END DO
          END DO
 …
       ! 2. North-Fold boundary conditions
       ! ----------------------------------
       CALL lbc_nfd( ztab_e(:,:), cd_type, psgn, pr2dj = jpr2dj )
+      CALL lbc_nfd( tab_e(:,:), cd_type, psgn, pr2dj = jpr2dj )
       ij = jpr2dj
 …
       ij  = ij +1
          DO ji= 1, nlci
             pt2d(ji,jj) = ztab_e(ji+nimpp-1,ij)
+            pt2d(ji,jj) = tab_e(ji+nimpp-1,ij)
          END DO
       END DO

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/LBC/mppini_2.h90

-                      r3818
+                      r4258
       irestj = 1 + MOD( jpjglo - nrecj -1 , jpnj )
+#if defined key_nemocice_decomp
+      ! Change padding to be consistent with CICE
+      ilci(1:jpni-1      ,:) = jpi
+      ilci(jpni          ,:) = jpiglo - (jpni - 1) * (jpi - nreci)
+      ilcj(:,      1:jpnj-1) = jpj
+      ilcj(:,          jpnj) = jpjglo - (jpnj - 1) * (jpj - nrecj)
+#else
       ilci(1:iresti      ,:) = jpi
       ilci(iresti+1:jpni ,:) = jpi-1
 …
       ilcj(:,      1:irestj) = jpj
       ilcj(:, irestj+1:jpnj) = jpj-1
+#endif
       IF(lwp) WRITE(numout,*)

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/SBC/geo2ocean.F90

-                      r2715
+                      r4258
          &      gsinf(jpi,jpj), gcosf(jpi,jpj), STAT=ierr )
       IF(lk_mpp)   CALL mpp_sum( ierr )
       IF( ierr /= 0 )   CALL ctl_stop('STOP', 'angle_msh_geo: unable to allocate arrays' )
+      IF( ierr /= 0 )   CALL ctl_stop('angle: unable to allocate arrays' )
       ! ============================= !
 …
             &      gsinlat(jpi,jpj,4) , gcoslat(jpi,jpj,4) , STAT=ierr )
          IF( lk_mpp    )   CALL mpp_sum( ierr )
          IF( ierr /= 0 )   CALL ctl_stop('STOP', 'angle_msh_geo: unable to allocate arrays' )
+         IF( ierr /= 0 )   CALL ctl_stop('geo2oce: unable to allocate arrays' )
       ENDIF
 …
       !!----------------------------------------------------------------------
       IF( ALLOCATED( gsinlon ) ) THEN
+      IF( .NOT. ALLOCATED( gsinlon ) ) THEN
          ALLOCATE( gsinlon(jpi,jpj,4) , gcoslon(jpi,jpj,4) ,   &
             &      gsinlat(jpi,jpj,4) , gcoslat(jpi,jpj,4) , STAT=ierr )
          IF( lk_mpp    )   CALL mpp_sum( ierr )
          IF( ierr /= 0 )   CALL ctl_stop('STOP', 'angle_msh_geo: unable to allocate arrays' )
+         IF( ierr /= 0 )   CALL ctl_stop('oce2geo: unable to allocate arrays' )
       ENDIF

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/SBC/sbc_oce.F90

-                      r3865
+                      r4258
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:) ::   sfx    , sfx_b    !: salt flux                                    [PSU/m2/s]
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:) ::   emp_tot           !: total E-P over ocean and ice                 [Kg/m2/s]
+   REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:) ::   fmmflx            !: freshwater budget: freezing/melting          [Kg/m2/s]
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:) ::   rnf    , rnf_b    !: river runoff   [Kg/m2/s]
    !!
 …
          &      qsr_tot(jpi,jpj) , qsr  (jpi,jpj) ,                        &
          &      emp    (jpi,jpj) , emp_b(jpi,jpj) ,                        &
          &      sfx    (jpi,jpj) , sfx_b(jpi,jpj) , emp_tot(jpi,jpj) , STAT=ierr(2) )
+         &      sfx    (jpi,jpj) , sfx_b(jpi,jpj) , emp_tot(jpi,jpj), fmmflx(jpi,jpj), STAT=ierr(2) )
+         !
       ALLOCATE( rnf  (jpi,jpj) , sbc_tsc  (jpi,jpj,jpts) , qsr_hc  (jpi,jpj,jpk) ,     &

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/SBC/sbccpl.F90

-                      r3680
+                      r4258
       SELECT CASE( TRIM( sn_rcv_emp%cldes ) )
       CASE( 'oce only'      )   ;   srcv(                                 jpr_oemp   )%laction = .TRUE.
+      CASE( 'conservative'  )   ;   srcv( (/jpr_rain, jpr_snow, jpr_ievp, jpr_tevp/) )%laction = .TRUE.
+      CASE( 'conservative'  )
+         srcv( (/jpr_rain, jpr_snow, jpr_ievp, jpr_tevp/) )%laction = .TRUE.
+         IF ( k_ice <= 1 )  srcv(jpr_ivep)%laction = .FALSE.
       CASE( 'oce and ice'   )   ;   srcv( (/jpr_ievp, jpr_sbpr, jpr_semp, jpr_oemp/) )%laction = .TRUE.
       CASE default              ;   CALL ctl_stop( 'sbc_cpl_init: wrong definition of sn_rcv_emp%cldes' )
 …
          CALL ctl_stop( 'sbc_cpl_init: namsbc_cpl namelist mismatch between sn_rcv_qns%cldes and sn_rcv_dqnsdt%cldes' )
       !                                                      ! ------------------------- !
-      !                                                      !    Ice Qsr penetration    !
-      !                                                      ! ------------------------- !
-      ! fraction of net shortwave radiation which is not absorbed in the thin surface layer
-      ! and penetrates inside the ice cover ( Maykut and Untersteiner, 1971 ; Elbert anbd Curry, 1993 )
-      ! Coupled case: since cloud cover is not received from atmosphere
-      !               ===> defined as constant value -> definition done in sbc_cpl_init
-      fr1_i0(:,:) = 0.18
-      fr2_i0(:,:) = 0.82
-      !                                                      ! ------------------------- !
       !                                                      !      10m wind module      !
       !                                                      ! ------------------------- !
 …
       ! Allocate taum part of frcv which is used even when not received as coupling field
       IF ( .NOT. srcv(jpr_taum)%laction ) ALLOCATE( frcv(jpr_taum)%z3(jpi,jpj,srcv(jn)%nct) )
+      ! Allocate itx1 and ity1 as they are used in sbc_cpl_ice_tau even if srcv(jpr_itx1)%laction = .FALSE.
+      IF( k_ice /= 0 ) THEN
+         IF ( .NOT. srcv(jpr_itx1)%laction ) ALLOCATE( frcv(jpr_itx1)%z3(jpi,jpj,srcv(jn)%nct) )
+         IF ( .NOT. srcv(jpr_ity1)%laction ) ALLOCATE( frcv(jpr_ity1)%z3(jpi,jpj,srcv(jn)%nct) )
+      END IF
       ! ================================ !
 …
       !!                 third  as  2 components on the cp_ice_msh point
       !!
       !!                In 'oce and ice' case, only one vector stress field
+      !!                Except in 'oce and ice' case, only one vector stress field
       !!             is received. It has already been processed in sbc_cpl_rcv
       !!             so that it is now defined as (i,j) components given at U-
       !!             and V-points, respectively. Therefore, here only the third
+      !!             and V-points, respectively. Therefore, only the third
       !!             transformation is done and only if the ice-grid is a 'I'-grid.
       !!
 …
       END SELECT
+      !    Ice Qsr penetration used (only?)in lim2 or lim3
+      ! fraction of net shortwave radiation which is not absorbed in the thin surface layer
+      ! and penetrates inside the ice cover ( Maykut and Untersteiner, 1971 ; Elbert anbd Curry, 1993 )
+      ! Coupled case: since cloud cover is not received from atmosphere
+      !               ===> defined as constant value -> definition done in sbc_cpl_init
+      fr1_i0(:,:) = 0.18
+      fr2_i0(:,:) = 0.82
       CALL wrk_dealloc( jpi,jpj, zcptn, ztmp, zicefr )
+      !

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/SBC/sbcmod.F90

-                      r3764
+                      r4258
       sfx(:,:) = 0.0_wp                            ! the salt flux due to freezing/melting will be computed (i.e. will be non-zero)
                                                    ! only if sea-ice is present
+      fmmflx(:,:) = 0.0_wp                        ! freezing-melting array initialisation
       !                                            ! restartability
 …
          IF( nsbc ==  6 )   WRITE(numout,*) '              MFS Bulk formulation'
       ENDIF
+      !
+                          CALL sbc_ssm_init               ! Sea-surface mean fields initialisation
+      !
       IF( ln_ssr      )   CALL sbc_ssr_init               ! Sea-Surface Restoring initialisation
 …
                                                                 ! (includes virtual salt flux beneath ice
                                                                 ! in linear free surface case)
+         CALL iom_put( "fmmflx", fmmflx  )                      ! Freezing-melting water flux
          CALL iom_put( "qt"    , qns  + qsr )                   ! total heat flux
          CALL iom_put( "qns"   , qns        )                   ! solar heat flux

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/SOL/solmat.F90

-                      r3609
+                      r4258
    USE lbclnk          ! lateral boudary conditions
    USE lib_mpp         ! distributed memory computing
+   USE c1d               ! 1D vertical configuration
    USE in_out_manager  ! I/O manager
    USE timing          ! timing
 …
       ! SOR and PCG solvers
+      IF( lk_c1d ) CALL lbc_lnk( gcdmat, 'T', 1._wp ) ! 1D case bmask =/0  but gcdmat not define everywhere
       DO jj = 1, jpj
          DO ji = 1, jpi

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/TRA/eosbn2.F90

-                      r3865
+                      r4258
    FUNCTION tfreez( psal ) RESULT( ptf )
+   FUNCTION tfreez( psal, pdep ) RESULT( ptf )
       !!----------------------------------------------------------------------
       !!                 ***  ROUTINE eos_init  ***
 …
       !!----------------------------------------------------------------------
       REAL(wp), DIMENSION(jpi,jpj), INTENT(in   ) ::   psal   ! salinity             [psu]
+      REAL(wp), DIMENSION(jpi,jpj), INTENT(in   ), OPTIONAL ::   pdep   ! depth      [decibars]
       ! Leave result array automatic rather than making explicitly allocated
       REAL(wp), DIMENSION(jpi,jpj)                ::   ptf    ! freezing temperature [Celcius]
 …
       ptf(:,:) = ( - 0.0575_wp + 1.710523e-3_wp * SQRT( psal(:,:) )   &
          &                     - 2.154996e-4_wp *       psal(:,:)   ) * psal(:,:)
+      IF ( PRESENT( pdep ) ) THEN
+         ptf(:,:) = ptf(:,:) - 7.53e-4_wp * pdep(:,:)
+      ENDIF
+      !
    END FUNCTION tfreez

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/OPA_SRC/step.F90

r4246	r4258
314	314	!
315	315	#if defined key_iomput
316		IF( kstp == nitend ) CALL xios_context_finalize() ! needed for XIOS+AGRIF
	316	IF( kstp == nitend .OR. indic < 0 ) CALL xios_context_finalize() ! needed for XIOS+AGRIF
317	317	#endif
318	318	!

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/SAS_SRC/daymod.F90

-                      r3851
+                      r4258
                nday_year = 1
                nsec_year = ndt05
+               IF( nsec1jan000 >= 2 * (2**30 - nsecd * nyear_len(1) / 2 ) ) THEN   ! test integer 4 max value
+                  CALL ctl_stop( 'The number of seconds between Jan. 1st 00h of nit000 year and Jan. 1st 00h ',   &
+                     &           'of the current year is exceeding the INTEGER 4 max VALUE: 2^31-1 -> 68.09 years in seconds', &
+                     & 'You must do a restart at higher frequency (or remove this STOP and recompile everything in I8)' )
+               ENDIF
                nsec1jan000 = nsec1jan000 + nsecd * nyear_len(1)
                IF( nleapy == 1 )   CALL day_mth

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/SAS_SRC/diawri.F90

-                      r3862
+                      r4258
          CALL histdef( nid_T, "sowaflup", "Net Upward Water Flux"              , "Kg/m2/s",   &  ! (emp-rnf)
             &          jpi, jpj, nh_T, 1  , 1, 1  , -99 , 32, clop, zsto, zout )
          CALL histdef( nid_T, "sowaflcd", "concentration/dilution water flux"  , "kg/m2/s",   &  ! (emps-rnf)
             &          jpi, jpj, nh_T, 1  , 1, 1  , -99 , 32, clop, zsto, zout )
+         CALL histdef( nid_T, "sosfldow", "downward salt flux"                 , "PSU/m2/s",  &  ! (sfx)
+             &         jpi, jpj, nh_T, 1  , 1, 1  , -99 , 32, clop, zsto, zout )
          CALL histdef( nid_T, "sohefldo", "Net Downward Heat Flux"             , "W/m2"   ,   &  ! qns + qsr
             &          jpi, jpj, nh_T, 1  , 1, 1  , -99 , 32, clop, zsto, zout )
 …
       CALL histwrite( nid_T, "sst_m", it, sst_m, ndim_hT, ndex_hT )   ! sea surface temperature
       CALL histwrite( nid_T, "sss_m", it, sss_m, ndim_hT, ndex_hT )   ! sea surface salinity
+      CALL histwrite( nid_T, "sowaflup", it, emp   , ndim_hT, ndex_hT )   ! upward water flux
+      CALL histwrite( nid_T, "sowaflcd", it, emps  , ndim_hT, ndex_hT )   ! c/d water flux
+      CALL histwrite( nid_T, "sowaflup", it, (emp - rnf )  , ndim_hT, ndex_hT )   ! upward water flux
+      CALL histwrite( nid_T, "sosfldow", it, sfx           , ndim_hT, ndex_hT )   ! downward salt flux
+                                                                                  ! (includes virtual salt flux beneath ice
+                                                                                  ! in linear free surface case)
       CALL histwrite( nid_T, "sohefldo", it, qns + qsr     , ndim_hT, ndex_hT )   ! total heat flux
       CALL histwrite( nid_T, "soshfldo", it, qsr           , ndim_hT, ndex_hT )   ! solar heat flux

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/SAS_SRC/nemogcm.F90

-                      r3769
+                      r4258
       USE diawri    , ONLY: dia_wri_alloc
       USE dom_oce   , ONLY: dom_oce_alloc
+      !
+      INTEGER :: ierr
+      USE oce       , ONLY : sshn, sshb, snwice_mass, snwice_mass_b, snwice_fmass
+      !
+      INTEGER :: ierr,ierr4
       !!----------------------------------------------------------------------
+      !
 …
       ierr = ierr + dom_oce_alloc   ()          ! ocean domain
       ierr = ierr + lib_mpp_alloc   (numout)    ! mpp exchanges
+      ALLOCATE( snwice_mass(jpi,jpj)  , snwice_mass_b(jpi,jpj),             &
+         &      snwice_fmass(jpi,jpj), STAT= ierr4 )
+      ierr = ierr + ierr4
+      !
       IF( lk_mpp    )   CALL mpp_sum( ierr )

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/SAS_SRC/sbcssm.F90

-                      r3364
+                      r4258
+      !
+      IF (kt == nn_it000 ) CALL sbc_ssm_init()
       IF( nn_timing == 1 )  CALL timing_start( 'sbc_ssm')
 …
       tsn(:,:,1,jp_tem) = sst_m(:,:)
       tsn(:,:,1,jp_sal) = sss_m(:,:)
+      IF ( nn_ice == 1 ) THEN
+         tsb(:,:,1,jp_tem) = sst_m(:,:)
+         tsb(:,:,1,jp_sal) = sss_m(:,:)
+      ENDIF
       ub (:,:,1       ) = ssu_m(:,:)
       vb (:,:,1       ) = ssv_m(:,:)
 …
       TYPE(FLD_N) :: sn_usp, sn_vsp, sn_ssh
+      !
       NAMELIST/namsbc_ssm/cn_dir, ln_3d_uv, sn_tem, sn_sal, sn_usp, sn_vsp, sn_ssh
+      NAMELIST/namsbc_sas/cn_dir, ln_3d_uv, sn_tem, sn_sal, sn_usp, sn_vsp, sn_ssh
       !!----------------------------------------------------------------------
 …
+      !
       REWIND( numnam )                          ! read in namlist namsbc_ssm
       READ  ( numnam, namsbc_ssm )
+      READ  ( numnam, namsbc_sas )
       !                                         ! store namelist information in an array
       !                                         ! Control print
       IF(lwp) THEN
          WRITE(numout,*)
          WRITE(numout,*) 'sbc_ssm : standalone surface scheme '
+         WRITE(numout,*) 'sbc_sas : standalone surface scheme '
          WRITE(numout,*) '~~~~~~~~~~~ '
          WRITE(numout,*) '   Namelist namsbc_ssm'
+         WRITE(numout,*) '   Namelist namsbc_sas'
          WRITE(numout,*)
       ENDIF
 …
       ! so allocate enough of arrays to use
+      !
+      ierr3 = 0
       jpm = MAX(jp_tem, jp_sal)
       ALLOCATE( tsn(jpi,jpj,1,jpm), STAT=ierr0 )
       ALLOCATE( ub(jpi,jpj,1)     , STAT=ierr1 )
       ALLOCATE( vb(jpi,jpj,1)     , STAT=ierr2 )
+      ierr = ierr0 + ierr1 + ierr2
+      IF ( nn_ice == 1 ) ALLOCATE( tsb(jpi,jpj,1,jpm), STAT=ierr3 )
+      ierr = ierr0 + ierr1 + ierr2 + ierr3
       IF( ierr > 0 ) THEN
          CALL ctl_stop('sbc_ssm_init: unable to allocate surface arrays')

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zfechem.F90

-                      r3780
+                      r4258
                   zoxy   = trn(ji,jj,jk,jpoxy) * ( rhop(ji,jj,jk) / 1.e3 )
                   ! Fe2+ oxydation rate from Santana-Casiano et al. (2005)
                   zkox   = 35.407 - 6.7109 * zph + 0.5342 * zph * zph - 5362.6 / ( tsn(ji,jj,1,jp_tem) + 273.15 )  &
+                  zkox   = 35.407 - 6.7109 * zph + 0.5342 * zph * zph - 5362.6 / ( tsn(ji,jj,jk,jp_tem) + 273.15 )  &
                     &    - 0.04406 * SQRT( tsn(ji,jj,jk,jp_sal) ) - 0.002847 * tsn(ji,jj,jk,jp_sal)
                   zkox   = ( 10.** zkox ) * spd
 …
                zdep    = MIN( 1., 1000. / fsdept(ji,jj,jk) )
                zlam1b  = xlam1 * MAX( 0.e0, ( trn(ji,jj,jk,jpfer) * 1.e9 - ztotlig(ji,jj,jk) ) )
                zcoag   = zfeequi * zlam1b * zstep + 1E-4 * ( 1. - zlamfac ) * zdep * zstep *zfecoll
+               zcoag   = zfeequi * zlam1b * zstep + 1E-4 * ( 1. - zlamfac ) * zdep * zstep * trn(ji,jj,jk,jpfer)
                !  Compute the coagulation of colloidal iron. This parameterization
 …
                tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zscave * zdenom1 + zaggdfea + zaggdfeb
 #else
                zlam1b = 3.53E3 *   trn(ji,jj,jk,jpgoc) * xdiss(ji,jj,jk) + 1E-4 * ( 1. - zlamfac ) * zdep
+               zlam1b = 3.53E3 *   trn(ji,jj,jk,jpgoc) * xdiss(ji,jj,jk)
                zaggdfeb = zlam1b * zstep * zfecoll
+               !

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zflx.F90

-                      r3481
+                      r4258
          ! then the first atmospheric CO2 record read is at years(1)
          zyr_dec = REAL( nyear + nn_offset, wp ) + REAL( nday_year, wp ) / REAL( nyear_len(1), wp )
          jm = 2
          DO WHILE( jm <= nmaxrec .AND. years(jm-1) < zyr_dec .AND. years(jm) >= zyr_dec ) ;  jm = jm + 1 ;  END DO
+         jm = 1
+         DO WHILE( jm <= nmaxrec .AND. years(jm) < zyr_dec ) ;  jm = jm + 1 ;  END DO
          iind = jm  ;   iindm1 = jm - 1
          zdco2dt = ( atcco2h(iind) - atcco2h(iindm1) ) / ( years(iind) - years(iindm1) + rtrn )
 …
       END DO
       t_oce_co2_flx = t_oce_co2_flx + glob_sum( oce_co2(:,:) )            ! Cumulative Total Flux of Carbon
       t_atm_co2_flx = glob_sum( satmco2(:,:) * patm(:,:) * e1e2t(:,:) )   ! Total atmospheric pCO2
+      t_oce_co2_flx = t_oce_co2_flx + glob_sum( oce_co2(:,:) )      ! Cumulative Total Flux of Carbon
+      t_atm_co2_flx = glob_sum( satmco2(:,:) * e1e2t(:,:) )         ! Total atmospheric pCO2
       IF(ln_ctl)   THEN  ! print mean trends (used for debugging)

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zmeso.F90

-                      r3856
+                      r4258
                !  ----------------------------------
 # if ! defined key_kriest
+               zgrazffeg = grazflux  * zstep * wsbio4(ji,jj,jk)      &
+!                 &                   * tgfunc2(ji,jj,jk) * trn(ji,jj,jk,jpgoc) * trn(ji,jj,jk,jpmes)
+               &                     * 2. *  trn(ji,jj,jk,jpgoc) * trn(ji,jj,jk,jpmes)
+               zgrazffeg = grazflux  * zstep * wsbio4(ji,jj,jk) * trn(ji,jj,jk,jpgoc) * trn(ji,jj,jk,jpmes)
                zgrazfffg = zgrazffeg * trn(ji,jj,jk,jpbfe) / (trn(ji,jj,jk,jpgoc) + rtrn)
 # endif
+               zgrazffep = grazflux  * zstep *  wsbio3(ji,jj,jk)     &
+!                 &                   * tgfunc2(ji,jj,jk) * trn(ji,jj,jk,jppoc) * trn(ji,jj,jk,jpmes)
+               &                     * 2. * trn(ji,jj,jk,jppoc) * trn(ji,jj,jk,jpmes)
+               zgrazffep = grazflux  * zstep *  wsbio3(ji,jj,jk) * trn(ji,jj,jk,jppoc) * trn(ji,jj,jk,jpmes)
                zgrazfffp = zgrazffep * trn(ji,jj,jk,jpsfe) / (trn(ji,jj,jk,jppoc) + rtrn)
+              !
 …
               ! Compute the proportion of filter feeders
               zproport  = (zgrazffep + zgrazffeg)/(rtrn + zgraztot)
+              ! Compute fractionation of aggregates. It is assumed that diatoms based aggregates are more prone to fractionation
+              ! since they are more porous (marine snow instead of fecal pellets)
               zratio    = trn(ji,jj,jk,jpgsi) / ( trn(ji,jj,jk,jpgoc) + rtrn )
               zratio2   = zratio * zratio
+!              zfrac =  zproport * 0.15 * zstep *                     &
+!                       ( 0.2 + 0.8 * zratio2 / ( 1.5**2 + zratio2 ) )   &
+!                      *trn(ji,jj,jk,jpmes)/3E-7 *trn(ji,jj,jk,jpgoc)
+              zfrac     = zproport * grazflux  * zstep * wsbio4(ji,jj,jk)      &
+                 &       * ( 0.1 + 3.9 * zratio2 / ( 1.**2 + zratio2 ) )       &
+                 &       * 2. * trn(ji,jj,jk,jpmes) * trn(ji,jj,jk,jpgoc)
+              zfrac     = zproport * zgrazffeg * ( 0.1 + 3.9 * zratio2 / ( 1.**2 + zratio2 ) )
               zfracfe   = zfrac * trn(ji,jj,jk,jpbfe) / (trn(ji,jj,jk,jpgoc) + rtrn)
 …
                zepshert  = epsher2 * MIN( 1., zncratio )
                zepsherv  = zepshert * MIN( 1., zgrasrat / ferat3 )
                zgrarem2  = zgraztot * ( 1. - zepsherv - unass2 ) + zrespz2  &
                &    + ( 1. - zepsherv - unass2 ) /( 1. - zepsherv + rtrn) * ztortz2
                zgrafer2  = zgraztot * MAX( 0. , ( 1. - unass2 ) * zgrasrat - ferat3 * zepsherv )    &
                &    + ferat3 * ( zrespz2 + ( 1. - zepsherv - unass2 ) /( 1. - zepsherv + rtrn) * ztortz2 )
+               zgrarem2  =  zgraztot * ( 1. - zepsherv - unass2 ) + zrespz2  &
+                  &       + ( 1. - zepsherv - unass2 ) /( 1. - zepsherv ) * ztortz2
+               zgrafer2  =  zgraztot * MAX( 0. , ( 1. - unass2 ) * zgrasrat - ferat3 * zepsherv )    &
+                  &       + ferat3 * ( zrespz2 + ( 1. - zepsherv - unass2 ) /( 1. - zepsherv ) * ztortz2 )
                zgrapoc2  = zgraztot * unass2
 …
                tra(ji,jj,jk,jpdic) = tra(ji,jj,jk,jpdic) + zgrarsig
                tra(ji,jj,jk,jptal) = tra(ji,jj,jk,jptal) + rno3 * zgrarsig
+#if defined key_kriest
+               tra(ji,jj,jk,jppoc) = tra(ji,jj,jk,jppoc) + zgrapoc2
+               tra(ji,jj,jk,jpnum) = tra(ji,jj,jk,jpnum) + zgrapoc2 * xkr_dmeso
+               tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zgraztotf * unass2
+#else
+               tra(ji,jj,jk,jpgoc) = tra(ji,jj,jk,jpgoc) + zgrapoc2 - zfrac
+               tra(ji,jj,jk,jppoc) = tra(ji,jj,jk,jppoc) + zfrac
+               tra(ji,jj,jk,jpbfe) = tra(ji,jj,jk,jpbfe) + zgraztotf * unass2 - zfracfe
+               tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zfracfe
+#endif
                zmortz2 = ztortz2 + zrespz2
                zmortzgoc = unass2 / ( 1. - zepsherv + rtrn ) * ztortz2
+               zmortzgoc = unass2 / ( 1. - zepsherv ) * ztortz2
                tra(ji,jj,jk,jpmes) = tra(ji,jj,jk,jpmes) - zmortz2 + zepsherv * zgraztot
                tra(ji,jj,jk,jpdia) = tra(ji,jj,jk,jpdia) - zgrazd
 …
 #if defined key_kriest
                znumpoc = trn(ji,jj,jk,jpnum) / ( trn(ji,jj,jk,jppoc) + rtrn )
                tra(ji,jj,jk,jppoc) = tra(ji,jj,jk,jppoc) + zmortzgoc - zgrazpoc - zgrazffep
                tra(ji,jj,jk,jpnum) = tra(ji,jj,jk,jpnum) - zgrazpoc * znumpoc &
                &   + zmortzgoc * xkr_dmeso - zgrazffep * znumpoc * wsbio4(ji,jj,jk) / ( wsbio3(ji,jj,jk) + rtrn )
                tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + ferat3 * zmortz2 - zgrazfffp - zgrazpof
+               tra(ji,jj,jk,jppoc) = tra(ji,jj,jk,jppoc) + zmortzgoc - zgrazpoc - zgrazffep + zgrapoc2
+               tra(ji,jj,jk,jpnum) = tra(ji,jj,jk,jpnum) - zgrazpoc * znumpoc + zgrapoc2 * xkr_dmeso      &
+               &                   + zmortzgoc * xkr_dmeso - zgrazffep * znumpoc * wsbio4(ji,jj,jk) / ( wsbio3(ji,jj,jk) + rtrn )
+               tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + ferat3 * zmortz2 - zgrazfffp - zgrazpof + zgraztotf * unass2
 #else
                tra(ji,jj,jk,jppoc) = tra(ji,jj,jk,jppoc) - zgrazpoc - zgrazffep
                tra(ji,jj,jk,jpgoc) = tra(ji,jj,jk,jpgoc) + zmortzgoc - zgrazffeg
                tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) - zgrazpof - zgrazfffp
                tra(ji,jj,jk,jpbfe) = tra(ji,jj,jk,jpbfe) + ferat3 * zmortzgoc - zgrazfffg
+               tra(ji,jj,jk,jppoc) = tra(ji,jj,jk,jppoc) - zgrazpoc - zgrazffep + zfrac
+               tra(ji,jj,jk,jpgoc) = tra(ji,jj,jk,jpgoc) + zmortzgoc - zgrazffeg + zgrapoc2 - zfrac
+               tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) - zgrazpof - zgrazfffp + zfracfe
+               tra(ji,jj,jk,jpbfe) = tra(ji,jj,jk,jpbfe) + ferat3 * zmortzgoc - zgrazfffg + zgraztotf * unass2 - zfracfe
 #endif
             END DO
          END DO

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zprod.F90

r3686	r4258
201	201	zconctemp2 = trn(ji,jj,jk,jpdia) - zconctemp
202	202	!
203		zpislopead (ji,jj,jk) = pislope * ( 1.+ zadap * EXP( enano(ji,jj,jk) ) )
	203	zpislopead (ji,jj,jk) = pislope * ( 1.+ zadap * EXP( -0.21 * enano(ji,jj,jk) ) )
204	204	zpislopead2(ji,jj,jk) = (pislope * zconctemp2 + pislope2 * zconctemp) / ( trn(ji,jj,jk,jpdia) + rtrn )
205	205

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zsed.F90

-                      r3751
+                      r4258
       REAL(wp) ::  zwflux, zfminus, zfplus
       REAL(wp) ::  zlim, zfact, zfactcal
       REAL(wp) ::  zo2, zno3, zflx, zpdenit, z1pdenit
+      REAL(wp) ::  zo2, zno3, zflx, zpdenit, z1pdenit, zdenitt, zolimit
       REAL(wp) ::  zsiloss, zcaloss, zwsbio3, zwsbio4, zwscal, zdep, zwstpoc
       REAL(wp) ::  ztrfer, ztrpo4, zwdust
 …
       IF( nn_timing == 1 )  CALL timing_start('p4z_sed')
+      !
       IF( kt == nit000 .AND. jnt == 1 )  THEN
+      IF( kt == nittrc000 .AND. jnt == 1 )  THEN
          ryyss    = nyear_len(1) * rday    ! number of seconds per year and per month
          rmtss    = ryyss / raamo
 …
             DO ji = 1, jpi
                zdep    = rfact2 / fse3t(ji,jj,1)
+    !           zwflux  = ( emps(ji,jj) - emp(ji,jj) ) &
+    !           &        * tsn(ji,jj,1,jp_sal) / ( tsn(ji,jj,1,jp_sal) - 6.0 ) / 1000.
+               zwflux = 0.
+               zfminus = MIN( 0., -zwflux ) * trn(ji,jj,1,jpfer) * zdep
+               zfplus  = MAX( 0., -zwflux ) * 10E-9 * zdep
+               zwflux  = fmmflx(ji,jj) / 1000._wp
+               zfminus = MIN( 0._wp, -zwflux ) * trn(ji,jj,1,jpfer) * zdep
+               zfplus  = MAX( 0._wp, -zwflux ) * icefeinput * zdep
                zironice(ji,jj) =  zfplus + zfminus
             END DO
 …
          ENDIF
          zsidep(:,:) = 8.8 * 0.075 * dust(:,:) * rfact2 / fse3t(:,:,1) / ( 28.1  * rmtss )
          zpdep (:,:) = 0.1 * 0.021 * dust(:,:) * rfact2 / fse3t(:,:,1) / ( 31.   * rmtss )
+         zpdep (:,:) = 0.1 * 0.021 * dust(:,:) * rfact2 / fse3t(:,:,1) / ( 31.   * rmtss ) / po4r
          !                                              ! Iron solubilization of particles in the water column
          zwdust = 0.005 / ( wdust * 55.85 * 30.42 ) / ( 45. * rday )
 …
 #endif
+      ! THEN this loss is scaled at each bottom grid cell for
+      ! equilibrating the total budget of silica in the ocean.
+      ! Thus, the amount of silica lost in the sediments equal
+      ! the supply at the surface (dust+rivers)
+      ! This loss is scaled at each bottom grid cell for equilibrating the total budget of silica in the ocean.
+      ! Thus, the amount of silica lost in the sediments equal the supply at the surface (dust+rivers)
       ! ------------------------------------------------------
 #if ! defined key_sed
 …
 #if ! defined key_sed
+            zpdenit  = MIN( ( trn(ji,jj,ikt,jpno3) - rtrn ) / rdenit, zdenit2d(ji,jj) * zwstpoc * zrivno3 )
+            ! The 0.5 factor in zpdenit and zdenitt is to avoid negative NO3 concentration after both denitrification
+            ! in the sediments and just above the sediments. Not very clever, but simpliest option.
+            zpdenit  = MIN( 0.5 * ( trn(ji,jj,ikt,jpno3) - rtrn ) / rdenit, zdenit2d(ji,jj) * zwstpoc * zrivno3 )
             z1pdenit = zwstpoc * zrivno3 - zpdenit
+            trn(ji,jj,ikt,jpdoc) = trn(ji,jj,ikt,jpdoc) + z1pdenit
+            trn(ji,jj,ikt,jppo4) = trn(ji,jj,ikt,jppo4) + zpdenit
+            trn(ji,jj,ikt,jpnh4) = trn(ji,jj,ikt,jpnh4) + zpdenit
+            trn(ji,jj,ikt,jpno3) = trn(ji,jj,ikt,jpno3) - rdenit * zpdenit
+            trn(ji,jj,ikt,jptal) = trn(ji,jj,ikt,jptal) + rno3 * ( 1. + rdenit ) * zpdenit
+            trn(ji,jj,ikt,jpdic) = trn(ji,jj,ikt,jpdic) + zpdenit
+            zolimit = MIN( ( trn(ji,jj,ikt,jpoxy) - rtrn ) / o2ut, z1pdenit * ( 1.- nitrfac(ji,jj,ikt) ) )
+            zdenitt = MIN(  0.5 * ( trn(ji,jj,ikt,jpno3) - rtrn ) / rdenit, z1pdenit * nitrfac(ji,jj,ikt) )
+            trn(ji,jj,ikt,jpdoc) = trn(ji,jj,ikt,jpdoc) + z1pdenit - zolimit - zdenitt
+            trn(ji,jj,ikt,jppo4) = trn(ji,jj,ikt,jppo4) + zpdenit + zolimit + zdenitt
+            trn(ji,jj,ikt,jpnh4) = trn(ji,jj,ikt,jpnh4) + zpdenit + zolimit + zdenitt
+            trn(ji,jj,ikt,jpno3) = trn(ji,jj,ikt,jpno3) - rdenit * (zpdenit + zdenitt)
+            trn(ji,jj,ikt,jpoxy) = trn(ji,jj,ikt,jpoxy) - zolimit * o2ut
+            trn(ji,jj,ikt,jptal) = trn(ji,jj,ikt,jptal) + rno3 * (zolimit + (1.+rdenit) * (zpdenit + zdenitt) )
+            trn(ji,jj,ikt,jpdic) = trn(ji,jj,ikt,jpdic) + zpdenit + zolimit + zdenitt
             zwork4(ji,jj) = rdenit * zpdenit * fse3t(ji,jj,ikt)
 #endif

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zsink.F90

-                      r3829
+                      r4258
             DO ji = 1, jpi
                IF( tmask(ji,jj,jk) == 1 ) THEN
                  zwsmax = 0.8 * fse3t(ji,jj,jk) / xstep
+                 zwsmax = 0.5 * fse3t(ji,jj,jk) / xstep
                  wsbio3(ji,jj,jk) = MIN( wsbio3(ji,jj,jk), zwsmax * FLOAT( iiter1 ) )
                  wsbio4(ji,jj,jk) = MIN( wsbio4(ji,jj,jk), zwsmax * FLOAT( iiter2 ) )
 …
                zaggdoc  = ( ( 0.369 * 0.3 * trn(ji,jj,jk,jpdoc) + 102.4 * trn(ji,jj,jk,jppoc) ) * zfact       &
                &            + 2.4 * zstep * trn(ji,jj,jk,jppoc) ) * 0.3 * trn(ji,jj,jk,jpdoc)
-!               zaggdoc  = ( 0.83 * trn(ji,jj,jk,jpdoc) + 271. * trn(ji,jj,jk,jppoc) ) * zfact * trn(ji,jj,jk,jpdoc)
                ! transfer of DOC to GOC :
                ! 1st term is shear aggregation
                ! 2nd term is differential settling
                zaggdoc2 = ( 3.53E3 * zfact + 0.1 * zstep ) * trn(ji,jj,jk,jpgoc) * 0.3 * trn(ji,jj,jk,jpdoc)
-!               zaggdoc2 = 1.07e4 * zfact * trn(ji,jj,jk,jpgoc) * trn(ji,jj,jk,jpdoc)
                ! tranfer of DOC to POC due to brownian motion
-!               zaggdoc3 =   0.02 * ( 16706. * trn(ji,jj,jk,jppoc) + 231. * trn(ji,jj,jk,jpdoc) ) * zstep * trn(ji,jj,jk,jpdoc)
                zaggdoc3 =  ( 5095. * trn(ji,jj,jk,jppoc) + 114. * 0.3 * trn(ji,jj,jk,jpdoc) ) *zstep * 0.3 * trn(ji,jj,jk,jpdoc)

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/P4Z/p4zsms.F90

-                      r3780
+                      r4258
       ENDIF
+      !
+      IF( ln_rsttr .AND. kt == nittrc000 )                         CALL p4z_rst( nittrc000, 'READ' )  !* read or initialize all required fields
+      IF( ln_rsttr  .AND. ln_pisclo )                              CALL p4z_clo            ! damping on closed seas
+      IF( kt == nittrc000 ) THEN
+        !
+        CALL p4z_che                              ! initialize the chemical constants
+        !
+        IF( .NOT. ln_rsttr ) THEN  ;   CALL p4z_ph_ini   !  set PH at kt=nit000
+        ELSE                       ;   CALL p4z_rst( nittrc000, 'READ' )  !* read or initialize all required fields
+        ENDIF
+        !
+      ENDIF
       IF( ln_pisdmp .AND. MOD( kt - nn_dttrc, nn_pisdmp ) == 0 )   CALL p4z_dmp( kt )      ! Relaxation of some tracers
+      !
 …
       NAMELIST/nampiskrp/ xkr_eta, xkr_zeta, xkr_ncontent, xkr_mass_min, xkr_mass_max
 #endif
       NAMELIST/nampisdmp/ ln_pisdmp, nn_pisdmp, ln_pisclo
+      NAMELIST/nampisdmp/ ln_pisdmp, nn_pisdmp
       NAMELIST/nampismass/ ln_check_mass
       !!----------------------------------------------------------------------
 …
       ln_pisdmp = .true.
       nn_pisdmp = 1
-      ln_pisclo = .false.
       REWIND( numnatp )
 …
          WRITE(numout,*) '    Relaxation of tracer to glodap mean value             ln_pisdmp      =', ln_pisdmp
          WRITE(numout,*) '    Frequency of Relaxation                               nn_pisdmp      =', nn_pisdmp
-         WRITE(numout,*) '    Restoring of tracer to initial value  on closed seas  ln_pisclo      =', ln_pisclo
          WRITE(numout,*) ' '
       ENDIF
 …
    END SUBROUTINE p4z_sms_init
+   SUBROUTINE p4z_ph_ini
+      !!---------------------------------------------------------------------
+      !!                   ***  ROUTINE p4z_ini_ph  ***
+      !!
+      !!  ** Purpose : Initialization of chemical variables of the carbon cycle
+      !!---------------------------------------------------------------------
+      INTEGER  ::  ji, jj, jk
+      REAL(wp) ::  zcaralk, zbicarb, zco3
+      REAL(wp) ::  ztmas, ztmas1
+      !!---------------------------------------------------------------------
+      ! Set PH from  total alkalinity, borat (???), akb3 (???) and ak23 (???)
+      ! --------------------------------------------------------
+      DO jk = 1, jpk
+         DO jj = 1, jpj
+            DO ji = 1, jpi
+               ztmas   = tmask(ji,jj,jk)
+               ztmas1  = 1. - tmask(ji,jj,jk)
+               zcaralk = trn(ji,jj,jk,jptal) - borat(ji,jj,jk) / (  1. + 1.E-8 / ( rtrn + akb3(ji,jj,jk) )  )
+               zco3    = ( zcaralk - trn(ji,jj,jk,jpdic) ) * ztmas + 0.5e-3 * ztmas1
+               zbicarb = ( 2. * trn(ji,jj,jk,jpdic) - zcaralk )
+               hi(ji,jj,jk) = ( ak23(ji,jj,jk) * zbicarb / zco3 ) * ztmas + 1.e-9 * ztmas1
+            END DO
+         END DO
+     END DO
+     !
+   END SUBROUTINE p4z_ph_ini
    SUBROUTINE p4z_rst( kt, cdrw )
       !!---------------------------------------------------------------------
 …
          ELSE
 !            hi(:,:,:) = 1.e-9
+            ! Set PH from  total alkalinity, borat (???), akb3 (???) and ak23 (???)
+            ! --------------------------------------------------------
+            DO jk = 1, jpk
+               DO jj = 1, jpj
+                  DO ji = 1, jpi
+                     ztmas   = tmask(ji,jj,jk)
+                     ztmas1  = 1. - tmask(ji,jj,jk)
+                     zcaralk = trn(ji,jj,jk,jptal) - borat(ji,jj,jk) / (  1. + 1.E-8 / ( rtrn + akb3(ji,jj,jk) )  )
+                     zco3    = ( zcaralk - trn(ji,jj,jk,jpdic) ) * ztmas + 0.5e-3 * ztmas1
+                     zbicarb = ( 2. * trn(ji,jj,jk,jpdic) - zcaralk )
+                     hi(ji,jj,jk) = ( ak23(ji,jj,jk) * zbicarb / zco3 ) * ztmas + 1.e-9 * ztmas1
+                  END DO
+               END DO
+            END DO
+            CALL p4z_ph_ini
          ENDIF
          CALL iom_get( numrtr, jpdom_autoglo, 'Silicalim', xksi(:,:) )
 …
 #endif
             &                    + trn(:,:,:,jpsfe)                     &
             &                    + trn(:,:,:,jpzoo)                     &
+            &                    + trn(:,:,:,jpzoo) * ferat3            &
             &                    + trn(:,:,:,jpmes) * ferat3            ) * cvol(:,:,:)  )
 …
    END SUBROUTINE p4z_chk_mass
-   SUBROUTINE p4z_clo
-      !!---------------------------------------------------------------------
-      !!                  ***  ROUTINE p4z_clo  ***
-      !!
-      !! ** Purpose :   Closed sea domain initialization
-      !!
-      !! ** Method  :   if a closed sea is located only in a model grid point
-      !!                we restore to initial data
-      !!
-      !! ** Action  :   ictsi1(), ictsj1() : south-west closed sea limits (i,j)
-      !!                ictsi2(), ictsj2() : north-east Closed sea limits (i,j)
-      !!----------------------------------------------------------------------
-      INTEGER, PARAMETER           ::   npicts   = 4        ! number of closed sea
-      INTEGER, DIMENSION(npicts)   ::   ictsi1, ictsj1      ! south-west closed sea limits (i,j)
-      INTEGER, DIMENSION(npicts)   ::   ictsi2, ictsj2      ! north-east closed sea limits (i,j)
-      INTEGER :: ji, jj, jk, jn, jl, jc                     ! dummy loop indices
-      INTEGER :: ierr                                       ! local integer
-      REAL(wp), POINTER, DIMENSION(:,:,:,:) ::  ztrcdta     ! 4D  workspace
-      !!----------------------------------------------------------------------
-      IF(lwp) WRITE(numout,*)
-      IF(lwp) WRITE(numout,*)' p4z_clo : closed seas '
-      IF(lwp) WRITE(numout,*)'~~~~~~~'
-      ! initial values
-      ictsi1(:) = 1  ;  ictsi2(:) = 1
-      ictsj1(:) = 1  ;  ictsj2(:) = 1
-      ! set the closed seas (in data domain indices)
-      ! -------------------
-      IF( cp_cfg == "orca" ) THEN
+         !
-         SELECT CASE ( jp_cfg )
-         !                                           ! =======================
-         CASE ( 2 )                                  !  ORCA_R2 configuration
-            !                                        ! =======================
-            !                                            ! Caspian Sea
-            ictsi1(1)   =  11  ;  ictsj1(1)   = 103
-            ictsi2(1)   =  17  ;  ictsj2(1)   = 112
-            !                                            ! Great North American Lakes
-            ictsi1(2)   =  97  ;  ictsj1(2)   = 107
-            ictsi2(2)   = 103  ;  ictsj2(2)   = 111
-            !                                            ! Black Sea 1 : west part of the Black Sea
-            ictsi1(3)   = 174  ; ictsj1(3)   = 107
-            ictsi2(3)   = 181  ; ictsj2(3)   = 112
-            !                                            ! Black Sea 2 : est part of the Black Sea
-            ictsi1(4)   =   2  ;  ictsj1(4)   = 107
-            ictsi2(4)   =   6  ;  ictsj2(4)   = 112
-            !                                        ! =======================
-         CASE ( 4 )                                  !  ORCA_R4 configuration
-            !                                        ! =======================
-            !                                            ! Caspian Sea
-            ictsi1(1)   =  4  ;  ictsj1(1)   = 53
-            ictsi2(1)   =  4  ;  ictsj2(1)   = 56
-            !                                            ! Great North American Lakes
-            ictsi1(2)   = 49  ;  ictsj1(2)   = 55
-            ictsi2(2)   = 51  ;  ictsj2(2)   = 56
-            !                                            ! Black Sea
-            ictsi1(3)   = 88  ;  ictsj1(3)   = 55
-            ictsi2(3)   = 91  ;  ictsj2(3)   = 56
-            !                                            ! Baltic Sea
-            ictsi1(4)   = 75  ;  ictsj1(4)   = 59
-            ictsi2(4)   = 76  ;  ictsj2(4)   = 61
-            !                                        ! =======================
-            !                                        ! =======================
-         CASE ( 025 )                                ! ORCA_R025 configuration
-            !                                        ! =======================
-                                                     ! Caspian + Aral sea
-            ictsi1(1)   = 1330 ; ictsj1(1)   = 645
-            ictsi2(1)   = 1400 ; ictsj2(1)   = 795
-            !                                        ! Azov Sea
-            ictsi1(2)   = 1284 ; ictsj1(2)   = 722
-            ictsi2(2)   = 1304 ; ictsj2(2)   = 747
+            !
-         END SELECT
+         !
-      ENDIF
-      ! convert the position in local domain indices
-      ! --------------------------------------------
-      DO jc = 1, npicts
-         ictsi1(jc)   = mi0( ictsi1(jc) )
-         ictsj1(jc)   = mj0( ictsj1(jc) )
-         ictsi2(jc)   = mi1( ictsi2(jc) )
-         ictsj2(jc)   = mj1( ictsj2(jc) )
-      END DO
-      ! Restore close seas values to initial data
-      IF( ln_trcdta .AND. nb_trcdta > 0 )  THEN   ! Initialisation of tracer from a file that may also be used for damping
+         !
-         CALL wrk_alloc( jpi, jpj, jpk, nb_trcdta, ztrcdta )   ! Memory allocation
+         !
-         CALL trc_dta( nittrc000, ztrcdta )   ! read tracer data at nittrc000
+         !
-         DO jn = 1, jptra
-            IF( ln_trc_ini(jn) ) THEN      ! update passive tracers arrays with input data read from file
-                jl = n_trc_index(jn)
-                DO jc = 1, npicts
-                   DO jk = 1, jpkm1
-                      DO jj = ictsj1(jc), ictsj2(jc)
-                         DO ji = ictsi1(jc), ictsi2(jc)
-                            trn(ji,jj,jk,jn) = ztrcdta(ji,jj,jk,jl) * tmask(ji,jj,jk)
-                            trb(ji,jj,jk,jn) = trn(ji,jj,jk,jn)
-                         ENDDO
-                      ENDDO
-                   ENDDO
-                ENDDO
-             ENDIF
-          ENDDO
-          CALL wrk_dealloc( jpi, jpj, jpk, nb_trcdta, ztrcdta )
-      ENDIF
+      !
-   END SUBROUTINE p4z_clo
 #else
    !!======================================================================

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/sms_pisces.F90

r3780	r4258
56	56	LOGICAL :: ln_pisdmp !: restoring or not of nutrients to a mean value
57	57	INTEGER :: nn_pisdmp !: frequency of relaxation or not of nutrients to a mean value
58		~~LOGICAL :: ln_pisclo !: Restoring or not of nutrients to initial value on closed seas~~
59	58
60	59	!!* Mass conservation

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/PISCES/trcini_pisces.F90

-                      r3757
+                      r4258
       rdenita =   3._wp /  5._wp
       o2ut    = 131._wp / 122._wp
-      CALL p4z_che        ! initialize the chemical constants
       ! Initialization of tracer concentration in case of  no restart
 …
          xksi(:,:)    = 2.e-6
          xksimax(:,:) = xksi(:,:)
+         ! Initialization of chemical variables of the carbon cycle
+         ! --------------------------------------------------------
+         DO jk = 1, jpk
+            DO jj = 1, jpj
+               DO ji = 1, jpi
+                  ztmas   = tmask(ji,jj,jk)
+                  ztmas1  = 1. - tmask(ji,jj,jk)
+                  zcaralk = trn(ji,jj,jk,jptal) - borat(ji,jj,jk) / (  1. + 1.E-8 / ( rtrn + akb3(ji,jj,jk) )  )
+                  zco3    = ( zcaralk - trn(ji,jj,jk,jpdic) ) * ztmas + 0.5e-3 * ztmas1
+                  zbicarb = ( 2. * trn(ji,jj,jk,jpdic) - zcaralk )
+                  hi(ji,jj,jk) = ( ak23(ji,jj,jk) * zbicarb / zco3 ) * ztmas + 1.e-9 * ztmas1
+               END DO
+            END DO
+         END DO
+         !
+        !
       END IF

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/TRP/trcdmp.F90

-                      r3294
+                      r4258
    !!            3.3  !  2010-06  (C. Ethe, G. Madec) merge TRA-TRC
    !!----------------------------------------------------------------------
+#if  defined key_top && defined key_trcdmp
+   !!----------------------------------------------------------------------
+   !!   key_trcdmp                                         internal damping
+#if  defined key_top
    !!----------------------------------------------------------------------
    !!   trc_dmp      : update the tracer trend with the internal damping
 …
    USE prtctl_trc      ! Print control for debbuging
    USE trdtra
+   USE trdmod_oce
    IMPLICIT NONE
 …
    PUBLIC trc_dmp            ! routine called by step.F90
+   PUBLIC trc_dmp_clo        ! routine called by step.F90
    PUBLIC trc_dmp_alloc      ! routine called by nemogcm.F90
-   LOGICAL , PUBLIC, PARAMETER ::   lk_trcdmp = .TRUE.   !: internal damping flag
    !                                !!* Namelist namtrc_dmp : passive tracer newtonian damping *
-   INTEGER  ::   nn_hdmp_tr =   -1   ! = 0/-1/'latitude' for damping over passive tracer
-   INTEGER  ::   nn_zdmp_tr =    0   ! = 0/1/2 flag for damping in the mixed layer
-   REAL(wp) ::   rn_surf_tr =   50.  ! surface time scale for internal damping        [days]
-   REAL(wp) ::   rn_bot_tr  =  360.  ! bottom time scale for internal damping         [days]
-   REAL(wp) ::   rn_dep_tr  =  800.  ! depth of transition between rn_surf and rn_bot [meters]
-   INTEGER  ::   nn_file_tr =    2   ! = 1 create a damping.coeff NetCDF file
    REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) ::   restotr   ! restoring coeff. on tracers (s-1)
+   INTEGER, PARAMETER           ::   npncts   = 5        ! number of closed sea
+   INTEGER, DIMENSION(npncts)   ::   nctsi1, nctsj1      ! south-west closed sea limits (i,j)
+   INTEGER, DIMENSION(npncts)   ::   nctsi2, nctsj2      ! north-east closed sea limits (i,j)
    !! * Substitutions
 …
       INTEGER, INTENT( in ) ::   kt      ! ocean time-step index
       !!
       INTEGER  ::   ji, jj, jk, jn       ! dummy loop indices
+      INTEGER  ::   ji, jj, jk, jn, jl       ! dummy loop indices
       REAL(wp) ::   ztra                 ! temporary scalars
       CHARACTER (len=22) :: charout
       REAL(wp), POINTER, DIMENSION(:,:,:) ::   ztrtrd
+      REAL(wp), POINTER, DIMENSION(:,:,:,:) ::  ztrcdta   ! 4D  workspace
       !!----------------------------------------------------------------------
+      !
 …
       IF( l_trdtrc )   CALL wrk_alloc( jpi, jpj, jpk, ztrtrd )   ! temporary save of trends
+      ! 1. Newtonian damping trends on tracer fields
+      ! --------------------------------------------
+      ! Initialize the input fields for newtonian damping
+      CALL trc_dta( kt )
+      !                                                          ! ===========
+      DO jn = 1, jptra                                           ! tracer loop
+         !                                                       ! ===========
+         IF( l_trdtrc ) ztrtrd(:,:,:) = tra(:,:,:,jn)    ! save trends
+         IF( lutini(jn) ) THEN
+      !
+      IF( nb_trcdta > 0 ) THEN  ! Initialisation of tracer from a file that may also be used for damping
+         !
+         CALL wrk_alloc( jpi, jpj, jpk, nb_trcdta, ztrcdta )    ! Memory allocation
+         CALL trc_dta( kt, ztrcdta )   ! read tracer data at nit000
+         !                                                          ! ===========
+         DO jn = 1, jptra                                           ! tracer loop
+            !                                                       ! ===========
+            IF( l_trdtrc ) ztrtrd(:,:,:) = tra(:,:,:,jn)    ! save trends
+            !
+            SELECT CASE ( nn_zdmp_trc )
+            !
+            CASE( 0 )                !==  newtonian damping throughout the water column  ==!
+               DO jk = 1, jpkm1
+                  DO jj = 2, jpjm1
+                     DO ji = fs_2, fs_jpim1   ! vector opt.
+                        ztra = restotr(ji,jj,jk) * ( trdta(ji,jj,jk,jn) - trb(ji,jj,jk,jn) )
+                        tra(ji,jj,jk,jn) = tra(ji,jj,jk,jn) + ztra
+            IF( ln_trc_ini(jn) ) THEN      ! update passive tracers arrays with input data read from file
+               jl = n_trc_index(jn)
+               SELECT CASE ( nn_zdmp_tr )
+               !
+               CASE( 0 )                !==  newtonian damping throughout the water column  ==!
+                  DO jk = 1, jpkm1
+                     DO jj = 2, jpjm1
+                        DO ji = fs_2, fs_jpim1   ! vector opt.
+                           ztra = restotr(ji,jj,jk) * ( ztrcdta(ji,jj,jk,jl) - trb(ji,jj,jk,jn) )
+                           tra(ji,jj,jk,jn) = tra(ji,jj,jk,jn) + ztra
+                        END DO
                      END DO
                   END DO
                END DO
+            !
             CASE ( 1 )                !==  no damping in the turbocline (avt > 5 cm2/s)  ==!
                DO jk = 1, jpkm1
                   DO jj = 2, jpjm1
                      DO ji = fs_2, fs_jpim1   ! vector opt.
                         IF( avt(ji,jj,jk) <= 5.e-4 )  THEN
                            ztra = restotr(ji,jj,jk) * ( trdta(ji,jj,jk,jn) - trb(ji,jj,jk,jn) )
                            tra(ji,jj,jk,jn) = tra(ji,jj,jk,jn) + ztra
                         ENDIF
+               !
+               CASE ( 1 )                !==  no damping in the turbocline (avt > 5 cm2/s)  ==!
+                  DO jk = 1, jpkm1
+                     DO jj = 2, jpjm1
+                        DO ji = fs_2, fs_jpim1   ! vector opt.
+                           IF( avt(ji,jj,jk) <= 5.e-4 )  THEN
+                              ztra = restotr(ji,jj,jk) * ( ztrcdta(ji,jj,jk,jl) - trb(ji,jj,jk,jn) )
+                              tra(ji,jj,jk,jn) = tra(ji,jj,jk,jn) + ztra
+                           ENDIF
+                        END DO
                      END DO
                   END DO
                END DO
+            !
             CASE ( 2 )               !==  no damping in the mixed layer   ==!
                DO jk = 1, jpkm1
                   DO jj = 2, jpjm1
                      DO ji = fs_2, fs_jpim1   ! vector opt.
                         IF( fsdept(ji,jj,jk) >= hmlp (ji,jj) ) THEN
                            ztra = restotr(ji,jj,jk,jn) * ( trdta(ji,jj,jk,jn) - trb(ji,jj,jk,jn) )
                            tra(ji,jj,jk,jn) = tra(ji,jj,jk,jn) + ztra
                         END IF
+               !
+               CASE ( 2 )               !==  no damping in the mixed layer   ==!
+                  DO jk = 1, jpkm1
+                     DO jj = 2, jpjm1
+                        DO ji = fs_2, fs_jpim1   ! vector opt.
+                           IF( fsdept(ji,jj,jk) >= hmlp (ji,jj) ) THEN
+                              ztra = restotr(ji,jj,jk) * ( ztrcdta(ji,jj,jk,jl) - trb(ji,jj,jk,jn) )
+                              tra(ji,jj,jk,jn) = tra(ji,jj,jk,jn) + ztra
+                           END IF
+                        END DO
                      END DO
                   END DO
+               END DO
+            !
+            END SELECT
+            !
+         ENDIF
+         !
+         IF( l_trdtrc ) THEN
+            ztrtrd(:,:,:) = tra(:,:,:,jn) -  ztrtrd(:,:,:)
+            CALL trd_tra( kt, 'TRC', jn, jptra_trd_dmp, ztrtrd )
+         END IF
+         !                                                       ! ===========
+      END DO                                                     ! tracer loop
+      !                                                          ! ===========
+               !
+               END SELECT
+               !
+            ENDIF
+            !
+            IF( l_trdtrc ) THEN
+               ztrtrd(:,:,:) = tra(:,:,:,jn) -  ztrtrd(:,:,:)
+               CALL trd_tra( kt, 'TRC', jn, jptra_trd_dmp, ztrtrd )
+            END IF
+            !                                                       ! ===========
+         END DO                                                     ! tracer loop
+         !                                                          ! ===========
+         CALL wrk_dealloc( jpi, jpj, jpk, nb_trcdta, ztrcdta )
+      ENDIF
+      !
       IF( l_trdtrc )  CALL wrk_dealloc( jpi, jpj, jpk, ztrtrd )
       !                                          ! print mean trends (used for debugging)
 …
+      !
    END SUBROUTINE trc_dmp
+   SUBROUTINE trc_dmp_clo( kt )
+      !!---------------------------------------------------------------------
+      !!                  ***  ROUTINE trc_dmp_clo  ***
+      !!
+      !! ** Purpose :   Closed sea domain initialization
+      !!
+      !! ** Method  :   if a closed sea is located only in a model grid point
+      !!                we restore to initial data
+      !!
+      !! ** Action  :   nctsi1(), nctsj1() : south-west closed sea limits (i,j)
+      !!                nctsi2(), nctsj2() : north-east Closed sea limits (i,j)
+      !!----------------------------------------------------------------------
+      INTEGER, INTENT( in ) ::   kt      ! ocean time-step index
+      !
+      INTEGER :: ji, jj, jk, jn, jl, jc                     ! dummy loop indicesa
+      REAL(wp), POINTER, DIMENSION(:,:,:,:) ::  ztrcdta     ! 4D  workspace
+      !!----------------------------------------------------------------------
+      IF( kt == nit000 ) THEN
+         ! initial values
+         nctsi1(:) = 1  ;  nctsi2(:) = 1
+         nctsj1(:) = 1  ;  nctsj2(:) = 1
+         ! set the closed seas (in data domain indices)
+         ! -------------------
+         IF( cp_cfg == "orca" ) THEN
+            !
+            SELECT CASE ( jp_cfg )
+            !                                           ! =======================
+            CASE ( 2 )                                  !  ORCA_R2 configuration
+               !                                        ! =======================
+               !                                            ! Caspian Sea
+               nctsi1(1)   =  11  ;  nctsj1(1)   = 103
+               nctsi2(1)   =  17  ;  nctsj2(1)   = 112
+               !                                            ! Great North American Lakes
+               nctsi1(2)   =  97  ;  nctsj1(2)   = 107
+               nctsi2(2)   = 103  ;  nctsj2(2)   = 111
+               !                                            ! Black Sea 1 : west part of the Black Sea
+               nctsi1(3)   = 174  ;  nctsj1(3)   = 107
+               nctsi2(3)   = 181  ;  nctsj2(3)   = 112
+              !                                            ! Black Sea 2 : est part of the Black Sea
+               nctsi1(4)   =   2  ;  nctsj1(4)   = 107
+               nctsi2(4)   =   6  ;  nctsj2(4)   = 112
+               !                                            ! Baltic Sea
+               nctsi1(5)   =  145 ;  nctsj1(5)   = 116
+               nctsi2(5)   =  150 ;  nctsj2(5)   = 126
+               !                                        ! =======================
+            CASE ( 4 )                                  !  ORCA_R4 configuration
+               !                                        ! =======================
+               !                                            ! Caspian Sea
+               nctsi1(1)   =  4  ;  nctsj1(1)   = 53
+               nctsi2(1)   =  4  ;  nctsj2(1)   = 56
+               !                                            ! Great North American Lakes
+               nctsi1(2)   = 49  ;  nctsj1(2)   = 55
+               nctsi2(2)   = 51  ;  nctsj2(2)   = 56
+               !                                            ! Black Sea
+               nctsi1(3)   = 88  ;  nctsj1(3)   = 55
+               nctsi2(3)   = 91  ;  nctsj2(3)   = 56
+               !                                            ! Baltic Sea
+               nctsi1(4)   = 75  ;  nctsj1(4)   = 59
+               nctsi2(4)   = 76  ;  nctsj2(4)   = 61
+               !                                        ! =======================
+            CASE ( 025 )                                ! ORCA_R025 configuration
+               !                                        ! =======================
+                                                     ! Caspian + Aral sea
+               nctsi1(1)   = 1330 ; nctsj1(1)   = 645
+               nctsi2(1)   = 1400 ; nctsj2(1)   = 795
+               !                                        ! Azov Sea
+               nctsi1(2)   = 1284 ; nctsj1(2)   = 722
+               nctsi2(2)   = 1304 ; nctsj2(2)   = 747
+               !
+            END SELECT
+            !
+         ENDIF
+         !
+         ! convert the position in local domain indices
+         ! --------------------------------------------
+         DO jc = 1, npncts
+            nctsi1(jc)   = mi0( nctsi1(jc) )
+            nctsj1(jc)   = mj0( nctsj1(jc) )
+            nctsi2(jc)   = mi1( nctsi2(jc) )
+            nctsj2(jc)   = mj1( nctsj2(jc) )
+         END DO
+         !
+      ENDIF
+      ! Restore close seas values to initial data
+      IF( ln_trcdta .AND. nb_trcdta > 0 )  THEN   ! Initialisation of tracer from a file that may also be used for damping
+         !
+         IF(lwp)  WRITE(numout,*)
+         IF(lwp)  WRITE(numout,*) ' trc_dmp_clo : Restoring of nutrients on close seas at time-step kt = ', kt
+         IF(lwp)  WRITE(numout,*)
+         !
+         CALL wrk_alloc( jpi, jpj, jpk, nb_trcdta, ztrcdta )   ! Memory allocation
+         !
+         CALL trc_dta( kt , ztrcdta )   ! read tracer data at nittrc000
+         !
+         DO jn = 1, jptra
+            IF( ln_trc_ini(jn) ) THEN      ! update passive tracers arrays with input data read from file
+                jl = n_trc_index(jn)
+                DO jc = 1, npncts
+                   DO jk = 1, jpkm1
+                      DO jj = nctsj1(jc), nctsj2(jc)
+                         DO ji = nctsi1(jc), nctsi2(jc)
+                            trn(ji,jj,jk,jn) = ztrcdta(ji,jj,jk,jl) * tmask(ji,jj,jk)
+                            trb(ji,jj,jk,jn) = trn(ji,jj,jk,jn)
+                         ENDDO
+                      ENDDO
+                   ENDDO
+                ENDDO
+             ENDIF
+          ENDDO
+          CALL wrk_dealloc( jpi, jpj, jpk, nb_trcdta, ztrcdta )
+      ENDIF
+      !
+   END SUBROUTINE trc_dmp_clo
 …
       END SELECT
+      IF( .NOT. lk_dtatrc )   &
+         &   CALL ctl_stop( 'no passive tracer data define key_dtatrc' )
+      IF( .NOT. lk_tradmp )   &
+      IF( .NOT. ln_tradmp )   &
          &   CALL ctl_stop( 'passive trace damping need key_tradmp to compute damping coef.' )
+      !
 …
+      !
    END SUBROUTINE trc_dmp_init
 #else
    !!----------------------------------------------------------------------
+   !!   Default key                                     NO internal damping
+   !!----------------------------------------------------------------------
+   LOGICAL , PUBLIC, PARAMETER ::   lk_trcdmp = .FALSE.    !: internal damping flag
+   !!  Dummy module :                                     No passive tracer
+   !!----------------------------------------------------------------------
 CONTAINS
    SUBROUTINE trc_dmp( kt )        ! Empty routine
 …
    END SUBROUTINE trc_dmp
 #endif
    !!======================================================================
 END MODULE trcdmp

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/TRP/trcnam_trp.F90

-                      r3718
+                      r4258
    !!   trc_nam_trp  : read the passive tracer namelist for transport
    !!----------------------------------------------------------------------
+   USE trc                 ! ocean passive tracers variables
+   USE oce_trc              ! shared ocean passive tracers variables
+   USE trc                 ! passive tracers variables
    USE in_out_manager      ! ocean dynamics and active tracers variables
 …
    INTEGER , PUBLIC ::   nn_trczdf_exp = 3             !: number of sub-time step (explicit time stepping)
-#if defined key_trcdmp
    !                                                 !!: ** newtonian damping namelist (nam_trcdmp) **
    INTEGER , PUBLIC ::   nn_hdmp_tr      =   -1       ! = 0/-1/'latitude' for damping over passive tracer
 …
    REAL(wp), PUBLIC ::   rn_dep_tr       =  800.      ! depth of transition between rn_surf and rn_bot [meters]
    INTEGER , PUBLIC ::   nn_file_tr      =    2       ! = 1 create a damping.coeff NetCDF file
-#endif
    !!----------------------------------------------------------------------
 …
       NAMELIST/namtrc_zdf/ ln_trczdf_exp  , nn_trczdf_exp
       NAMELIST/namtrc_rad/ ln_trcrad
+#if defined key_trcdmp
+      NAMELIST/namtrc_dmp/ ln_trcdmp, nn_hdmp_tr, nn_zdmp_tr, rn_surf_tr, &
+      NAMELIST/namtrc_dmp/ nn_hdmp_tr, nn_zdmp_tr, rn_surf_tr, &
         &                  rn_bot_tr , rn_dep_tr , nn_file_tr
-#endif
       !!----------------------------------------------------------------------
 …
-# if defined key_trcdmp
       REWIND ( numnat )                  ! Read Namelist namtra_dmp : temperature and salinity damping term
       READ   ( numnat, namtrc_dmp )
       IF( lzoom )   nn_zdmp_trc = 0           ! restoring to climatology at closed north or south boundaries
+      IF( lzoom )   nn_zdmp_tr = 0           ! restoring to climatology at closed north or south boundaries
       IF(lwp) THEN                       ! Namelist print
 …
          WRITE(numout,*) '~~~~~~~'
          WRITE(numout,*) '   Namelist namtrc_dmp : set damping parameter'
-         WRITE(numout,*) '      add a damping term or not      ln_trcdmp = ', ln_trcdmp
          WRITE(numout,*) '      tracer damping option          nn_hdmp_tr = ', nn_hdmp_tr
          WRITE(numout,*) '      mixed layer damping option     nn_zdmp_tr = ', nn_zdmp_tr, '(zoom: forced to 0)'
 …
          WRITE(numout,*) '      create a damping.coeff file    nn_file_tr = ', nn_file_tr
       ENDIF
-#endif
+      !
    END SUBROUTINE trc_nam_trp

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/TRP/trctrp.F90

-                      r3680
+                      r4258
                                 CALL trc_sbc( kstp )            ! surface boundary condition
          IF( lk_trabbl )        CALL trc_bbl( kstp )            ! advective (and/or diffusive) bottom boundary layer scheme
+         IF( lk_trcdmp )        CALL trc_dmp( kstp )            ! internal damping trends
+         IF( ln_trcdmp )        CALL trc_dmp( kstp )            ! internal damping trends
+         IF( ln_trcdmp_clo )    CALL trc_dmp_clo( kstp )        ! internal damping trends on closed seas only
                                 CALL trc_adv( kstp )            ! horizontal & vertical advection
                                 CALL trc_ldf( kstp )            ! lateral mixing

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/oce_trc.F90

r3865	r4258
92	92	USE sbc_oce , ONLY : emp => emp !: freshwater budget: volume flux [Kg/m2/s]
93	93	USE sbc_oce , ONLY : emp_b => emp_b !: freshwater budget: volume flux [Kg/m2/s]
94		USE sbc_oce , ONLY : ~~sfx => sfx !: downward salt flux [PSU~~/m2/s]
	94	USE sbc_oce , ONLY : fmmflx => fmmflx !: freshwater budget: volume flux [Kg/m2/s]
95	95	USE sbc_oce , ONLY : rnf => rnf !: river runoff [Kg/m2/s]
96	96	USE sbc_oce , ONLY : ln_dm2dc => ln_dm2dc !: Daily mean to Diurnal Cycle short wave (qsr)

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/trc.F90

-                      r3770
+                      r4258
    INTEGER, PUBLIC                                                 ::   numrtr        !: logical unit for trc restart (read )
    INTEGER, PUBLIC                                                 ::   numrtw        !: logical unit for trc restart ( write )
-   LOGICAL, PUBLIC                                                 ::   ln_top_euler  !: boolean term for euler integration in the first timestep
    !! passive tracers fields (before,now,after)
 …
    CHARACTER(len = 80) , PUBLIC                                    ::  cn_trcrst_out  !: suffix of pass. tracer restart name (output)
    REAL(wp)            , PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:)   ::  rdttrc         !: vertical profile of passive tracer time step
+   LOGICAL             , PUBLIC                                    ::  ln_top_euler  !: boolean term for euler integration
    LOGICAL             , PUBLIC                                    ::  ln_trcdta      !: Read inputs data from files
    LOGICAL             , PUBLIC                                    ::  ln_trcdmp      !: internal damping flag
+   LOGICAL             , PUBLIC                                    ::  ln_trcdmp_clo  !: internal damping flag on closed seas
    INTEGER             , PUBLIC                                    ::  nittrc000       !: first time step of passive tracers model
 …
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  fr_i_tm    !: average ice fraction     [m/s]
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  emp_tm     !: freshwater budget: volume flux [Kg/m2/s]
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  sfx_tm     !: downward salt flux [PSU/m2/s]
+   REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  fmmflx_tm  !: freshwater budget: freezing/melting [Kg/m2/s]
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  emp_b_hold !: hold emp from the beginning of each sub-stepping[m]
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  qsr_tm     !: solar radiation average [m]
 …
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:)   ::  hdivb_temp, rotb_temp
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  hmld_temp, qsr_temp, fr_i_temp,wndm_temp
    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  emp_temp, sfx_temp, emp_b_temp
+   REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:)     ::  emp_temp, fmmflx_temp, emp_b_temp
+   !
 #if defined key_trabbl

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/trcdta.F90

-                      r3862
+                      r4258
             ENDDO
          ENDIF
+         !
          IF( .NOT.ln_trcdmp ) THEN                   !==   deallocate data structure   ==!
+         IF( .NOT.ln_trcdmp .AND. .NOT.ln_trcdmp_clo ) THEN      !==   deallocate data structure   ==!
             !                                              (data used only for initialisation)
             IF(lwp) WRITE(numout,*) 'trc_dta: deallocate data arrays as they are only use to initialize the run'

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/trcnam.F90

-                      r3749
+                      r4258
       !!
       NAMELIST/namtrc/ nn_dttrc, nn_writetrc, ln_rsttr, nn_rsttr, &
          &             cn_trcrst_in, cn_trcrst_out, sn_tracer, ln_trcdta, ln_trcdmp, &
          &             ln_top_euler
+         &             cn_trcrst_in, cn_trcrst_out, sn_tracer, ln_trcdta, &
+         &             ln_trcdmp, ln_trcdmp_clo, ln_top_euler
 #if defined key_trdmld_trc  || defined key_trdtrc
       NAMELIST/namtrc_trd/ nn_trd_trc, nn_ctls_trc, rn_ucf_trc, &
 …
          sn_tracer(jn)%llsave  = .TRUE.
       END DO
+      ln_trcdta = .FALSE.
+      ln_trcdmp = .FALSE.
+      ln_trcdta     = .FALSE.
+      ln_trcdmp     = .FALSE.
+      ln_trcdmp_clo = .FALSE.
 …
          WRITE(numout,*) '   Read inputs data from file (y/n)             ln_trcdta     = ', ln_trcdta
          WRITE(numout,*) '   Damping of passive tracer (y/n)              ln_trcdmp     = ', ln_trcdmp
+         WRITE(numout,*) '   Restoring of tracer on closed seas           ln_trcdmp_clo = ', ln_trcdmp_clo
          WRITE(numout,*) '   Use euler integration for TRC (y/n)          ln_top_euler  = ', ln_top_euler
          WRITE(numout,*) ' '
 …
+      IF( ln_trcdmp .AND. .NOT.ln_trcdta ) THEN
+         CALL ctl_warn( 'trc_nam: passive tracer damping requires data from files we set ln_trcdta to TRUE' )
+         ln_trcdta = .TRUE.
+      ENDIF
+      !
+      IF( ln_rsttr .AND. .NOT.ln_trcdmp .AND. ln_trcdta ) THEN
+          CALL ctl_warn( 'trc_nam: passive tracer restart and  data intialisation, ',   &
+             &           'we keep the restart values and set ln_trcdta to FALSE' )
+         ln_trcdta = .FALSE.
+      ENDIF
+      IF( ln_rsttr )                      ln_trcdta = .FALSE.   ! restart : no need of clim data
+      !
+      IF( ln_trcdmp .OR. ln_trcdmp_clo )  ln_trcdta = .TRUE.   ! damping : need to have clim data
+      !
       IF( .NOT.ln_trcdta ) THEN
 …
          IF( ln_rsttr ) THEN
             WRITE(numout,*)
+            WRITE(numout,*) '    read a restart file for passive tracer : ', TRIM( cn_trcrst_in )
+            WRITE(numout,*)
+         ELSE
+            IF( .NOT.ln_trcdta ) THEN
+                WRITE(numout,*)
+                WRITE(numout,*) '  All the passive tracers are initialised with constant values '
+                WRITE(numout,*)
+            ENDIF
+            WRITE(numout,*) '  Read a restart file for passive tracer : ', TRIM( cn_trcrst_in )
+            WRITE(numout,*)
+         ENDIF
+         IF( ln_trcdta .AND. .NOT.ln_rsttr ) THEN
+            WRITE(numout,*)
+            WRITE(numout,*) '  Some of the passive tracers are initialised from climatologies '
+            WRITE(numout,*)
+         ENDIF
+         IF( .NOT.ln_trcdta ) THEN
+            WRITE(numout,*)
+            WRITE(numout,*) '  All the passive tracers are initialised with constant values '
+            WRITE(numout,*)
          ENDIF
       ENDIF

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/NEMO/TOP_SRC/trcsub.F90

-                      r3680
+                      r4258
           fr_i_tm  (:,:)         = fr_i_tm  (:,:)         + fr_i  (:,:)
           emp_tm   (:,:)         = emp_tm   (:,:)         + emp   (:,:)
           sfx_tm   (:,:)         = sfx_tm   (:,:)         + sfx   (:,:)
+          fmmflx_tm(:,:)         = fmmflx_tm(:,:)         + fmmflx(:,:)
           qsr_tm   (:,:)         = qsr_tm   (:,:)         + qsr   (:,:)
           wndm_tm  (:,:)         = wndm_tm  (:,:)         + wndm  (:,:)
 …
          emp_temp   (:,:)        = emp   (:,:)
          emp_b_temp (:,:)        = emp_b (:,:)
          sfx_temp   (:,:)        = sfx   (:,:)
+         fmmflx_temp(:,:)        = fmmflx(:,:)
          qsr_temp   (:,:)        = qsr   (:,:)
          wndm_temp  (:,:)        = wndm  (:,:)
 …
          fr_i_tm  (:,:)          = fr_i_tm    (:,:)       + fr_i  (:,:)
          emp_tm   (:,:)          = emp_tm     (:,:)       + emp   (:,:)
          sfx_tm   (:,:)          = sfx_tm     (:,:)       + sfx   (:,:)
+         fmmflx_tm(:,:)          = fmmflx_tm  (:,:)       + fmmflx(:,:)
          qsr_tm   (:,:)          = qsr_tm     (:,:)       + qsr   (:,:)
          wndm_tm  (:,:)          = wndm_tm    (:,:)       + wndm  (:,:)
 …
             qsr   (:,:)          = qsr_tm     (:,:) * r1_ndttrc
             emp   (:,:)          = emp_tm     (:,:) * r1_ndttrc
             sfx   (:,:)          = sfx_tm     (:,:) * r1_ndttrc
+            fmmflx(:,:)          = fmmflx_tm  (:,:) * r1_ndttrc
             fr_i  (:,:)          = fr_i_tm    (:,:) * r1_ndttrc
 # if defined key_trabbl
 …
             qsr   (:,:)          = qsr_tm     (:,:) * r1_ndttrcp1
             emp   (:,:)          = emp_tm     (:,:) * r1_ndttrcp1
             sfx   (:,:)          = sfx_tm     (:,:) * r1_ndttrcp1
+            fmmflx(:,:)          = fmmflx_tm  (:,:) * r1_ndttrcp1
             fr_i  (:,:)          = fr_i_tm    (:,:) * r1_ndttrcp1
 # if defined key_trabbl
 …
          CALL lbc_lnk( emp   (:,:)         , 'T', 1. )
          CALL lbc_lnk( emp_b (:,:)         , 'T', 1. )
          CALL lbc_lnk( sfx   (:,:)         , 'T', 1. )
+         CALL lbc_lnk( fmmflx(:,:)         , 'T', 1. )
          CALL lbc_lnk( qsr   (:,:)         , 'T', 1. )
          CALL lbc_lnk( wndm  (:,:)         , 'T', 1. )
 …
       fr_i_tm(:,:) = 0._wp
       emp_tm (:,:) = 0._wp
       sfx_tm(:,:)  = 0._wp
+      fmmflx_tm(:,:)  = 0._wp
       qsr_tm (:,:) = 0._wp
       wndm_tm(:,:) = 0._wp
 …
       fr_i  (:,:)     =  fr_i_temp  (:,:)
       emp   (:,:)     =  emp_temp   (:,:)
       sfx   (:,:)     =  sfx_temp   (:,:)
+      fmmflx(:,:)     =  fmmflx_temp(:,:)
       emp_b (:,:)     =  emp_b_temp (:,:)
       qsr   (:,:)     =  qsr_temp   (:,:)
 …
       fr_i_tm    (:,:) = fr_i  (:,:)
       emp_tm     (:,:) = emp   (:,:)
       sfx_tm     (:,:) = sfx   (:,:)
+      fmmflx_tm  (:,:) = fmmflx(:,:)
       qsr_tm     (:,:) = qsr   (:,:)
       wndm_tm    (:,:) = wndm  (:,:)
 …
          &      rnf_temp(jpi,jpj)           ,  h_rnf_temp(jpi,jpj) ,     &
          &      tsn_temp(jpi,jpj,jpk,2)     ,  emp_b_temp(jpi,jpj),      &
          &      emp_temp(jpi,jpj)           ,  sfx_temp(jpi,jpj)  ,      &
+         &      emp_temp(jpi,jpj)           ,  fmmflx_temp(jpi,jpj),     &
          &      hmld_temp(jpi,jpj)          ,  qsr_temp(jpi,jpj) ,       &
          &      fr_i_temp(jpi,jpj)          ,  fr_i_tm(jpi,jpj) ,        &
 …
          &      sshv_n_tm(jpi,jpj)          ,  sshv_b_hold(jpi,jpj),     &
          &      tsn_tm(jpi,jpj,jpk,2)       ,                            &
          &      emp_tm(jpi,jpj)             ,  sfx_tm(jpi,jpj)  ,        &
+         &      emp_tm(jpi,jpj)             ,  fmmflx_tm(jpi,jpj)  ,     &
          &      emp_b_hold(jpi,jpj)         ,                            &
          &      hmld_tm(jpi,jpj)            ,  qsr_tm(jpi,jpj) ,         &

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/SETTE/iodef_sette.xml

-                      r3764
+                      r4258
     -->
     <file_definition type="multiple_file" sync_freq="1d" min_digits="4">
+    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4">
       <file_group id="1h" output_freq="1h"  output_level="10" enabled=".FALSE."/> <!-- 1h files -->
 …
    <axis_definition>
       <axis id="deptht" long_name="Vertical T levels" unit="m"  /><!-- positive=".FALSE." -->
       <axis id="depthu" long_name="Vertical U levels" unit="m"  /><!-- positive=".FALSE." -->
       <axis id="depthv" long_name="Vertical V levels" unit="m"  /><!-- positive=".FALSE." -->
       <axis id="depthw" long_name="Vertical W levels" unit="m"  /><!-- positive=".FALSE." -->
+      <axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" />
+      <axis id="depthu" long_name="Vertical U levels" unit="m" positive="down" />
+      <axis id="depthv" long_name="Vertical V levels" unit="m" positive="down" />
+      <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
       <axis id="nfloat" long_name="Float number"      unit="-"  />
+      <axis id="icbcla" long_name="Iceberg class"     unit="-"  />
    </axis_definition>

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/TOOLS/COMPILE/Fcheck_archfile.sh

-                      r3862
+                      r4258
 # ::
+#
 #  $ ./Fcheck_archfile.sh ARCHFILE COMPILER
+#  $ ./Fcheck_archfile.sh ARCHFILE CPPFILE COMPILER
+#
+#
 …
+#
 #-
+cpeval ()
+{
+    cat > $2 << EOF
+if [ ${#2} -eq 0 ]; then
+   if [ ! -f ${COMPIL_DIR}/$1 ]; then
+   echo "Warning !!!"
+   echo "NO compiler chosen"
+   echo "Try makenemo -h for help"
+   echo "EXITING..."
+   exit 1
+   fi
+#==========================================================
+#    Automatically generated by Fcheck_archfile.sh from
+#    $1
+#==========================================================
+EOF
+    while read line
+    do
+   eval "echo \"$line\" >> $2"
+    done < $1
+}
+# cleaning related to the old version
+rm -f $( find ${COMPIL_DIR} -type l -name $1 -print )
+#
+if [ ${#3} -eq 0 ]; then # arch not specified
+    if [ ! -f ${COMPIL_DIR}/arch.history ]; then
+   echo "Warning !!!"
+   echo "NO compiler chosen"
+   echo "Try makenemo -h for help"
+   echo "EXITING..."
+   exit 1
+    else # use the arch file defined in arch.history
+   myarch=$( cat ${COMPIL_DIR}/arch.history )
+   if [ ! -f $myarch ]; then
+       echo "Warning !!!"
+       echo "previously used arch file no more found:"
+       echo $myarch
+       echo "EXITING..."
+       exit 1
+   else
+       if [ -f ${COMPIL_DIR}/$1 ]; then
+      if [ "$2" != "nocpp" ]
+      then
+          # has the cpp keys file been changed since we copied the arch file in ${COMPIL_DIR}?
+          mycpp=$( ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" )
+          if [ "$mycpp" != "$( cat ${COMPIL_DIR}/cpp.history )" ]; then
+         echo $mycpp > ${COMPIL_DIR}/cpp.history
+         cpeval ${myarch} ${COMPIL_DIR}/$1
+          fi
+          # has the cpp keys file been updated since we copied the arch file in ${COMPIL_DIR}?
+          mycpp=$( find -L ${COMPIL_DIR} -cnewer ${COMPIL_DIR}/$1 -name $2 -print )
+          [ ${#mycpp} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+      fi
+      # has myarch file been updated since we copied it in ${COMPIL_DIR}?
+      myarchdir=$( dirname ${myarch} )
+      myarchname=$( basename ${myarch} )
+      myarch=$( find -L $myarchdir -cnewer ${COMPIL_DIR}/$1 -name $myarchname -print )
+      [ ${#myarch} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+       else
+      cpeval ${myarch} ${COMPIL_DIR}/$1
+       fi
+   fi
+    fi
+else
+    nb=$( find ${MAIN_DIR}/ARCH -name arch-${3}.fcm -print | wc -l )
+    if [ $nb -eq 0 ]; then # no arch file found
+   echo "Warning !!!"
+   echo "Compiler not existing"
+   echo "Try makenemo -h for help"
+   echo "EXITING..."
+   exit 1
+    fi
+    if [ $nb -gt 1 ]; then # more than 1 arch file found
+   echo "Warning !!!"
+   echo "more than 1 arch file for the same compiler have been found"
+   find ${MAIN_DIR}/ARCH -name arch-${3}.fcm -print
+   echo "keep only 1"
+   echo "EXITING..."
+   exit 1
+    fi
+    myarch=$( find ${MAIN_DIR}/ARCH -name arch-${3}.fcm -print )
+    # we were already using this arch file ?
+    if [ "$myarch" == "$( cat ${COMPIL_DIR}/arch.history )" ]; then
+   if [ -f ${COMPIL_DIR}/$1 ]; then
+       if [ "$2" != "nocpp" ]
+       then
+      # has the cpp keys file been changed since we copied the arch file in ${COMPIL_DIR}?
+      mycpp=$( ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" )
+      if [ "$mycpp" != "$( cat ${COMPIL_DIR}/cpp.history )" ]; then
+          echo $mycpp > ${COMPIL_DIR}/cpp.history
+          cpeval ${myarch} ${COMPIL_DIR}/$1
+      fi
+      # has the cpp keys file been updated since we copied the arch file in ${COMPIL_DIR}?
+      mycpp=$( find -L ${COMPIL_DIR} -cnewer ${COMPIL_DIR}/$1 -name $2 -print )
+      [ ${#mycpp} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+       fi
+       # has myarch file been updated since we copied it in ${COMPIL_DIR}?
+       myarch=$( find -L ${MAIN_DIR}/ARCH -cnewer ${COMPIL_DIR}/$1 -name arch-${3}.fcm -print )
+       [ ${#myarch} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+   else
+       cpeval ${myarch} ${COMPIL_DIR}/$1
+   fi
+    else
+   if [ "$2" != "nocpp" ]
+   then
+       ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" > ${COMPIL_DIR}/cpp.history
+   fi
+   echo ${myarch} > ${COMPIL_DIR}/arch.history
+   cpeval ${myarch} ${COMPIL_DIR}/$1
+    fi
+fi
+#- do we need xios library?
+if [ "$2" != "nocpp" ]
+then
+    use_iom=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$2 | grep -c key_iomput )
 else
+   myfile=$( find -L ${MAIN_DIR}/ARCH -name arch-${2}.fcm -print )
+   if [ ${#myfile} -gt 0 ]; then
+      ln -sf  ${myfile} ${COMPIL_DIR}/$1
+   else
+      echo "Warning !!!"
+      echo "Compiler not existing"
+      echo "Try makenemo -h for help"
+      echo "EXITING..."
+      pwd
+      echo "find ${MAIN_DIR}/ARCH -name arch-${2}.fcm -print"
+      exit 1
+   fi
+    use_iom=0
 fi
+have_lxios=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$1 | grep -c "\-lxios" )
+if [[ ( $use_iom -eq 0 ) && ( $have_lxios -ge 1 ) ]]
+then
+    sed -e "s/-lxios//g" ${COMPIL_DIR}/$1 > ${COMPIL_DIR}/tmp$$
+    mv -f ${COMPIL_DIR}/tmp$$ ${COMPIL_DIR}/$1
+fi
+#- do we need oasis libraries?
+if [ "$2" != "nocpp" ]
+then
+    use_oasis=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$2 | grep -c key_oasis3 )
+else
+    use_oasis=0
+fi
+for liboa in psmile.MPI1 mct mpeu scrip mpp_io
+do
+    have_liboa=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$1 | grep -c "\-l${liboa}" )
+    if [[ ( $use_oasis -eq 0 ) && ( $have_liboa -ge 1 ) ]]
+    then
+   sed -e "s/-l${liboa}//g" ${COMPIL_DIR}/$1 > ${COMPIL_DIR}/tmp$$
+   mv -f ${COMPIL_DIR}/tmp$$ ${COMPIL_DIR}/$1
+    fi
+done

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/TOOLS/COMPILE/Flist_archfile.sh

-                      r3294
+                      r4258
 echo "Available compilers for -m option :"
 for file in  $(ls ${MAIN_DIR}/ARCH | grep fcm )
+for file in  $(ls ${MAIN_DIR}/ARCH | grep "fcm$" )
 do
 zvar1=${file#arch-}
 …
 if [ "$1" == "all" ]; then
    for dir  in  $(ls ${MAIN_DIR}/ARCH | grep -v fcm )
+   for dir  in  $(ls ${MAIN_DIR}/ARCH | grep -v "fcm$" )
    do
       echo "Available compilers at ${dir} :"
       for file in  $(ls ${MAIN_DIR}/ARCH/${dir} | grep  fcm )
+      for file in  $(ls ${MAIN_DIR}/ARCH/${dir} | grep "fcm$" )
       do
       zvar1=${file#arch-}
 …
 elif [ -d ${MAIN_DIR}/ARCH/${1} ]; then
       echo "Available compilers at $1 :"
       for file in  $(ls ${MAIN_DIR}/ARCH/$1 | grep fcm )
+      for file in  $(ls ${MAIN_DIR}/ARCH/$1 | grep "fcm$" )
       do
       zvar1=${file#arch-}
 …
 else
       echo "Available consortium member sub-directories :"
       for dir  in  $(ls ${MAIN_DIR}/ARCH | grep -v fcm )
+      for dir  in  $(ls ${MAIN_DIR}/ARCH | grep -v "fcm$" )
       do
          echo ${dir}

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/TOOLS/MISCELLANEOUS/chk_iomput.sh

-                      r2404
+                      r4258
        echo ' --insrc              only print all variable definitions found in the source code'
        echo 'Examples'
        echo '      chk_iomput.sh'
        echo '      chk_iomput.sh --help'
        echo '      chk_iomput.sh ../../CONFIG/ORCA2_LIM/EXP00/iodef.xml "../../NEMO/OPA_SRC/ ../../NEMO/LIM_SRC_2/"'
+       echo '      ./chk_iomput.sh'
+       echo '      ./chk_iomput.sh --help'
+       echo '      ./chk_iomput.sh ../../CONFIG/ORCA2_LIM/EXP00/iodef.xml "../../NEMO/OPA_SRC/ ../../NEMO/LIM_SRC_2/"'
        echo
        exit ;;
 …
 #------------------------------------------------
+#
+[ $inxml -eq 1 ] && grep "< *field * id *=" $xmlfile
+external=$( grep -c "<field_definition  *\([^ ].* \)*src=" $xmlfile )
+if [ $external -eq 1 ]
+then
+    xmlfield_def=$( grep "<field_definition  *\([^ ].* \)*src=" $xmlfile | sed -e 's/.*src="\([^"]*\)".*/\1/' )
+    xmlfield_def=$( dirname $xmlfile )/$xmlfield_def
+else
+    xmlfield_def=$xmlfile
+fi
+[ $inxml -eq 1 ] && grep "< *field  *\([^ ].* \)*id *=" $xmlfield_def
 [ $insrc -eq 1 ] && find $srcdir -name "*.[Ffh]90" -exec grep -iH "^[^\!]*call  *iom_put *(" {} \;
 [ $(( $insrc + $inxml )) -ge 1 ] && exit
 …
 # list of variables used in "CALL iom_put"
+#
+varlistsrc=$( find $srcdir -name "*.[Ffh]90" -exec grep -i  "^[^\!]*call  *iom_put *(" {} \; | sed -e "s/.*iom_put *( *[\"\']\([^\"\']*\)[\"\'] *,.*/\1/" | sort -d )
+badvarsrc=$( find $srcdir -name "*.[Ffh]90" -exec grep -i  "^[^\!]*call  *iom_put *(" {} \; | sed -e "s/.*iom_put *( *[\"\']\([^\"\']*\)[\"\'] *,.*/\1/" | grep -ic iom_put )
+if [ $badvarsrc -ne 0 ]
+then
+    echo "The following call to iom_put cannot be checked"
+    echo
+    find $srcdir -name "*.[Ffh]90" -exec grep -i  "^[^\!]*call  *iom_put *(" {} \; | sed -e "s/.*iom_put *( *[\"\']\([^\"\']*\)[\"\'] *,.*/\1/" | grep -i iom_put | sort -d
+    echo
+fi
+varlistsrc=$( find $srcdir -name "*.[Ffh]90" -exec grep -i  "^[^\!]*call  *iom_put *(" {} \; | sed -e "s/.*iom_put *( *[\"\']\([^\"\']*\)[\"\'] *,.*/\1/" | grep -vi iom_put | sort -d )
+#
 # list of variables defined in the xml file
+#
 varlistxml=$( grep "< *field * id *=" $xmlfile  | sed -e "s/^.*< *field * id *= *[\"\']\([^\"\']*\)[\"\'].*/\1/" | sort -d )
+varlistxml=$( grep "< *field  *\([^ ].* \)*id *=" $xmlfield_def  | sed -e "s/^.*< *field .*id *= *[\"\']\([^\"\']*\)[\"\'].*/\1/" | sort -d )
+#
 # list of variables to be outputed in the xml file
+#
 varlistout=$( grep "< *field * ref *=" $xmlfile  | sed -e "s/^.*< *field * ref *= *[\"\']\([^\"\']*\)[\"\'].*/\1/" | sort -d )
+varlistout=$( grep "< *field  *\([^ ].* \)*field_ref *=" $xmlfile  | sed -e "s/^.*< *field .*field_ref *= *[\"\']\([^\"\']*\)[\"\'].*/\1/" | sort -d )
+#
 echo "--------------------------------------------------"
 echo  check if all iom_put found in $srcdir
 echo  have a corresponding variable definition in $xmlfile
+echo  have a corresponding variable definition in $xmlfield_def
 echo "--------------------------------------------------"
 for var in $varlistsrc
 …
     if [ $tst -ne 1 ]
     then
    echo "problem with $var: $tst lines corresponding to its definition in $xmlfile, but defined in the code in"
+   echo "problem with $var: $tst lines corresponding to its definition in $xmlfield_def, but defined in the code in"
    for f in $srclist
    do

branches/2013/dev_r3858_NOC_ZTC/NEMOGCM/TOOLS/maketools

r3294	r4258
146	146
147	147	#- When used for the first time, choose a compiler ---
148		. ${COMPIL_DIR}/Fcheck_archfile.sh arch_tools.fcm ${CMP_NAM} \|\| exit
	148	. ${COMPIL_DIR}/Fcheck_archfile.sh arch_tools.fcm nocpp ${CMP_NAM} \|\| exit
149	149
150	150	#- Choose a default tool if needed ---

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