Changeset 3294 for trunk/DOC/TexFiles/Chapters/Chap_DIA.tex

Timestamp:

2012-01-28T17:44:18+01:00 (12 years ago)

Author:

rblod

Message:

Merge of 3.4beta into the trunk

File:

• trunk/DOC/TexFiles/Chapters/Chap_DIA.tex (modified) (5 diffs, 1 prop)

trunk/DOC/TexFiles/Chapters/Chap_DIA.tex

@@ -236 +236 @@
 \item[group]: define a group of file or field. Accept the same attributes as file or field.
 
-\item[file]: define the output fileÕs characteristics. Accepted attributes are description, enable, 
+\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.
 
@@ -321 +321 @@
 \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 wonÕt be output even if they are listed in the file.  
+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 
@@ -681 +681 @@
 numeric of the code, so that the trajectories never intercept the bathymetry. 
 
+\subsubsection{ Input data: initial coordinates }
+
+Initial coordinates can be given with Ariane Tools convention ( IJK coordinates ,(\np{ln\_ariane}=true) )
+or with longitude and latitude.
+
+
+In case of Ariane convention, input filename is \np{"init\_float\_ariane"}. Its format is:
+
+\texttt{ I J K nisobfl itrash itrash }
+
+\noindent with: 
+
+ - I,J,K  : indexes of initial position
+
+ - nisobfl: 0 for an isobar float, 1 for a float following the w velocity  
+
+ - itrash : set to zero; it is a dummy variable to respect Ariane Tools convention
+
+ - itrash :set to zero; it is a dummy variable to respect Ariane Tools convention
+
+\noindent Example:\\
+\noindent \texttt{ 100.00000  90.00000  -1.50000 1.00000   0.00000}\\
+\texttt{ 102.00000  90.00000  -1.50000 1.00000   0.00000}\\
+\texttt{ 104.00000  90.00000  -1.50000 1.00000   0.00000}\\
+\texttt{ 106.00000  90.00000  -1.50000 1.00000   0.00000}\\
+\texttt{ 108.00000  90.00000  -1.50000 1.00000   0.00000}\\
+
+
+In the other case ( longitude and latitude ), input filename is \np{"init\_float"}. Its format is:
+
+\texttt{ Long Lat depth nisobfl ngrpfl itrash}
+
+\noindent with:
+
+ - Long, Lat, depth  : Longitude, latitude, depth
+
+ - nisobfl: 0 for an isobar float, 1 for a float following the w velocity
+
+ - ngrpfl : number to identify searcher group
+
+ - itrash :set to 1; it is a dummy variable.
+
+\noindent Example:
+
+\noindent\texttt{  20.0 0.0 0.0 0 1 1 }\\
+\texttt{ -21.0 0.0 0.0 0 1 1 }\\
+\texttt{ -22.0 0.0 0.0 0 1 1 }\\
+\texttt{ -23.0 0.0 0.0 0 1 1 }\\
+\texttt{ -24.0 0.0 0.0 0 1 1 }\\
+
+\np{jpnfl} is the total number of floats during the run.
+When initial positions are read in a restart file ( \np{ln\_rstflo= .TRUE.} ),  \np{jpnflnewflo}
+can be added in the initialization file. 
+
+\subsubsection{ Output data }
+
+\np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} 
+is the frequency of creation of the float restart file.
+
+Output data can be written in ascii files (\np{ln\_flo\_ascii = .TRUE.} ). In that case, 
+output filename is \np{is trajec\_float}.
+
+Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii = .FALSE.} ). There are 2 possibilities:
+
+ - if (\key{iomput}) is used, outputs are selected in  \np{iodef.xml}. Here it is an example of specification 
+   to put in files description section:
+
+\vspace{-30pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+
+     <group id="1d\_grid\_T" name="auto" description="ocean T grid variables" >   }
+       <file id="floats"  description="floats variables"> }\\
+           <field ref="traj\_lon"   name="floats\_longitude"   freq\_op="86400" />}
+           <field ref="traj\_lat"   name="floats\_latitude"    freq\_op="86400" />}
+           <field ref="traj\_dep"   name="floats\_depth"       freq\_op="86400" />}
+           <field ref="traj\_temp"  name="floats\_temperature" freq\_op="86400" />}
+           <field ref="traj\_salt"  name="floats\_salinity"    freq\_op="86400" />}
+           <field ref="traj\_dens"  name="floats\_density"     freq\_op="86400" />}
+           <field ref="traj\_group" name="floats\_group"       freq\_op="86400" />}
+       </file>}
+  </group>}
+
+\end{verbatim}
+}}\end{alltt}
+
+
+ -  if (\key{iomput}) is not used, a file called \np{trajec\_float.nc} will be created by IOIPSL library.
+
+
+
 See also \href{http://stockage.univ-brest.fr/~grima/Ariane/}{here} the web site describing 
 the off-line use of this marvellous diagnostic tool.
+
+
+% -------------------------------------------------------------------------------------------------------------
+%       Harmonic analysis of tidal constituents
+% -------------------------------------------------------------------------------------------------------------
+\section{Harmonic analysis of tidal constituents (\key{diaharm}) }
+\label{DIA_diag_harm}
+
+A module is available to compute the amplitude and phase for tidal waves. 
+This diagnostic is actived with \key{diaharm}.
+
+%------------------------------------------namdia_harm----------------------------------------------------
+\namdisplay{namdia_harm}
+%----------------------------------------------------------------------------------------------------------
+
+Concerning the on-line Harmonic analysis, some parameters are available in namelist:
+
+- \texttt{nit000\_han} is the first time step used for harmonic analysis
+
+- \texttt{nitend\_han} is the last time step used for harmonic analysis
+
+- \texttt{nstep\_han} is the time step frequency for harmonic analysis
+
+- \texttt{nb\_ana} is the number of harmonics to analyse
+
+- \texttt{tname} is an array with names of tidal constituents to analyse
+
+\texttt{nit000\_han} and \texttt{nitend\_han} must be between \texttt{nit000} and \texttt{nitend} of the simulation.
+The restart capability is not implemented.
+
+The Harmonic analysis solve this equation:
+\begin{equation}
+h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i}
+\end{equation}
+
+With $A_{j}$,$\nu_{j}$,$\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error.
+$h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\
+We can rewrite this equation:
+\begin{equation}
+h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i}
+\end{equation}
+with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ et $\phi_{j}=arctan(S_{j}/C_{j})$.
+
+We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave.
+
+% -------------------------------------------------------------------------------------------------------------
+%       Sections transports
+% -------------------------------------------------------------------------------------------------------------
+\section{Transports across sections (\key{diadct}) }
+\label{DIA_diag_dct}
+
+A module is available to compute the transport of volume, heat and salt through sections. This diagnostic
+is actived with \key{diadct}.
+
+Each section is defined by the coordinates of its 2 extremities. The pathways between them are contructed
+using tools which can be found in  \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT} and are written in a binary file
+ \texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is later read in by NEMO to compute on-line transports.
+
+The on-line transports module creates three output ascii files: 
+
+- \texttt{volume\_transport} for volume transports (  unit: $10^{6} m^{3} s^{-1}$ )
+
+- \texttt{heat\_transport}   for heat transports   (  unit: $10^{15} W $ )
+
+- \texttt{salt\_transport}   for salt transports   (  unit: $10^{9}g s^{-1}$ )\\
+
+
+Namelist parameters control how frequently the flows are summed and the time scales over which
+ they are averaged, as well as the level of output for debugging:
+
+%------------------------------------------namdct----------------------------------------------------
+\namdisplay{namdct}
+%-------------------------------------------------------------------------------------------------------------
+
+\texttt{nn\_dct}: frequency of instantaneous transports computing
+
+\texttt{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
+
+\texttt{nn\_debug}: debugging of the section
+
+\subsubsection{ To create a binary file containing the pathway of each section }
+
+In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run}, the file \texttt{ {list\_sections.ascii\_global}}
+contains a list of all the sections that are to be computed (this list of sections is based on MERSEA project metrics).
+
+Another file is available for the GYRE configuration (\texttt{ {list\_sections.ascii\_GYRE}}). 
+
+Each section is defined by:
+
+\noindent \texttt{ long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name }\\
+with:
+
+- \texttt{long1 lat1} , coordinates of the first extremity of the section;
+
+- \texttt{long2 lat2} , coordinates of the second extremity of the section;
+
+- \texttt{nclass} the number of bounds of your classes (e.g. 3 bounds for 2 classes);
+
+- \texttt{okstrpond} to compute heat and salt transport, \texttt{nostrpond} if no;
+
+- \texttt{ice}  to compute surface and volume ice transports, \texttt{noice} if no. \\
+
+
+\noindent The results of the computing of transports, and the directions of positive
+ and negative flow do not depend on the order of the 2 extremities in this file.\\ 
+
+
+\noindent If nclass =/ 0,the next lines contain the class type and the nclass bounds:
+
+\texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}
+
+\texttt{classtype}
+
+\texttt{zbound1}
+
+\texttt{zbound2}
+
+\texttt{.}
+
+\texttt{.}
+
+\texttt{nclass-1}
+
+\texttt{nclass}
+
+\noindent where \texttt{classtype} can be:
+
+- \texttt{zsal} for salinity classes
+
+- \texttt{ztem} for temperature classes
+
+- \texttt{zlay} for depth classes
+
+- \texttt{zsigi} for insitu density classes
+
+- \texttt{zsigp} for potential density classes \\
+
+  
+The script \texttt{job.ksh} computes the pathway for each section and creates a binary file 
+\texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is read by NEMO. \\
+
+It is possible to use this tools for new configuations: \texttt{job.ksh} has to be updated 
+with the coordinates file name and path. \\
+
+
+Examples of two sections, the ACC\_Drake\_Passage with no classes, and the
+ ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown:
+
+\noindent \texttt{ -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage}
+
+\noindent \texttt{ -80.5    22.5   -80.5    25.5  05 nostrpond noice ATL\_Cuba\_Florida}
+
+\noindent \texttt{ztem}
+
+\noindent \texttt{-2.0}
+
+\noindent \texttt{ 4.5}
+
+\noindent \texttt{ 7.0}
+
+\noindent \texttt{12.0}
+
+\noindent \texttt{40.0}
+
+
+\subsubsection{ To read the output files }
+
+The output format is :
+ 
+{\small\texttt{date, time-step number, section number, section name, section slope coefficient, class number, 
+class name, class bound 1 , classe bound2, transport\_direction1 ,  transport\_direction2, transport\_total}}\\
+
+
+For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class 
+and the last line corresponds to the total transport summed over all classes. For sections with no classes, class number
+\texttt{ 1 } corresponds to \texttt{ total class } and this class is called  \texttt{N}, meaning \texttt{none}.\\
+
+
+\noindent \texttt{ transport\_direction1 } is the positive part of the transport ( \texttt{ > = 0 } ).
+
+\noindent \texttt{ transport\_direction2 } is the negative part of the transport ( \texttt{ < = 0 } ).\\
+
+
+\noindent The \texttt{section slope coefficient} gives information about the significance of transports signs and direction:\\
+
+
+
+\begin{tabular}{|c|c|c|c|p{4cm}|}
+\hline
+section slope coefficient & section type & direction 1 & direction 2 & total transport \\ \hline
+0.    &  horizontal & northward & southward & postive: northward  \\ \hline
+1000. &  vertical   & eastward  & westward  & postive: eastward  \\ \hline                
+\texttt{=/0, =/ 1000.}   &  diagonal   & eastward  & westward  & postive: eastward  \\ \hline                
+\end{tabular}
+
+
 
 % -------------------------------------------------------------------------------------------------------------
@@ -726 +1013 @@
 are removed from the sub-basins. Note also that the Arctic Ocean has been split 
 into Atlantic and Pacific basins along the North fold line.  }
-\end{center}   \end{figure}
+\end{center}   \end{figure}  
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
@@ -733 +1020 @@
 (see Section \ref{MISC_steric} below for one of them). 
 Activating those outputs requires to define the \key{diaar5} CPP key.
+\\
+\\