manual/s_phys_pkgs/diagnostics.tex

\section{Diagnostics--A Flexible Infrastructure}
\label{sec:pkg:diagnostics}
\begin{rawhtml}
<!-- CMIREDIR:package_diagnostics: -->
\end{rawhtml}

\subsection{Introduction}

\noindent
This section of the documentation describes the Diagnostics package available within 
the GCM.  A large selection of model diagnostics is available for output.  
In addition to the diagnostic quantities pre-defined in the GCM, there exists
the option, in any experiment, to define a new diagnostic quantity and include it
as part of the diagnostic output with the addition of a single subroutine call in the
routine where the field is computed. As a matter of philosophy, no diagnostic is enabled 
as default, thus each user must specify the exact diagnostic information required for an 
experiment.  This is accomplished by enabling the specific diagnostic of interest cataloged 
in the Diagnostic Menu (see Section \ref{sec:diagnostics:menu}). Instructions for enabling
diagnostic output and defining new diagnostic quantities are found in Section 
\ref{sec:diagnostics:usersguide} of this document.

\noindent
The Diagnostic Menu in this section of the manual is a listing of diagnostic quantities available 
within the main (dynamics) part of the GCM. Additional diagnostic quantities, defined within the
different GCM packages, are available and are listed in the diagnostic menu subsection of 
the manual section associated with each relevant package. Once a diagnostic is enabled, the 
GCM will continually increment an array specifically allocated for that diagnostic whenever the 
appropriate quantity is computed.  A counter is defined which records how many times each diagnostic 
quantity has been incremented.  Several special diagnostics are included in the menu. Quantities 
refered to as ``Counter Diagnostics'', are defined for selected diagnostics which record the 
frequency at which a diagnostic is incremented separately for each model grid location.
Quantitied refered to as ``User Diagnostics'' are included in the menu to facilitate
defining new diagnostics for a particular experiment.

\subsection{Equations}
Not relevant.

\subsection{Key Subroutines and Parameters}
\label{sec:diagnostics:diagover}

\noindent
There are several utilities within the GCM available to users to enable, disable,
clear, write and retrieve model diagnostics, and may be called from any routine.  
The available utilities and the CALL sequences are listed below.

\noindent
{\bf diagnostics\_fill}:  This is the main user interface routine to the diagnostics
package. This routine will increment the specified diagnostic quantity with a field 
sent through the argument list.

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\>        call diagnostics\_fill (arrayin, chardiag, levflg, nlevs, \\
\>              bibjflg, bi, bj, myThid) \\
\\
where \>  arrayin  \>= Field to increment diagnostics array \\
      \>  chardiag \>= Character *8 expression for diag to fill \\
      \>  levflg   \>= Integer flag for vertical levels: \\
      \>           \>= 0 indicates multiple (nlevs) levels incremented \\
      \>           \>= -1 indicates multiple (nlevs) levels incremented, \\
      \>           \> but in reverse vertical order \\
      \>           \> positive integer - WHICH single level to increment. \\
      \>  nlevs    \>= indicates Number of levels to be filled (1 if levflg gt 0) \\
      \>  bibjflg  \>= Integer flag to indicate instructions for bi bj loop \\
      \>           \>= 0 indicates that the bi-bj loop must be done here \\
      \>           \>= 1 indicates that the bi-bj loop is done OUTSIDE \\
      \>           \>= 2 indicates that the bi-bj loop is done OUTSIDE \\
      \>           \>    AND that we have been sent a local array \\
      \>           \>    AND that the array has the shadow regions \\
      \>           \>= 3 indicates that the bi-bj loop is done OUTSIDE \\
      \>           \>    AND that we have been sent a local array \\
      \>           \>    AND that the array has no shadow regions \\
      \>  bi       \>= X-direction process(or) number - used for bibjflg=1-3 \\
      \>  bj       \>= Y-direction process(or) number - used for bibjflg=1-3 \\
      \>  myThid   \>= Current Thread number \\
\end{tabbing}

\noindent
{\bf diagnostics\_scale\_fill}:  This is a possible alternative routine to
diagnostics\_fill which performs the same functions and has an additional option
to scale the field before filling or raise the field to a power before filling.

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\>        call diagnostics\_scale\_fill (arrayin, scalefactor, power, chardiag, \\
\>        levflg, nlevs, bibjflg, bi, bj, myThid) \\
\\
where \>  All the arguments are the same as for diagnostics\_fill with the addition of: \\
      \>  scalefactor \>= Factor to scale field \\
      \>  power       \>= Integer power to which to raise the input field \\
\end{tabbing}

\noindent
{\bf diagnostics\_is\_on}: Function call to inquire whether a diagnostic is active
and can be incremented. Useful when there is a computation that must be done locally
before a call to diagnostics\_fill. The call sequence:

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\> flag = diagnostics\_is\_on( diagName, myThid )
\\
where \>  diagName \>= Character *8 expression for diagnostic \\
      \>  myThid   \>= Current Thread number \\
\end{tabbing}

\noindent
{\bf diagnostics\_get\_pointers}:  This subroutine retrieves the value of a the diagnostics
pointers that other routines require as input - can be useful if the diagnostics common
blocks are not local to a routine.

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\> call diagnostics\_get\_pointers( diagName, ipoint, jpoint, myThid )
\\
where \>  diagName \>= Character *8 expression of diagnostic \\
      \>  ipoint   \>= Pointer into qdiag array - from idiag array in common \\
      \>  jpoint   \>= Pointer into diagnostics menu - from jdiag array in common \\
      \>  myThid   \>= Current Thread number \\
\end{tabbing}

\noindent
{\bf getdiag}:  This subroutine retrieves the value of a model diagnostic.  This routine 
is particulary useful when called from a user output routine, although it can be called 
from any routine.  This routine returns the time-averaged value of the diagnostic by
dividing the current accumulated diagnostic value by its corresponding counter.  This 
routine does not change the value of the diagnostic itself, that is, it does not replace 
the diagnostic with its time-average.  The calling sequence for this routine is givin by:

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\>        call getdiag (lev, undef, qtmp, ipoint, mate, bi, bj, myThid) \\
\\
where \>  lev     \>= Model Level at which the diagnostic is desired \\
      \>  undef   \>= Fill value to be used when diagnostic is undefined \\
      \>  qtmp    \>= Time-Averaged Diagnostic Output \\
      \>  ipoint  \>= Pointer into qdiag array - from idiag array in common \\
      \>  mate    \>= Diagnostic mate pointer number \\
      \>  bi      \>= X-direction process(or) number \\
      \>  bj      \>= Y-direction process(or) number \\
      \>  myThid  \>= Current Thread number \\
\end{tabbing}

\noindent
{\bf diagnostics\_add2list}:  This subroutine enables a diagnostic from the Diagnostic Menu, meaning 
that space is allocated for the diagnostic and the model routines will increment the 
diagnostic value during execution.  This routine is the underlying interface routine
for defining a new permanent diagnostic in the main model or in a package.  The calling sequence is:

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\>        call diagnostics\_add2list( diagNum,diagName, diagCode, \\
\>        diagUnits, diagTitle, myThid ) \\
\\
where \> diagNum   \>=Diagnostic number - Output from routine \\
      \> diagName  \>=character*8 diagnostic name \\
      \> diagCode  \>=character*16 parsing code (see description of gdiag below) \\
      \> diagUnits \>=Diagnostic units (character*16) \\
      \> diagTitle \>=Diagnostic title or long name (up to character*80) \\
      \> myThid    \>=Current Thread number \\
\end{tabbing}

\noindent
{\bf clrdiag}:  This subroutine initializes the values of model diagnostics to zero, and is
particularly useful when called from user output routines to re-initialize diagnostics 
during the run.  The calling sequence is:

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\>        call diagnostics\_clrdiag (jpoint, ipoint, myThid) \\
\\
where \>  jpoint \>= Diagnostic number from menu - from jdiag array \\
          ipoint \>= Pointer number into qdiag array - from idiag array \\
      \>  myThid \>=Current Thread number \\
\end{tabbing}

\noindent
The diagnostics are computed at various times and places within the GCM. Because the
MIT GCM may employ a staggered grid, diagnostics may be computed at grid box centers,
corners, or edges, and at the middle or edge in the vertical. Some diagnostics are scalars, 
while others are components of vectors. An internal array is defined which contains 
information concerning various grid attributes of each diagnostic. The GDIAG
array (in common block \\diagnostics in file diagnostics.h) is internally defined as a 
character*8 variable, and is equivalenced to a character*1 "parse" array in output in 
order to extract the grid-attribute information.  The GDIAG array is described in 
Table \ref{tab:diagnostics:gdiag.tabl}.

\begin{table}
\caption{Diagnostic Parsing Array}
\label{tab:diagnostics:gdiag.tabl}
\begin{center}
\begin{tabular}{ |c|c|l| }
\hline
\multicolumn{3}{|c|}{\bf Diagnostic Parsing Array} \\ 
\hline
\hline
Array & Value & Description \\
\hline
  parse(1)   & $\rightarrow$ S &  Scalar Diagnostic                 \\ 
             & $\rightarrow$ U &  U-vector component Diagnostic     \\ 
             & $\rightarrow$ V &  V-vector component Diagnostic     \\ \hline
  parse(2)   & $\rightarrow$ U &  C-Grid U-Point                    \\ 
             & $\rightarrow$ V &  C-Grid V-Point                    \\ 
             & $\rightarrow$ M &  C-Grid Mass Point                 \\ 
             & $\rightarrow$ Z &  C-Grid Vorticity (Corner) Point   \\ \hline
  parse(3)   & $\rightarrow$ R &  Not Currently in Use              \\ \hline
  parse(4)   & $\rightarrow$ P &  Positive Definite Diagnostic      \\ \hline
  parse(5)   & $\rightarrow$ C &  Counter Diagnostic                \\
             & $\rightarrow$ D &  Disabled Diagnostic for output    \\ \hline
  parse(6-8) & $\rightarrow$ C &  3-digit integer corresponding to  \\
             &                 &  vector or counter component mate  \\ \hline
\end{tabular}
\addcontentsline{lot}{section}{Table 3:  Diagnostic Parsing Array}
\end{center}
\end{table}


\noindent
As an example, consider a diagnostic whose associated GDIAG parameter is equal
to ``UU  002''.  From GDIAG we can determine that this diagnostic is a 
U-vector component located at the C-grid U-point.
Its corresponding V-component diagnostic is located in Diagnostic \# 002.

\noindent
In this way, each Diagnostic in the model has its attributes (ie. vector or scalar,
C-grid location, etc.) defined internally.  The Output routines use this information 
in order to determine what type of transformations need to be performed.  Any 
interpolations are done at the time of output rather than during each model step.
In this way the User has flexibility in determining the type of gridded data which 
is output.

\subsection{Usage Notes}
\label{sec:diagnostics:usersguide}

\noindent
To use the diagnostics package, other than enabling it in packages.conf
and turning the usediagnostics flag in data.pkg to .TRUE., there are two
further steps the user must take to enable the diagnostics package for
output of quantities that are already defined in the GCM under an experiment's
configuration of packages.  A namelist must be supplied in the run directory 
called data.diagnostics, and the file DIAGNOSTICS\_SIZE.h must be included in the 
code directory.  The steps for defining a new (permanent or experiment-specific 
temporary) diagnostic quantity will be outlined later. 

\noindent The namelist will activate a user-defined list of diagnostics quantities 
to be computed, specify the frequency and type of output, the number of levels, and 
the name of all the separate output files. A sample data.diagnostics namelist file:

\noindent
$\#$ Diagnostic Package Choices \\
 $\&$diagnostics\_list \\
  frequency(1) = 86400., \ \\
   levels(1,1) = 1., \ \\
   fields(1,1) = 'RSURF   ', \ \\
   filename(1) = 'surface', \ \\
  frequency(2) = 86400., \ \\
   levels(1,2) = 1.,2.,3.,4.,5., \ \\
   fields(1,2) = 'UVEL    ','VVEL    ', \ \\
   filename(2) = 'diagout1', \ \\
  frequency(3) = 3600., \ \\
   fields(1,3) = 'UVEL    ','VVEL    ','PRESSURE', \ \\
   filename(3) = 'diagout2', \ \\
  fileflags(3) = ' P1     ', \ \\
 $\&$end \ \\

\noindent
In this example, there are two output files that will be generated
for each tile and for each output time. The first set of output files
has the prefix diagout1, does time averaging every 86400. seconds,
(frequency is 86400.), and will write fields which are multiple-level 
fields at output levels 1-5. The names of diagnostics quantities are 
UVEL and VVEL.  The second set of output files
has the prefix diagout2, does time averaging every 3600. seconds,
includes fields which are multiple-level fields, levels output are 1-5,
and the names of diagnostics quantities are THETA and SALT.

\noindent
The user must assure that enough computer memory is allocated for the diagnostics 
and the output streams selected for a particular experiment.  This is acomplished by
modifying the file DIAGNOSTICS\_SIZE.h and including it in the experiment code directory.
The parameters that should be checked are called numdiags, numlists, numperlist, and
diagSt\_size. 

\noindent numdiags (and diagSt\_size): \\
\noindent All GCM diagnostic quantities are stored in the single diagnostic array QDIAG 
which is located in the file \\ \filelink{pkg/diagnostics/diagnostics.h}{pkg-diagnostics-diagnostics.h}.\\
and has the form:\\
common /diagnostics/ qdiag(1-Olx,sNx+Olx,1-Olx,sNx+Olx,numdiags,Nsx,Nsy) \\
\noindent
The first two-dimensions of qdiag correspond to the horizontal dimension of a given diagnostic, 
and the third dimension of qdiag is used to identify diagnostic fields and levels combined. In 
order to minimize the memory requirement of the model for diagnostics, the default GCM 
executable is compiled with room for only one horizontal diagnostic array, or with
numdiags set to Nr. In order for the User to enable more than 1 three-dimensional diagnostic,
the size of the diagnostics common must be expanded to accomodate the desired diagnostics.
This can be accomplished by manually changing the parameter numdiags in the
file \filelink{pkg/diagnostics/DIAGNOSTICS\_SIZE.h}{pkg-diagnostics-DIAGNOSTICS\_SIZE.h}.
numdiags should be set greater than or equal to the sum of all the diagnostics activated
for output each multiplied by the number of levels defined for that diagnostic quantity.
For the above example, there are 4 multiple level fields, which the diagnostics menu
(see below) indicates are defined at the GCM vertical resolution, Nr. The value of
numdiag in DIAGNOSTICS\_SIZE.h would therefore be equal to 4*Nr, or, say 40 if $Nr=10$.

\noindent numlists and numperlist: \\
\noindent The parameter numlists must be set greater than or equal to the number of
separate output streams that the user specifies in the namelist file data.diagnostics.
The parameter numperlist corresponds to the number of diagnostics requested in each
output stream.

\noindent
In order to define and include as part of the diagnostic output any field
that is desired for a particular experiment, two steps must be taken. The
first is to enable the ``User Diagnostic'' in data.diagnostics. This is
accomplished by adding one of the ``User Diagnostic'' field names (UDIAG1 through 
UDIAG10, for multi-level fields, or SDIAG1 through SDIAG10 for single level
fields) to the data.diagnostics namelist in one of the output streams. These 
fields are listed in the diagnostics menu. The second step is to
add a call to diagnostics\_fill from the subroutine in which the quantity
desired for diagnostic output is computed. 

\noindent
In order to add a new diagnostic to the permanent set of diagnostics that the
main model or any package contains as part of its diagnostics menu, the subroutine
diagnostics\_add2list should be called during the initialization phase of the
main model or package. For the main model, the call should be made from
subroutine diagnostics\_main\_init, and for a package, the call should probably
be made from somewhere in the packages\_init\_fixed sequence (probaby from inside
the particular package's init\_fixed routine). A typical code sequence to set the
input arguments to diagnostics\_add2list would look like:

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\>      diagName  = 'THETA   ' \\
\>      diagTitle = 'Potential Temperature (degC,K)' \\
\>      diagUnits = 'Degrees K       ' \\
\>      diagCode  = 'SM      MR      ' \\
\>      CALL DIAGNOSTICS\_ADD2LIST( diagNum, \\
\>     I          diagName, diagCode, diagUnits, diagTitle, myThid ) \\
\\
\end{tabbing}

\noindent If the new diagnostic quantity is associated with either a vector
pair or a diagnostic counter, the diagCode argument must be filled with the
proper index for the ``mate''. The output argument from diagnostics\_add2list
that is called diagNum here contains a running total of the number of diagnostics
defined in the code up to any point during the run. The sequence number for the
next two diagnostics defined (the two components of the vector pair, for instance)
will be diagNum+1 and diagNum+2. The definition of the first component of the vector
pair must fill the ``mate'' segment of the diagCode as diagnostic number diagNum+2. 
Since the subroutine increments diagNum, the definition of the second component of 
the vector fills the ``mate'' part of diagCode with diagNum. A code sequence for 
this case would look like:

\noindent
\begin{tabbing}
XXXXXXXXX\=XXXXXX\= \kill
\>      diagName  = 'UVEL    ' \\
\>      diagTitle = 'Zonal Velocity                ' \\
\>      diagUnits = 'm / sec         ' \\
\>      diagCode  = 'SM      MR      ' \\
\>      write(diagCode,'(A,I3.3,A)') 'VV   ', diagNum+2 ,'MR      ' \\
\>      call diagnostics\_add2list( diagNum, \\
\>     I          diagName, diagCode, diagUnits, diagTitle, myThid ) \\
\>      diagName  = 'VVEL    ' \\
\>      diagTitle = 'Meridional Velocity           ' \\
\>      diagUnits = 'm / sec         ' \\
\>      diagCode  = 'SM      MR      ' \\
\>      write(diagCode,'(A,I3.3,A)') 'VV   ', diagNum ,'MR      ' \\
\>      call diagnostics\_add2list( diagNum, \\
\>     I          diagName, diagCode, diagUnits, diagTitle, myThid ) \\
\\
\end{tabbing}


\newpage

\subsubsection{GCM Diagnostic Menu}
\label{sec:diagnostics:menu}

\begin{tabular}{llll}
\hline\hline
 NAME & UNITS & LEVELS & DESCRIPTION \\
\hline

&\\
 SDIAG1   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-1} 
         \end{minipage}\\
 SDIAG2   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-2} 
         \end{minipage}\\
 UDIAG1   &             &    Nrphys
         &\begin{minipage}[t]{3in}
          {User-Defined Upper-Air Diagnostic-1} 
         \end{minipage}\\
 UDIAG2   &             &    Nrphys
         &\begin{minipage}[t]{3in}
          {User-Defined Upper-Air Diagnostic-2} 
         \end{minipage}\\
 SDIAG3   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-3} 
         \end{minipage}\\
 SDIAG4   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-4} 
         \end{minipage}\\
 SDIAG5   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-5} 
         \end{minipage}\\
 SDIAG6   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-6} 
         \end{minipage}\\
 SDIAG7   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-7} 
         \end{minipage}\\
 SDIAG8   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-8} 
         \end{minipage}\\
 SDIAG9   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-9} 
         \end{minipage}\\
 SDIAG10  &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Surface Diagnostic-1-} 
         \end{minipage}\\
 UDIAG3   &             &    Nrphys  
         &\begin{minipage}[t]{3in}
          {User-Defined Multi-Level Diagnostic-3} 
         \end{minipage}\\
 UDIAG4   &             &    Nrphys  
         &\begin{minipage}[t]{3in}
          {User-Defined Multi-Level Diagnostic-4} 
         \end{minipage}\\
 UDIAG5   &             &    Nrphys  
         &\begin{minipage}[t]{3in}
          {User-Defined Multi-Level Diagnostic-5} 
         \end{minipage}\\
 UDIAG6   &             &    Nrphys  
         &\begin{minipage}[t]{3in}
          {User-Defined Multi-Level Diagnostic-6} 
         \end{minipage}\\
 UDIAG7   &             &    Nrphys  
         &\begin{minipage}[t]{3in}
          {User-Defined Multi-Level Diagnostic-7} 
         \end{minipage}\\
 UDIAG8   &             &    Nrphys  
         &\begin{minipage}[t]{3in}
          {User-Defined Multi-Level Diagnostic-8} 
         \end{minipage}\\
 UDIAG9   &             &    Nrphys  
         &\begin{minipage}[t]{3in}
          {User-Defined Multi-Level Diagnostic-9} 
         \end{minipage}\\
 UDIAG10  &             &    Nrphys  
         &\begin{minipage}[t]{3in}
          {User-Defined Multi-Level Diagnostic-10} 
         \end{minipage}\\
 SDIAGC   &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Counted Surface Diagnostic} 
         \end{minipage}\\
 SDIAGCC  &             &    1  
         &\begin{minipage}[t]{3in}
          {User-Defined Counted Surface Diagnostic Counter} 
         \end{minipage}\\
 ETAN     & $(hPa,m)$ &    1
         &\begin{minipage}[t]{3in}
          {Perturbation of Surface (pressure, height)} 
         \end{minipage}\\
 ETANSQ   & $(hPa^2,m^2)$ & 1
         &\begin{minipage}[t]{3in}
          {Square of Perturbation of Surface (pressure, height)} 
         \end{minipage}\\
 DETADT2  & ${r-unit}^2/s^2$ & 1
         &\begin{minipage}[t]{3in}
          {Square of Eta (Surf.P,SSH) Tendency} 
         \end{minipage}\\
 THETA    & $deg K$ & Nr
         &\begin{minipage}[t]{3in}
          {Potential Temperature} 
         \end{minipage}\\
 SST      & $deg K$ & 1
         &\begin{minipage}[t]{3in}
          {Sea Surface Temperature} 
         \end{minipage}\\
 SALT     & $g/kg$ & Nr
         &\begin{minipage}[t]{3in}
          {Salt (or Water Vapor Mixing Ratio)} 
         \end{minipage}\\
 SSS      & $g/kg$ & 1
         &\begin{minipage}[t]{3in}
          {Sea Surface Salinity} 
         \end{minipage}\\
 SALTanom & $g/kg$ & Nr
         &\begin{minipage}[t]{3in}
          {Salt anomaly (=SALT-35)} 
         \end{minipage}\\
\end{tabular}
\vspace{1.5in}
\vfill

\newpage
\vspace*{\fill}
\begin{tabular}{llll}
\hline\hline
 NAME & UNITS & LEVELS & DESCRIPTION \\
\hline

&\\
 UVEL     & $m/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {U-Velocity} 
         \end{minipage}\\
 VVEL     & $m/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {V-Velocity} 
         \end{minipage}\\
 UVEL\_k2  & $m/sec$ & 1
         &\begin{minipage}[t]{3in}
          {U-Velocity} 
         \end{minipage}\\
 VVEL\_k2  & $m/sec$ & 1
         &\begin{minipage}[t]{3in}
          {V-Velocity} 
         \end{minipage}\\
 WVEL     & $m/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Vertical-Velocity} 
         \end{minipage}\\
 THETASQ  & $deg^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Square of Potential Temperature} 
         \end{minipage}\\
 SALTSQ   & $g^2/{kg}^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Square of Salt (or Water Vapor Mixing Ratio)} 
         \end{minipage}\\
 SALTSQan & $g^2/{kg}^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Square of Salt anomaly (=SALT-35)} 
         \end{minipage}\\
 UVELSQ   & $m^2/sec^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Square of U-Velocity} 
         \end{minipage}\\
 VVELSQ   & $m^2/sec^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Square of V-Velocity} 
         \end{minipage}\\
 WVELSQ   & $m^2/sec^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Square of Vertical-Velocity} 
         \end{minipage}\\
 UV\_VEL\_C & $m^2/sec^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Meridional Transport of Zonal Momentum (cell center)} 
         \end{minipage}\\
 UV\_VEL\_Z & $m^2/sec^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Meridional Transport of Zonal Momentum (corner)} 
         \end{minipage}\\
 WU\_VEL   & $m^2/sec^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Vertical Transport of Zonal Momentum (cell center)} 
         \end{minipage}\\
 WV\_VEL   & $m^2/sec^2$ & Nr
         &\begin{minipage}[t]{3in}
          {Vertical Transport of Meridional Momentum (cell center)} 
         \end{minipage}\\
 UVELMASS & $m/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Zonal Mass-Weighted Component of Velocity} 
         \end{minipage}\\
 VVELMASS & $m/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Meridional Mass-Weighted Component of Velocity} 
         \end{minipage}\\
 WVELMASS & $m/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Vertical Mass-Weighted Component of Velocity} 
         \end{minipage}\\
 UTHMASS  & $m-deg/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Zonal Mass-Weight Transp of Pot Temp} 
         \end{minipage}\\
 VTHMASS  & $m-deg/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Meridional Mass-Weight Transp of Pot Temp} 
         \end{minipage}\\
 WTHMASS  & $m-deg/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Vertical Mass-Weight Transp of Pot Temp} 
         \end{minipage}\\
 USLTMASS & $m-kg/sec-kg$ & Nr
         &\begin{minipage}[t]{3in}
          {Zonal Mass-Weight Transp of Salt (or W.Vap Mix Rat.)} 
         \end{minipage}\\
 VSLTMASS & $m-kg/sec-kg$ & Nr
         &\begin{minipage}[t]{3in}
          {Meridional Mass-Weight Transp of Salt (or W.Vap Mix Rat.)} 
         \end{minipage}\\
 WSLTMASS & $m-kg/sec-kg$ & Nr
         &\begin{minipage}[t]{3in}
          {Vertical Mass-Weight Transp of Salt (or W.Vap Mix Rat.)} 
         \end{minipage}\\
 UVELTH   & $m-deg/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Zonal Transp of Pot Temp} 
         \end{minipage}\\
 VVELTH   & $m-deg/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Meridional Transp of Pot Temp} 
         \end{minipage}\\
 WVELTH   & $m-deg/sec$ & Nr
         &\begin{minipage}[t]{3in}
          {Vertical Transp of Pot Temp} 
         \end{minipage}\\
 UVELSLT  & $m-kg/sec-kg$ & Nr
         &\begin{minipage}[t]{3in}
          {Zonal Transp of Salt (or W.Vap Mix Rat.)} 
         \end{minipage}\\
 VVELSLT  & $m-kg/sec-kg$ & Nr
         &\begin{minipage}[t]{3in}
          {Meridional Transp of Salt (or W.Vap Mix Rat.)} 
         \end{minipage}\\
 WVELSLT  & $m-kg/sec-kg$ & Nr
         &\begin{minipage}[t]{3in}
          {Vertical Transp of Salt (or W.Vap Mix Rat.)} 
         \end{minipage}\\
\end{tabular}
\vspace{1.5in}
\vfill

\newpage
\vspace*{\fill}
\begin{tabular}{llll}
\hline\hline
 NAME & UNITS & LEVELS & DESCRIPTION \\
\hline

&\\
 RHOAnoma & $kg/m^3  $  &  Nr  
         &\begin{minipage}[t]{3in}
          {Density Anomaly (=Rho-rhoConst)}
         \end{minipage}\\
 RHOANOSQ & $kg^2/m^6$  &  Nr  
         &\begin{minipage}[t]{3in}
          {Square of Density Anomaly (=(Rho-rhoConst))}
         \end{minipage}\\
 URHOMASS & $kg/m^2/s$  &  Nr  
         &\begin{minipage}[t]{3in}
          {Zonal Transport of Density}
         \end{minipage}\\
 VRHOMASS & $kg/m^2/s$  &  Nr  
         &\begin{minipage}[t]{3in}
          {Meridional Transport of Density}
         \end{minipage}\\
 WRHOMASS & $kg/m^2/s$  &  Nr  
         &\begin{minipage}[t]{3in}
          {Vertical Transport of Potential Density}
         \end{minipage}\\
 PHIHYD   & $m^2/s^2 $  &  Nr  
         &\begin{minipage}[t]{3in}
          {Hydrostatic (ocean) pressure / (atmos) geo-Potential}
         \end{minipage}\\
 PHIHYDSQ & $m^4/s^4 $  &  Nr  
         &\begin{minipage}[t]{3in}
          {Square of Hyd. (ocean) press / (atmos) geoPotential}
         \end{minipage}\\
 PHIBOT   & $m^2/s^2 $  &  Nr  
         &\begin{minipage}[t]{3in}
          {ocean bottom pressure / top. atmos geo-Potential}
         \end{minipage}\\
 PHIBOTSQ & $m^4/s^4 $  &  Nr  
         &\begin{minipage}[t]{3in}
          {Square of ocean bottom pressure / top. geo-Potential}
         \end{minipage}\\
 DRHODR   & $kg/m^3/{r-unit}$ & Nr
         &\begin{minipage}[t]{3in}
          {Stratification: d.Sigma/dr} 
         \end{minipage}\\
 VISCA4   & $m^4/sec$ & 1
         &\begin{minipage}[t]{3in}
          {Biharmonic Viscosity Coefficient} 
         \end{minipage}\\
 VISCAH   & $m^2/sec$ & 1
         &\begin{minipage}[t]{3in}
          {Harmonic Viscosity Coefficient} 
         \end{minipage}\\
 TAUX     & $N/m^2        $ & 1 
         &\begin{minipage}[t]{3in}
          {zonal surface wind stress, >0 increases uVel}
         \end{minipage}\\
 TAUY     & $N/m^2        $ & 1 
         &\begin{minipage}[t]{3in}
          {meridional surf. wind stress, >0 increases vVel}
         \end{minipage}\\
 TFLUX    & $W/m^2        $ & 1 
         &\begin{minipage}[t]{3in}
          {net surface heat flux, >0 increases theta}
         \end{minipage}\\
 TRELAX   & $W/m^2        $ & 1 
         &\begin{minipage}[t]{3in}
          {surface temperature relaxation, >0 increases theta}
         \end{minipage}\\
 TICE     & $W/m^2        $ & 1 
         &\begin{minipage}[t]{3in}
          {heat from melt/freeze of sea-ice, >0 increases theta}
         \end{minipage}\\
 SFLUX    & $g/m^2/s      $ & 1 
         &\begin{minipage}[t]{3in}
          {net surface salt flux, >0 increases salt}
         \end{minipage}\\
 SRELAX   & $g/m^2/s      $ & 1 
         &\begin{minipage}[t]{3in}
          {surface salinity relaxation, >0 increases salt}
         \end{minipage}\\
 PRESSURE & $Pa           $ & Nr 
         &\begin{minipage}[t]{3in}
          {Atmospheric Pressure (Pa)}
         \end{minipage}\\
 ADVr\_TH  & $K.Pa.m^2/s   $ & Nr 
         &\begin{minipage}[t]{3in}
          {Vertical   Advective Flux of Pot.Temperature}
         \end{minipage}\\
 ADVx\_TH  & $K.Pa.m^2/s   $ & Nr 
         &\begin{minipage}[t]{3in}
          {Zonal      Advective Flux of Pot.Temperature}
         \end{minipage}\\
 ADVy\_TH  & $K.Pa.m^2/s   $ & Nr 
         &\begin{minipage}[t]{3in}
          {Meridional Advective Flux of Pot.Temperature}
         \end{minipage}\\
 DFrE\_TH  & $K.Pa.m^2/s   $ & Nr 
         &\begin{minipage}[t]{3in}
          {Vertical Diffusive Flux of Pot.Temperature (Explicit part)}
         \end{minipage}\\
 DIFx\_TH  & $K.Pa.m^2/s   $ & Nr 
         &\begin{minipage}[t]{3in}
          {Zonal      Diffusive Flux of Pot.Temperature}
         \end{minipage}\\
 DIFy\_TH  & $K.Pa.m^2/s   $ & Nr 
         &\begin{minipage}[t]{3in}
          {Meridional Diffusive Flux of Pot.Temperature}
         \end{minipage}\\
 DFrI\_TH  & $K.Pa.m^2/s   $ & Nr 
         &\begin{minipage}[t]{3in}
          {Vertical Diffusive Flux of Pot.Temperature (Implicit part)}
         \end{minipage}\\
 ADVr\_SLT & $g/kg.Pa.m^2/s$ & Nr 
         &\begin{minipage}[t]{3in}
          {Vertical   Advective Flux of Water-Vapor}
         \end{minipage}\\
 ADVx\_SLT & $g/kg.Pa.m^2/s$ & Nr 
         &\begin{minipage}[t]{3in}
          {Zonal      Advective Flux of Water-Vapor}
         \end{minipage}\\
 ADVy\_SLT & $g/kg.Pa.m^2/s$ & Nr 
         &\begin{minipage}[t]{3in}
          {Meridional Advective Flux of Water-Vapor}
         \end{minipage}\\
\end{tabular}
\vspace{1.5in}
\vfill

\newpage
\vspace*{\fill}
\begin{tabular}{llll}
\hline\hline
 NAME & UNITS & LEVELS & DESCRIPTION \\
\hline

&\\
 DFrE\_SLT & $g/kg.Pa.m^2/s$ & Nr 
         &\begin{minipage}[t]{3in}
          {Vertical Diffusive Flux of Water-Vapor (Explicit part)}
         \end{minipage}\\
 DIFx\_SLT & $g/kg.Pa.m^2/s$ & Nr 
         &\begin{minipage}[t]{3in}
          {Zonal      Diffusive Flux of Water-Vapor}
         \end{minipage}\\
 DIFy\_SLT & $g/kg.Pa.m^2/s$ & Nr 
         &\begin{minipage}[t]{3in}
          {Meridional Diffusive Flux of Water-Vapor}
         \end{minipage}\\
 DFrI\_SLT & $g/kg.Pa.m^2/s$ & Nr 
         &\begin{minipage}[t]{3in}
          {Vertical Diffusive Flux of Water-Vapor (Implicit part)}
         \end{minipage}\\
\end{tabular}
\vspace{1.5in}
\vfill

\newpage

\subsubsection{Diagnostic Description}

In this section we list and describe the diagnostic quantities available within the 
GCM.  The diagnostics are listed in the order that they appear in the 
Diagnostic Menu, Section \ref{sec:diagnostics:menu}.
In all cases, each diagnostic as currently archived on the output datasets
is time-averaged over its diagnostic output frequency:

\[
{\bf DIAGNOSTIC} = {1 \over TTOT} \sum_{t=1}^{t=TTOT} diag(t)
\]
where $TTOT = {{\bf NQDIAG} \over \Delta t}$, {\bf NQDIAG} is the 
output frequency of the diagnostic, and $\Delta t$ is
the timestep over which the diagnostic is updated.  

\subsection{Dos and Donts}

\subsection{Diagnostics Reference}
