/[MITgcm]/manual/s_phys_pkgs/mnc.tex

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-revision 1.6 by edhill,
Fri Feb 13 21:35:59 2004 UTC
+revision 1.11 by edhill,
Wed Sep 22 15:11:32 2004 UTC
 Line 99 
 where the terms \textit{H0}, \textit{H1}
  \begin{center}
    \begin{tabular}[h]{|ccc|c|c|}\hline
      \multicolumn{3}{|c|}{Horizontal} & Vertical & Time \\
-     \textit{H0}: location & \textit{H1}: dimensions & \textit{H2}: halo
+     \textbf{H0}: location & \textbf{H1}: dimensions & \textbf{H2}: halo
-           & \textit{V}: location & \textit{T}: level  \\\hline
+           & \textbf{V}: location & \textbf{T}: level  \\\hline
      \texttt{-} & xy & Hn & \texttt{-} & \texttt{-} \\
      U  &  x  &  Hy  &  i  &  t  \\
      V  &  y  &      &  c  &     \\
 Line 114 
 file
    \texttt{pkg/mnc/pre-defined\_grids.txt}.
  \end{center}
+ The variable type is an association between a variable type name and the
+ following items:
+ \begin{center}
+   \begin{tabular}[h]{|l|l|}\hline
+     \textbf{Item}  & \textbf{Purpose}  \\\hline
+     grid type  &  defines the in-memory arrangement  \\
+     \texttt{bi,bj} dimensions  &  tiling indices, if present  \\\hline
+   \end{tabular}
+ \end{center}
+ and is used by the \texttt{mnc\_cw\_*\_[R|W]} subroutines for reading
+ and writing variables.
  \subsubsection{An Example}
-Line 125 
 dimensions.  The second function call wi
+Line 137 
 dimensions.  The second function call wi
  necessary, the current time level within the model.
  Examples of the initialization calls can be found in the file
- \filelink{model/src/initialise\_fixed.F}{model-src-initialise_fixed.F}
+ \filelink{model/src/ini\_mnc\_io.F}{model-src-ini_mnc_io.F}
- where these four function calls:
+ where these function calls:
  {\footnotesize
  \begin{verbatim}
-   C     Create MNC definitions for DYNVARS.h variables
+ C     Create MNC definitions for DYNVARS.h variables
-         CALL MNC_CW_ADD_VNAME(myThid, 'iter', '-_-_--__-__t', 0,0)
+       CALL MNC_CW_ADD_VNAME('iter', '-_-_--__-__t', 0,0, myThid)
-         CALL MNC_CW_ADD_VATTR_TEXT(myThid,'iter',1,
+       CALL MNC_CW_ADD_VATTR_TEXT('iter',1,
-        &     'long_name','iteration_count')
+      &     'long_name','iteration_count', myThid)
-         CALL MNC_CW_ADD_VNAME(myThid, 'U', 'U_xy_Hn__C__t', 4,5)
-         CALL MNC_CW_ADD_VATTR_TEXT(myThid,'U',1,'units','m/s')
+       CALL MNC_CW_ADD_VNAME('model_time', '-_-_--__-__t', 0,0, myThid)
+       CALL MNC_CW_ADD_VATTR_TEXT('model_time',1,
+      &     'long_name','Model Time', myThid)
+       CALL MNC_CW_ADD_VATTR_TEXT('model_time',1,'units','s', myThid)
+       CALL MNC_CW_ADD_VNAME('U', 'U_xy_Hn__C__t', 4,5, myThid)
+       CALL MNC_CW_ADD_VATTR_TEXT('U',1,'units','m/s', myThid)
+       CALL MNC_CW_ADD_VATTR_TEXT('U',1,
+      &     'coordinates','XU YU RC iter', myThid)
+       CALL MNC_CW_ADD_VNAME('T', 'Cen_xy_Hn__C__t', 4,5, myThid)
+       CALL MNC_CW_ADD_VATTR_TEXT('T',1,'units','degC', myThid)
+       CALL MNC_CW_ADD_VATTR_TEXT('T',1,'long_name',
+      &     'potential_temperature', myThid)
+       CALL MNC_CW_ADD_VATTR_TEXT('T',1,
+      &     'coordinates','XC YC RC iter', myThid)
  \end{verbatim}
  }
- {\noindent initialize two \texttt{VNAME}s and add one NetCDF
+ {\noindent initialize four \texttt{VNAME}s and add one or more NetCDF
-   attribute to each.}
+   attributes to each.}
- The two variables defined above are subsequently written at specific
+ The four variables defined above are subsequently written at specific
  time steps within
  \filelink{model/src/write\_state.F}{model-src-write_state.F}
  using the function calls:
  {\footnotesize
  \begin{verbatim}
-   C     Write the DYNVARS.h variables using the MNC package
+ C       Write dynvars using the MNC package
-         mnc_iter = myIter
+         CALL MNC_CW_SET_UDIM('state', -1, myThid)
-         CALL MNC_CW_RL_W_R(myThid,'state',0,0,'iter',-1,mnc_iter)
+         CALL MNC_CW_I_W('I','state',0,0,'iter', myIter, myThid)
-         CALL MNC_CW_RL_W_D(myThid,'state',0,0,'U', 0, uVel)
+         CALL MNC_CW_SET_UDIM('state', 0, myThid)
+         CALL MNC_CW_RL_W('D','state',0,0,'model_time',myTime, myThid)
+         CALL MNC_CW_RL_W('D','state',0,0,'U', uVel, myThid)
+         CALL MNC_CW_RL_W('D','state',0,0,'T', theta, myThid)
  \end{verbatim}
  }
- \subsection{Key subroutines, parameters and files}
+ \subsubsection{Parameters}
- All of the variables used to implement the lookup tables are described
+ Most of the MNC--related parameters are contained within a Fortran
- in \filelink{model/src/write\_state.F}{model-src-write_state.F}
+ namelist file called \texttt{data.mnc}.  If this file does not exist,
+ then the MNC package will interpret that as an indication that it is
+ not to be used.  If the \texttt{data.mnc} file does exist, then it may
+ contain the following parameters:
+ \begin{center}
+   {\footnotesize
+     \begin{tabular}[htb]{|l|c|l|l|}\hline
+       \textbf{Name}  &  \textbf{T}  &
+       \textbf{Default}  &  \textbf{Description}  \\\hline
+       &  &  &  \\
+       \texttt{useMNC}  &  L  & \texttt{.FALSE.}  &
+       \textbf{overall MNC ON/OFF switch}  \\
+       \texttt{mnc\_echo\_gvtypes}  &  L  & \texttt{.FALSE.}  &
+       echo pre-defined ``types'' (debugging)   \\
+       \texttt{mnc\_use\_outdir}  &  L  & \texttt{.FALSE.}  &
+       create a directory for output  \\
+       \texttt{mnc\_outdir\_str}  &  S  & \texttt{'mnc\_'}  &
+       output directory name \\
+       \texttt{mnc\_outdir\_date}  &  L  & \texttt{.FALSE.}  &
+       embed date in the output dir name  \\
+       \texttt{pickup\_write\_mnc}  &  L  & \texttt{.FALSE.}  &
+       use MNC to write (create) pickup files  \\
+       \texttt{pickup\_read\_mnc}  &  L  & \texttt{.FALSE.}  &
+       use MNC to read pickup files  \\
+       \texttt{mnc\_use\_indir}  &  L  & \texttt{.FALSE.}  &
+       use a directory (path) for input  \\
+       \texttt{mnc\_indir\_str}  &  S  & \texttt{''}  &
+       input directory (or path) name  \\
+       \texttt{snapshot\_mnc}  &  L  & \texttt{.FALSE.}  &
+       write \texttt{snapshot} (instantaneous) w/MNC  \\
+       \texttt{monitor\_mnc}  &  L  & \texttt{.FALSE.}  &
+       write \texttt{monitor} w/MNC  \\
+       \texttt{timeave\_mnc}  &  L  & \texttt{.FALSE.}  &
+       write \texttt{timeave} w/MNC  \\\hline
+     \end{tabular}
+   }
+ \end{center}
+ Additional MNC--related parameters are contained within the main
+ \texttt{data} namelist file and in some of the namelist files for
+ individual packages.  These options are:
+ \begin{center}
+   {\footnotesize
+     \begin{tabular}[htb]{|l|c|l|l|}\hline
+       \textbf{Name}  &  \textbf{T}  &
+       \textbf{Default}  &  \textbf{Description}  \\\hline
+       \multicolumn{4}{|c|}{\ }  \\
+       \multicolumn{4}{|c|}{Main namelist file:
+         ``\textbf{data}''}  \\\hline
+       \texttt{snapshot\_ioinc}  &  L  & \texttt{.FALSE.}  &
+       write \texttt{snapshot} ``inclusively''  \\
+       \texttt{timeave\_ioinc}  &  L  & \texttt{.FALSE.}  &
+       write \texttt{timeave} ``inclusively''  \\
+       \texttt{monitor\_ioinc}  &  L  & \texttt{.FALSE.}  &
+       write \texttt{monitor} ``inclusively''  \\\hline
+       \multicolumn{4}{|c|}{\ }  \\
+       \multicolumn{4}{|c|}{Diagnostics namelist file:
+         ``\textbf{data.diagnostics}''}  \\\hline
+       \texttt{diag\_mnc}  &  L  & \texttt{.FALSE.}  &
+       write \texttt{diagnostics} w/MNC  \\
+       \texttt{diag\_ioinc}  &  L  & \texttt{.FALSE.}  &
+       write \texttt{diagnostics} ``inclusively''  \\\hline
+     \end{tabular}
+   }
+ \end{center}
- \subsection{Package Reference}
+ By default, turning on MNC for a particular output stream will result
+ in turning off all the corresponding (usually, default) MDSIO or
+ STDOUT output mechanisms.  In other words, output defaults to being an
+ exclusive selection.  To enable multiple kinds of simultaneous output,
+ flags of the form \texttt{NAME\_ioinc} can be used where \texttt{NAME}
+ corresponds to the various MNC output flags.  When a
+ \texttt{NAME\_ioinc} flag is set to \texttt{.TRUE.}, then multiple
+ forms of output are allowed for the \texttt{NAME} output mechanism.
+ The intent of this design is that typical users will only want one
+ kind of output while people debugging the code (particularly the I/O
+ routines) may want simultaneous types of output.
+ This ``inclusive'' versus ``exclusive'' design is easily applied in
+ cases where three or more kinds of output may be generated.  Thus, it
+ can be readily extended to additional new output types (eg. HDF5).
+ Input types are always exclusive.

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