/[MITgcm]/manual/s_phys_pkgs/mnc.tex
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revision 1.5 by edhill, Thu Feb 12 03:35:05 2004 UTC revision 1.7 by edhill, Fri Apr 2 15:56:02 2004 UTC
# Line 1  Line 1 
1  % $Header$  % $Header$
2  % $Name$  % $Name$
3    
4  \section{NetCDF I/O Integration}  \section{NetCDF I/O Integration: MNC}
5  \label{sec:pkg:mnc}  \label{sec:pkg:mnc}
6    
7  The \texttt{mnc} package is a set of convenience routines written to  The \texttt{mnc} package is a set of convenience routines written to
# Line 23  http://www.unidata.ucar.edu/packages/net Line 23  http://www.unidata.ucar.edu/packages/net
23  The \texttt{mnc} package is a two-level convenience library (or  The \texttt{mnc} package is a two-level convenience library (or
24  ``wrapper'') for most of the NetCDF Fortran API.  Its purpose is to  ``wrapper'') for most of the NetCDF Fortran API.  Its purpose is to
25  streamline the user interface to NetCDF by maintaining internal  streamline the user interface to NetCDF by maintaining internal
26  relations (``look-up tables'') keyed with strings (or ``names'') and  relations (look-up tables) keyed with strings (or names) and entities
27  entities such as NetCDF files, variables, and attributes.  such as NetCDF files, variables, and attributes.
28    
29  The two levels of the \texttt{mnc} package are:  The two levels of the \texttt{mnc} package are:
30  \begin{description}  \begin{description}
# Line 34  The two levels of the \texttt{mnc} packa Line 34  The two levels of the \texttt{mnc} packa
34    The upper level contains information about two kinds of    The upper level contains information about two kinds of
35    associations:    associations:
36    \begin{description}    \begin{description}
37    \item[Grid type] is lookup table indexed with a grid type name.    \item[grid type] is lookup table indexed with a grid type name.
38      Each grid type name is associated with a number of dimensions, the      Each grid type name is associated with a number of dimensions, the
39      dimension sizes (one of which may be unlimited), and starting and      dimension sizes (one of which may be unlimited), and starting and
40      ending index arrays.  The intent is to store all the necessary      ending index arrays.  The intent is to store all the necessary
# Line 44  The two levels of the \texttt{mnc} packa Line 44  The two levels of the \texttt{mnc} packa
44      shown in Figures \ref{fig:communication_primitives} and      shown in Figures \ref{fig:communication_primitives} and
45      \ref{fig:tiling-strategy}).      \ref{fig:tiling-strategy}).
46        
47    \item[Variable type] is a lookup table indexed by a variable type    \item[variable type] is a lookup table indexed by a variable type
48      name.  For each name, the table contains a reference to a grid      name.  For each name, the table contains a reference to a grid
49      type for the variable and the names and values of various      type for the variable and the names and values of various
50      attributes.      attributes.
# Line 68  The two levels of the \texttt{mnc} packa Line 68  The two levels of the \texttt{mnc} packa
68    
69  \subsection{Using MNC}  \subsection{Using MNC}
70    
71  \subsubsection{``Grid--Types'' and ``Variable--Types''}  \subsubsection{Grid--Types and Variable--Types}
72    
73  As a convenience for users, the MNC package includes numerous routines  As a convenience for users, the MNC package includes numerous routines
74  to aid in the writing of data to NetCDF format.  Probably the biggest  to aid in the writing of data to NetCDF format.  Probably the biggest
# Line 94  string follows the format Line 94  string follows the format
94  \begin{center}  \begin{center}
95    \texttt{H0\_H1\_H2\_\_V\_\_T}    \texttt{H0\_H1\_H2\_\_V\_\_T}
96  \end{center}  \end{center}
97  where the terms \textit{H0,H1,H2,V,T} can be almost any combination of  where the terms \textit{H0}, \textit{H1}, \textit{H2}, \textit{V},
98  the following:  \textit{T} can be almost any combination of the following:
99  \begin{center}  \begin{center}
100    \begin{tabular}[h]{|ccc|c|c|}\hline    \begin{tabular}[h]{|ccc|c|c|}\hline
101      \multicolumn{3}{|c|}{Horizontal} & Vertical &  \\      \multicolumn{3}{|c|}{Horizontal} & Vertical & Time \\
102      Location & Direction & Halo & Location & Time  \\\hline      \textbf{H0}: location & \textbf{H1}: dimensions & \textbf{H2}: halo
103      H0  &  H1  &  H2  &  V  &  T  \\\hline            & \textbf{V}: location & \textbf{T}: level  \\\hline
104      \texttt{-} & xy & Hn & \texttt{-} & \texttt{-} \\      \texttt{-} & xy & Hn & \texttt{-} & \texttt{-} \\
105      U  &  x  &  Hy  &  i  &  t  \\      U  &  x  &  Hy  &  i  &  t  \\
106      V  &  y  &      &  c  &     \\      V  &  y  &      &  c  &     \\
# Line 114  file Line 114  file
114    \texttt{pkg/mnc/pre-defined\_grids.txt}.    \texttt{pkg/mnc/pre-defined\_grids.txt}.
115  \end{center}  \end{center}
116    
117    The variable type is an association between a variable type name and the
118    following items:
119    \begin{center}
120      \begin{tabular}[h]{|ll|}\hline
121        \textbf{Item}  & \textbf{Purpose}  \\\hline
122        grid type  &  defines the in-memory arrangement  \\
123        \texttt{bi,bj} dimensions  &  tiling indices, if present  \\\hline
124      \end{tabular}
125    \end{center}
126    and is used by the \texttt{mnc\_cw\_*\_[R|W]} subroutines for reading
127    and writing variables.
128    
129    
130  \subsubsection{An Example}  \subsubsection{An Example}
131    
132  Writing variables to NetCDF files can be accomplished in as few as two  Writing variables to NetCDF files can be accomplished in as few as two
133  function calls.  The first function call defines a variable type,  function calls.  The first function call defines a variable type,
134  associates it with a name (character string), and provides additional  associates it with a name (character string), and provides additional
135  information about the indicies for \texttt{bi,bj} dimensions.  The  information about the indicies for the tile (\texttt{bi},\texttt{bj})
136  second function call will write variable at, if necessary, the  dimensions.  The second function call will write the data at, if
137  current time level within the model.  necessary, the current time level within the model.
138    
139  Examples of the initialization calls can be found in the file  Examples of the initialization calls can be found in the file
140  \begin{center}  \filelink{model/src/initialise\_fixed.F}{model-src-initialise_fixed.F}
141    \filelink{model/src/initialise\_fixed.F}{model-src-initialise_fixed.F}  where these four function calls:
142  \end{center}  {\footnotesize
 where these four function calls: {\footnotesize  
143  \begin{verbatim}  \begin{verbatim}
144    C     Create MNC definitions for DYNVARS.h variables    C     Create MNC definitions for DYNVARS.h variables
145          CALL MNC_CW_ADD_VNAME(myThid, 'iter', '-_-_--__-__t', 0,0)          CALL MNC_CW_ADD_VNAME(myThid, 'iter', '-_-_--__-__t', 0,0)
# Line 136  where these four function calls: {\footn Line 147  where these four function calls: {\footn
147         &     'long_name','iteration_count')         &     'long_name','iteration_count')
148          CALL MNC_CW_ADD_VNAME(myThid, 'U', 'U_xy_Hn__C__t', 4,5)          CALL MNC_CW_ADD_VNAME(myThid, 'U', 'U_xy_Hn__C__t', 4,5)
149          CALL MNC_CW_ADD_VATTR_TEXT(myThid,'U',1,'units','m/s')          CALL MNC_CW_ADD_VATTR_TEXT(myThid,'U',1,'units','m/s')
150  \end{verbatim} }  \end{verbatim}
151  {\noindent initialize two \texttt{VNAME}s and add one attribute to each.}  }
152    {\noindent initialize two \texttt{VNAME}s and add one NetCDF
153      attribute to each.}
154            
155  The two variables are subsequently written at specific time steps  The two variables defined above are subsequently written at specific
156  within  time steps within
157  \begin{center}  \filelink{model/src/write\_state.F}{model-src-write_state.F}
158    \filelink{model/src/write\_state.F}{model-src-write_state.F}  using the function calls:
159  \end{center}  {\footnotesize
 using the function calls: {\footnotesize  
160  \begin{verbatim}  \begin{verbatim}
161    C     Write the DYNVARS.h variables using the MNC package    C     Write the DYNVARS.h variables using the MNC package
162          mnc_iter = myIter          mnc_iter = myIter
163          CALL MNC_CW_RL_W_R(myThid,'state',0,0,'iter',-1,mnc_iter)          CALL MNC_CW_RL_W_R(myThid,'state',0,0,'iter',-1,mnc_iter)
164          CALL MNC_CW_RL_W_D(myThid,'state',0,0,'U', 0, uVel)          CALL MNC_CW_RL_W_D(myThid,'state',0,0,'U', 0, uVel)
165  \end{verbatim} }  \end{verbatim}
166    }
167    
168    
169  \subsection{Key subroutines, parameters and files}  \subsection{Key subroutines, parameters and files}
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