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

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-revision 1.8 by molod,
Thu Oct 28 22:41:16 2004 UTC
+revision 1.11 by molod,
Fri Jul 15 18:58:21 2005 UTC
 Line 20 
 diagnostic output and defining new diagn
  \ref{sec:diagnostics:usersguide} of this document.
  \noindent
- The Diagnostic Menu is a hard-wired enumeration of diagnostic quantities available within
+ The Diagnostic Menu in this section of the manual is a listing of diagnostic quantities available
- the GCM. Once a diagnostic is enabled, the GCM will continually increment an array
+ within the main (dynamics) part of the GCM. Additional diagnostic quantities, defined within the
- specifically allocated for that diagnostic whenever the appropriate quantity is computed.
+ different GCM packages, are available and are listed in the diagnostic menu subsection of
- A counter is defined which records how many times each diagnostic quantity has been
+ the manual section associated with each relevant package. Once a diagnostic is enabled, the
- incremented.  Several special diagnostics are included in the menu. Quantities refered to
+ GCM will continually increment an array specifically allocated for that diagnostic whenever the
- as ``Counter Diagnostics'', are defined for selected diagnostics which record 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.
-Line 37 
 Not relevant.
+Line 39 
 Not relevant.
  \label{sec:diagnostics:diagover}
  \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.
- \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 fill\_diagnostics}:  This routine will increment the specified diagnostic
+ {\bf diagnostics\_fill}:  This is the main user interface routine to the diagnostics
- quantity with a field sent through the argument list.
+ package. This routine will increment the specified diagnostic quantity with a field
+ sent through the argument list.
  \noindent
  \begin{tabbing}
  XXXXXXXXX\=XXXXXX\= \kill
- \>        call fill\_diagnostics (myThid, chardiag, levflg, nlevs, \\
+ \>        call diagnostics\_fill (arrayin, chardiag, levflg, nlevs, \\
-                 bibjflg, bi, bj, arrayin) \\
+ \>              bibjflg, bi, bj, myThid) \\
  \\
- where \>  myThid   \>= Current Process(or) \\
+ where \>  arrayin  \>= Field to increment diagnostics array \\
        \>  chardiag \>= Character *8 expression for diag to fill \\
        \>  levflg   \>= Integer flag for vertical levels: \\
-       \>           \> 0 indicates multiple levels incremented in qdiag \\
+       \>           \>= 0 indicates multiple (nlevs) levels incremented \\
-       \>           \> non-0 (any integer) - WHICH single level to increment. \\
+       \>           \>= -1 indicates multiple (nlevs) levels incremented, \\
-       \>           \> negative integer - the input data array is single-leveled \\
+       \>           \> but in reverse vertical order \\
-       \>           \> positive integer - the input data array is multi-leveled \\
+       \>           \> positive integer - WHICH single level to increment. \\
-       \>  nlevs    \>= indicates Number of levels to be filled (1 if levflg <> 0) \\
+       \>  nlevs    \>= indicates Number of levels to be filled (1 if levflg gt 0) \\
-       \>           \> positive: fill in "nlevs" levels in the same order as \\
-       \>           \> the input array \\
-       \>           \> negative: fill in -nlevs levels in reverse order. \\
        \>  bibjflg  \>= Integer flag to indicate instructions for bi bj loop \\
-       \>           \> 0 indicates that the bi-bj loop must be done here \\
+       \>           \>= 0 indicates that the bi-bj loop must be done here \\
-       \>           \> 1 indicates that the bi-bj loop is done OUTSIDE \\
+       \>           \>= 1 indicates that the bi-bj loop is done OUTSIDE \\
-       \>           \> 2 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 \\
-       \>           \> 3 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 \\
-       \>  arrayin  \>= Field to increment diagnostics array \\
+       \>  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
- {\bf setdiag}:  This subroutine enables a diagnostic from the Diagnostic Menu, meaning
+ \begin{tabbing}
- that space is allocated for the diagnostic and the model routines will increment the
+ XXXXXXXXX\=XXXXXX\= \kill
- diagnostic value during execution.  This routine is the underlying interface
+ \>        call diagnostics\_scale\_fill (arrayin, scalefactor, power, chardiag, \\
- between the user and the desired diagnostic.  The diagnostic is referenced by its diagnostic
+ \>        levflg, nlevs, bibjflg, bi, bj, myThid) \\
- number from the menu, and its calling sequence is given by:
+ \\
+ 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 setdiag (num) \\
+ \> call diagnostics\_get\_pointers( diagName, ipoint, jpoint, myThid )
  \\
- where \>  num   \>= Diagnostic number from menu \\
+ 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
-Line 161 
 the diagnostic with its time-average.  T
+Line 133 
 the diagnostic with its time-average.  T
  \noindent
  \begin{tabbing}
  XXXXXXXXX\=XXXXXX\= \kill
- \>        call getdiag (lev,num,qtmp,undef) \\
+ \>        call getdiag (lev, undef, qtmp, ipoint, mate, bi, bj, myThid) \\
  \\
- where \>  lev   \>= Model Level at which the diagnostic is desired \\
+ where \>  lev     \>= Model Level at which the diagnostic is desired \\
-       \>  num   \>= Diagnostic number from menu \\
+       \>  undef   \>= Fill value to be used when diagnostic is undefined \\
-       \>  qtmp  \>= Time-Averaged Diagnostic Output \\
+       \>  qtmp    \>= Time-Averaged Diagnostic Output \\
-       \>  undef \>= Fill value to be used when diagnostic is undefined \\
+       \>  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 clrdiag}:  This subroutine initializes the values of model diagnostics to zero, and is
+ {\bf diagnostics\_add2list}:  This subroutine enables a diagnostic from the Diagnostic Menu, meaning
- particularly useful when called from user output routines to re-initialize diagnostics
+ that space is allocated for the diagnostic and the model routines will increment the
- during the run.  The calling sequence is:
+ 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 clrdiag (num) \\
+ \>        call diagnostics\_add2list( diagNum,diagName, diagCode, \\
+ \>        diagUnits, diagTitle, myThid ) \\
  \\
- where \>  num   \>= Diagnostic number from menu \\
+ 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 zapdiag}:  This entry into subroutine SETDIAG disables model diagnostics, meaning
+ {\bf clrdiag}:  This subroutine initializes the values of model diagnostics to zero, and is
- that the diagnostic is no longer available to the user.  The memory previously allocated
+ particularly useful when called from user output routines to re-initialize diagnostics
- to the diagnostic is released when ZAPDIAG is invoked.  The calling sequence is given by:
+ during the run.  The calling sequence is:
  \noindent
  \begin{tabbing}
  XXXXXXXXX\=XXXXXX\= \kill
- \>        call zapdiag (NUM) \\
+ \>        call diagnostics\_clrdiag (jpoint, ipoint, myThid) \\
  \\
- where \>  num   \>= Diagnostic number from menu \\
+ 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}
- \subsection{Usage Notes}
- \label{sec:diagnostics:usersguide}
  \noindent
- We begin this section with a discussion on the manner in which computer
+ As an example, consider a diagnostic whose associated GDIAG parameter is equal
- memory is allocated for diagnostics. All GCM diagnostic quantities are stored in the
+ to ``UU  002''.  From GDIAG we can determine that this diagnostic is a
- single diagnostic array QDIAG which is located in the file \\
+ U-vector component located at the C-grid U-point.
- \filelink{pkg/diagnostics/diagnostics.h}{pkg-diagnostics-diagnostics.h}.
+ Its corresponding V-component diagnostic is located in Diagnostic \# 002.
- and has the form:
- common /diagnostics/ qdiag(1-Olx,sNx+Olx,1-Olx,sNx+Olx,numdiags,Nsx,Nsy)
  \noindent
- where numdiags is an Integer variable which should be set equal to the number of
+ In this way, each Diagnostic in the model has its attributes (ie. vector or scalar,
- enabled diagnostics, and qdiag is a three-dimensional array.  The first two-dimensions
+ C-grid location, etc.) defined internally.  The Output routines use this information
- of qdiag correspond to the horizontal dimension of a given diagnostic, while the third
+ in order to determine what type of transformations need to be performed.  Any
- dimension of qdiag is used to identify diagnostic fields and levels combined. In order
+ interpolations are done at the time of output rather than during each model step.
- to minimize the memory requirement of the model for diagnostics, the default GCM
+ In this way the User has flexibility in determining the type of gridded data which
- executable is compiled with room for only one horizontal diagnostic array, or with
+ is output.
- numdiags set to 1. In order for the User to enable more than 1 two-dimensional diagnostic,
- the size of the diagnostics common must be expanded to accomodate the desired diagnostics.
+ \subsection{Usage Notes}
- This can be accomplished by manually changing the parameter numdiags in the
+ \label{sec:diagnostics:usersguide}
- 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.
- This is illustrated in the example below:
  \noindent
  To use the diagnostics package, other than enabling it in packages.conf
- and turning the usediagnostics flag in data.pkg to .TRUE., a namelist
+ and turning the usediagnostics flag in data.pkg to .TRUE., there are two
- must be supplied in the run directory called data.diagnostics. The namelist
+ further steps the user must take to enable the diagnostics package for
- will activate a user-defined list of diagnostics quantities to be computed,
+ output of quantities that are already defined in the GCM under an experiment's
- specify the frequency of output, the number of levels, and the name of
+ configuration of packages.  A namelist must be supplied in the run directory
- up to 10 separate output files. A sample data.diagnostics namelist file:
+ 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) = 10, \ \\
+   frequency(1) = 86400., \ \\
-    levels(1,1) = 1.,2.,3.,4.,5., \ \\
+    levels(1,1) = 1., \ \\
-    fields(1,1) = 'UVEL    ','VVEL    ', \ \\
+    fields(1,1) = 'RSURF   ', \ \\
-    filename(1) = 'diagout1', \ \\
+    filename(1) = 'surface', \ \\
-   frequency(2) = 100, \ \\
+   frequency(2) = 86400., \ \\
     levels(1,2) = 1.,2.,3.,4.,5., \ \\
-    fields(1,2) = 'THETA   ','SALT    ', \ \\
+    fields(1,2) = 'UVEL    ','VVEL    ', \ \\
-    filename(2) = 'diagout2', \ \\
+    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 10 time steps
+ has the prefix diagout1, does time averaging every 86400. seconds,
- (frequency is 10), they will write fields which are multiple-level
+ (frequency is 86400.), and will write fields which are multiple-level
- fields and output levels 1-5. The names of diagnostics quantities are
+ 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 100 time steps,
+ has the prefix diagout2, does time averaging every 3600. seconds,
- they include fields which are multiple-level fields, levels output are 1-5,
+ 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 setting one of the fields slots to either UDIAG1 through
+ 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. These are listed in the diagnostics menu. The second step is to
+ fields) to the data.diagnostics namelist in one of the output streams. These
- add a call to fill\_diagnostics from the subroutine in which the quantity
+ 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}{lllll}
+ \begin{tabular}{llll}
  \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
+  NAME & UNITS & LEVELS & DESCRIPTION \\
  \hline
  &\\
-& UFLUX    &   $Newton/m^2$  &    1
+  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}
-           {Surface U-Wind Stress on the atmosphere}
+           {User-Defined Surface Diagnostic-4}
           \end{minipage}\\
-& VFLUX    &   $Newton/m^2$  &    1
+  SDIAG5   &             &    1
           &\begin{minipage}[t]{3in}
-           {Surface V-Wind Stress on the atmosphere}
+           {User-Defined Surface Diagnostic-5}
           \end{minipage}\\
-& HFLUX    &   $Watts/m^2$  &    1
+  SDIAG6   &             &    1
           &\begin{minipage}[t]{3in}
-           {Surface Flux of Sensible Heat}
+           {User-Defined Surface Diagnostic-6}
           \end{minipage}\\
-& EFLUX    &   $Watts/m^2$  &    1
+  SDIAG7   &             &    1
           &\begin{minipage}[t]{3in}
-           {Surface Flux of Latent Heat}
+           {User-Defined Surface Diagnostic-7}
           \end{minipage}\\
-& QICE     &   $Watts/m^2$  &    1
+  SDIAG8   &             &    1
           &\begin{minipage}[t]{3in}
-           {Heat Conduction through Sea-Ice}
+           {User-Defined Surface Diagnostic-8}
           \end{minipage}\\
-& RADLWG   &   $Watts/m^2$ &    1
+  SDIAG9   &             &    1
           &\begin{minipage}[t]{3in}
-           {Net upward LW flux at the ground}
+           {User-Defined Surface Diagnostic-9}
           \end{minipage}\\
-& RADSWG   &   $Watts/m^2$  &    1
+  SDIAG10  &             &    1
           &\begin{minipage}[t]{3in}
-           {Net downward SW flux at the ground}
+           {User-Defined Surface Diagnostic-1-}
           \end{minipage}\\
-& RI       &  $dimensionless$ &  Nrphys
+  UDIAG3   &             &    Nrphys
           &\begin{minipage}[t]{3in}
-           {Richardson Number}
+           {User-Defined Multi-Level Diagnostic-3}
           \end{minipage}\\
-& CT       &  $dimensionless$ &  1
+  UDIAG4   &             &    Nrphys
           &\begin{minipage}[t]{3in}
-           {Surface Drag coefficient for T and Q}
+           {User-Defined Multi-Level Diagnostic-4}
           \end{minipage}\\
-& CU       & $dimensionless$ &  1
+  UDIAG5   &             &    Nrphys
           &\begin{minipage}[t]{3in}
-           {Surface Drag coefficient for U and V}
+           {User-Defined Multi-Level Diagnostic-5}
           \end{minipage}\\
-& ET       &  $m^2/sec$ &  Nrphys
+  UDIAG6   &             &    Nrphys
           &\begin{minipage}[t]{3in}
-           {Diffusivity coefficient for T and Q}
+           {User-Defined Multi-Level Diagnostic-6}
           \end{minipage}\\
-& EU       &  $m^2/sec$ &  Nrphys
+  UDIAG7   &             &    Nrphys
           &\begin{minipage}[t]{3in}
-           {Diffusivity coefficient for U and V}
+           {User-Defined Multi-Level Diagnostic-7}
           \end{minipage}\\
-& TURBU    &  $m/sec/day$ &  Nrphys
+  UDIAG8   &             &    Nrphys
           &\begin{minipage}[t]{3in}
-           {U-Momentum Changes due to Turbulence}
+           {User-Defined Multi-Level Diagnostic-8}
           \end{minipage}\\
-& TURBV    &  $m/sec/day$ &  Nrphys
+  UDIAG9   &             &    Nrphys
           &\begin{minipage}[t]{3in}
-           {V-Momentum Changes due to Turbulence}
+           {User-Defined Multi-Level Diagnostic-9}
           \end{minipage}\\
-& TURBT    &  $deg/day$ &  Nrphys
+  UDIAG10  &             &    Nrphys
           &\begin{minipage}[t]{3in}
-           {Temperature Changes due to Turbulence}
+           {User-Defined Multi-Level Diagnostic-10}
           \end{minipage}\\
-& TURBQ    &  $g/kg/day$ &  Nrphys
+  SDIAGC   &             &    1
           &\begin{minipage}[t]{3in}
-           {Specific Humidity Changes due to Turbulence}
+           {User-Defined Counted Surface Diagnostic}
           \end{minipage}\\
-& MOISTT   &   $deg/day$ &  Nrphys
+  SDIAGCC  &             &    1
           &\begin{minipage}[t]{3in}
-           {Temperature Changes due to Moist Processes}
+           {User-Defined Counted Surface Diagnostic Counter}
           \end{minipage}\\
-& MOISTQ   &  $g/kg/day$ &  Nrphys
+  ETAN     & $(hPa,m)$ &    1
           &\begin{minipage}[t]{3in}
-           {Specific Humidity Changes due to Moist Processes}
+           {Perturbation of Surface (pressure, height)}
           \end{minipage}\\
-& RADLW    &  $deg/day$ &  Nrphys
+  ETANSQ   & $(hPa^2,m^2)$ & 1
           &\begin{minipage}[t]{3in}
-           {Net Longwave heating rate for each level}
+           {Square of Perturbation of Surface (pressure, height)}
           \end{minipage}\\
-& RADSW    &  $deg/day$ &  Nrphys
+  DETADT2  & ${r-unit}^2/s^2$ & 1
           &\begin{minipage}[t]{3in}
-           {Net Shortwave heating rate for each level}
+           {Square of Eta (Surf.P,SSH) Tendency}
           \end{minipage}\\
-& PREACC   &  $mm/day$ &  1
+  THETA    & $deg K$ & Nr
           &\begin{minipage}[t]{3in}
-           {Total Precipitation}
+           {Potential Temperature}
           \end{minipage}\\
-& PRECON   &  $mm/day$ &  1
+  SST      & $deg K$ & 1
           &\begin{minipage}[t]{3in}
-           {Convective Precipitation}
+           {Sea Surface Temperature}
           \end{minipage}\\
-& TUFLUX   &  $Newton/m^2$ &  Nrphys
+  SALT     & $g/kg$ & Nr
           &\begin{minipage}[t]{3in}
-           {Turbulent Flux of U-Momentum}
+           {Salt (or Water Vapor Mixing Ratio)}
           \end{minipage}\\
-& TVFLUX   &  $Newton/m^2$ &  Nrphys
+  SSS      & $g/kg$ & 1
           &\begin{minipage}[t]{3in}
-           {Turbulent Flux of V-Momentum}
+           {Sea Surface Salinity}
           \end{minipage}\\
-& TTFLUX   &  $Watts/m^2$ &  Nrphys
+  SALTanom & $g/kg$ & Nr
           &\begin{minipage}[t]{3in}
-           {Turbulent Flux of Sensible Heat}
+           {Salt anomaly (=SALT-35)}
           \end{minipage}\\
  \end{tabular}
+ \vspace{1.5in}
+ \vfill
  \newpage
  \vspace*{\fill}
- \begin{tabular}{lllll}
+ \begin{tabular}{llll}
  \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
+  NAME & UNITS & LEVELS & DESCRIPTION \\
  \hline
  &\\
-& TQFLUX   &  $Watts/m^2$ &  Nrphys
+  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}
-           {Turbulent Flux of Latent Heat}
+           {U-Velocity}
           \end{minipage}\\
-& CN       &  $dimensionless$ &  1
+  VVEL\_k2  & $m/sec$ & 1
           &\begin{minipage}[t]{3in}
-           {Neutral Drag Coefficient}
+           {V-Velocity}
           \end{minipage}\\
-& WINDS     &  $m/sec$ &  1
+  WVEL     & $m/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Surface Wind Speed}
+           {Vertical-Velocity}
           \end{minipage}\\
-& DTSRF     &  $deg$ &  1
+  THETASQ  & $deg^2$ & Nr
           &\begin{minipage}[t]{3in}
-           {Air/Surface virtual temperature difference}
+           {Square of Potential Temperature}
           \end{minipage}\\
-& TG        &  $deg$ &  1
+  SALTSQ   & $g^2/{kg}^2$ & Nr
           &\begin{minipage}[t]{3in}
-           {Ground temperature}
+           {Square of Salt (or Water Vapor Mixing Ratio)}
           \end{minipage}\\
-& TS        &  $deg$ &  1
+  SALTSQan & $g^2/{kg}^2$ & Nr
           &\begin{minipage}[t]{3in}
-           {Surface air temperature (Adiabatic from lowest model layer)}
+           {Square of Salt anomaly (=SALT-35)}
           \end{minipage}\\
-& DTG       &  $deg$ &  1
+  UVELSQ   & $m^2/sec^2$ & Nr
           &\begin{minipage}[t]{3in}
-           {Ground temperature adjustment}
+           {Square of U-Velocity}
           \end{minipage}\\
+  VVELSQ   & $m^2/sec^2$ & Nr
-& QG        &  $g/kg$ &  1
+          &\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}
-           {Ground specific humidity}
+           {Meridional Transport of Zonal Momentum (corner)}
           \end{minipage}\\
-& QS        &  $g/kg$ &  1
+  WU\_VEL   & $m^2/sec^2$ & Nr
           &\begin{minipage}[t]{3in}
-           {Saturation surface specific humidity}
+           {Vertical Transport of Zonal Momentum (cell center)}
           \end{minipage}\\
-& TGRLW    &    $deg$   &    1
+  WV\_VEL   & $m^2/sec^2$ & Nr
           &\begin{minipage}[t]{3in}
-           {Instantaneous ground temperature used as input to the
+           {Vertical Transport of Meridional Momentum (cell center)}
-            Longwave radiation subroutine}
           \end{minipage}\\
-& ST4      &   $Watts/m^2$  &    1
+  UVELMASS & $m/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Upward Longwave flux at the ground ($\sigma T^4$)}
+           {Zonal Mass-Weighted Component of Velocity}
           \end{minipage}\\
-& OLR      &   $Watts/m^2$  &    1
+  VVELMASS & $m/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Net upward Longwave flux at the top of the model}
+           {Meridional Mass-Weighted Component of Velocity}
           \end{minipage}\\
-& OLRCLR   &   $Watts/m^2$  &    1
+  WVELMASS & $m/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Net upward clearsky Longwave flux at the top of the model}
+           {Vertical Mass-Weighted Component of Velocity}
           \end{minipage}\\
-& LWGCLR   &   $Watts/m^2$  &    1
+  UTHMASS  & $m-deg/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Net upward clearsky Longwave flux at the ground}
+           {Zonal Mass-Weight Transp of Pot Temp}
           \end{minipage}\\
-& LWCLR    &  $deg/day$ &  Nrphys
+  VTHMASS  & $m-deg/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Net clearsky Longwave heating rate for each level}
+           {Meridional Mass-Weight Transp of Pot Temp}
           \end{minipage}\\
-& TLW      &    $deg$   &  Nrphys
+  WTHMASS  & $m-deg/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Instantaneous temperature used as input to the Longwave radiation
+           {Vertical Mass-Weight Transp of Pot Temp}
-           subroutine}
           \end{minipage}\\
-& SHLW     &    $g/g$   &  Nrphys
+  USLTMASS & $m-kg/sec-kg$ & Nr
           &\begin{minipage}[t]{3in}
-           {Instantaneous specific humidity used as input to the Longwave radiation
+           {Zonal Mass-Weight Transp of Salt (or W.Vap Mix Rat.)}
-           subroutine}
           \end{minipage}\\
-& OZLW     &    $g/g$   &  Nrphys
+  VSLTMASS & $m-kg/sec-kg$ & Nr
           &\begin{minipage}[t]{3in}
-           {Instantaneous ozone used as input to the Longwave radiation
+           {Meridional Mass-Weight Transp of Salt (or W.Vap Mix Rat.)}
-           subroutine}
           \end{minipage}\\
-& CLMOLW   &    $0-1$   &  Nrphys
+  WSLTMASS & $m-kg/sec-kg$ & Nr
           &\begin{minipage}[t]{3in}
-           {Maximum overlap cloud fraction used in the Longwave radiation
+           {Vertical Mass-Weight Transp of Salt (or W.Vap Mix Rat.)}
-           subroutine}
           \end{minipage}\\
-& CLDTOT   &    $0-1$   &  Nrphys
+  UVELTH   & $m-deg/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Total cloud fraction used in the Longwave and Shortwave radiation
+           {Zonal Transp of Pot Temp}
-           subroutines}
           \end{minipage}\\
-& LWGDOWN  &    $Watts/m^2$   &  1
+  VVELTH   & $m-deg/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Downwelling Longwave radiation at the ground}
+           {Meridional Transp of Pot Temp}
           \end{minipage}\\
-& GWDT     &    $deg/day$ &  Nrphys
+  WVELTH   & $m-deg/sec$ & Nr
           &\begin{minipage}[t]{3in}
-           {Temperature tendency due to Gravity Wave Drag}
+           {Vertical Transp of Pot Temp}
           \end{minipage}\\
-& RADSWT   &    $Watts/m^2$   &  1
+  UVELSLT  & $m-kg/sec-kg$ & Nr
           &\begin{minipage}[t]{3in}
-           {Incident Shortwave radiation at the top of the atmosphere}
+           {Zonal Transp of Salt (or W.Vap Mix Rat.)}
           \end{minipage}\\
-& TAUCLD   &    $per 100 mb$   &  Nrphys
+  VVELSLT  & $m-kg/sec-kg$ & Nr
           &\begin{minipage}[t]{3in}
-           {Counted Cloud Optical Depth (non-dimensional) per 100 mb}
+           {Meridional Transp of Salt (or W.Vap Mix Rat.)}
           \end{minipage}\\
-& TAUCLDC  &    $Number$   &  Nrphys
+  WVELSLT  & $m-kg/sec-kg$ & Nr
           &\begin{minipage}[t]{3in}
-           {Cloud Optical Depth Counter}
+           {Vertical Transp of Salt (or W.Vap Mix Rat.)}
           \end{minipage}\\
  \end{tabular}
+ \vspace{1.5in}
  \vfill
  \newpage
  \vspace*{\fill}
- \begin{tabular}{lllll}
+ \begin{tabular}{llll}
  \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
+  NAME & UNITS & LEVELS & DESCRIPTION \\
  \hline
  &\\
-& CLDLOW   &    $0-1$   &  Nrphys
+  RHOAnoma & $kg/m^3  $  &  Nr
           &\begin{minipage}[t]{3in}
-           {Low-Level ( 1000-700 hPa) Cloud Fraction  (0-1)}
+           {Density Anomaly (=Rho-rhoConst)}
           \end{minipage}\\
-& EVAP     &    $mm/day$   &  1
+  RHOANOSQ & $kg^2/m^6$  &  Nr
           &\begin{minipage}[t]{3in}
-           {Surface evaporation}
+           {Square of Density Anomaly (=(Rho-rhoConst))}
           \end{minipage}\\
-& DPDT     &    $hPa/day$ &  1
+  URHOMASS & $kg/m^2/s$  &  Nr
           &\begin{minipage}[t]{3in}
-           {Surface Pressure tendency}
+           {Zonal Transport of Density}
           \end{minipage}\\
-& UAVE     &    $m/sec$ &  Nrphys
+  VRHOMASS & $kg/m^2/s$  &  Nr
           &\begin{minipage}[t]{3in}
-           {Average U-Wind}
+           {Meridional Transport of Density}
           \end{minipage}\\
-& VAVE     &    $m/sec$ &  Nrphys
+  WRHOMASS & $kg/m^2/s$  &  Nr
           &\begin{minipage}[t]{3in}
-           {Average V-Wind}
+           {Vertical Transport of Potential Density}
           \end{minipage}\\
-& TAVE     &    $deg$ &  Nrphys
+  PHIHYD   & $m^2/s^2 $  &  Nr
           &\begin{minipage}[t]{3in}
-           {Average Temperature}
+           {Hydrostatic (ocean) pressure / (atmos) geo-Potential}
           \end{minipage}\\
-& QAVE     &    $g/kg$ &  Nrphys
+  PHIHYDSQ & $m^4/s^4 $  &  Nr
           &\begin{minipage}[t]{3in}
-           {Average Specific Humidity}
+           {Square of Hyd. (ocean) press / (atmos) geoPotential}
           \end{minipage}\\
-& OMEGA    &    $hPa/day$ &  Nrphys
+  PHIBOT   & $m^2/s^2 $  &  Nr
           &\begin{minipage}[t]{3in}
-           {Vertical Velocity}
+           {ocean bottom pressure / top. atmos geo-Potential}
           \end{minipage}\\
-& DUDT     &    $m/sec/day$ &  Nrphys
+  PHIBOTSQ & $m^4/s^4 $  &  Nr
           &\begin{minipage}[t]{3in}
-           {Total U-Wind tendency}
+           {Square of ocean bottom pressure / top. geo-Potential}
           \end{minipage}\\
-& DVDT     &    $m/sec/day$ &  Nrphys
+  DRHODR   & $kg/m^3/{r-unit}$ & Nr
           &\begin{minipage}[t]{3in}
-           {Total V-Wind tendency}
+           {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}\\
-& DTDT     &    $deg/day$ &  Nrphys
+  TRELAX   & $W/m^2        $ & 1
           &\begin{minipage}[t]{3in}
-           {Total Temperature tendency}
+           {surface temperature relaxation, >0 increases theta}
           \end{minipage}\\
-& DQDT     &    $g/kg/day$ &  Nrphys
+  TICE     & $W/m^2        $ & 1
           &\begin{minipage}[t]{3in}
-           {Total Specific Humidity tendency}
+           {heat from melt/freeze of sea-ice, >0 increases theta}
           \end{minipage}\\
-& VORT     &    $10^{-4}/sec$ &  Nrphys
+  SFLUX    & $g/m^2/s      $ & 1
           &\begin{minipage}[t]{3in}
-           {Relative Vorticity}
+           {net surface salt flux, >0 increases salt}
           \end{minipage}\\
-& NOT USED &    $$ &
+  SRELAX   & $g/m^2/s      $ & 1
           &\begin{minipage}[t]{3in}
-           {}
+           {surface salinity relaxation, >0 increases salt}
           \end{minipage}\\
-& DTLS     &    $deg/day$ &  Nrphys
+  PRESSURE & $Pa           $ & Nr
           &\begin{minipage}[t]{3in}
-           {Temperature tendency due to Stratiform Cloud Formation}
+           {Atmospheric Pressure (Pa)}
           \end{minipage}\\
-& DQLS     &    $g/kg/day$ &  Nrphys
+  ADVr\_TH  & $K.Pa.m^2/s   $ & Nr
           &\begin{minipage}[t]{3in}
-           {Specific Humidity tendency due to Stratiform Cloud Formation}
+           {Vertical   Advective Flux of Pot.Temperature}
           \end{minipage}\\
-& USTAR    &    $m/sec$ &  1
+  ADVx\_TH  & $K.Pa.m^2/s   $ & Nr
           &\begin{minipage}[t]{3in}
-           {Surface USTAR wind}
+           {Zonal      Advective Flux of Pot.Temperature}
           \end{minipage}\\
-& Z0       &    $m$ &  1
+  ADVy\_TH  & $K.Pa.m^2/s   $ & Nr
           &\begin{minipage}[t]{3in}
-           {Surface roughness}
+           {Meridional Advective Flux of Pot.Temperature}
           \end{minipage}\\
-& FRQTRB   &    $0-1$ &  Nrphys-1
+  DFrE\_TH  & $K.Pa.m^2/s   $ & Nr
           &\begin{minipage}[t]{3in}
-           {Frequency of Turbulence}
+           {Vertical Diffusive Flux of Pot.Temperature (Explicit part)}
           \end{minipage}\\
-& PBL      &    $mb$ &  1
+  DIFx\_TH  & $K.Pa.m^2/s   $ & Nr
           &\begin{minipage}[t]{3in}
-           {Planetary Boundary Layer depth}
+           {Zonal      Diffusive Flux of Pot.Temperature}
           \end{minipage}\\
-& SWCLR    &  $deg/day$ &  Nrphys
+  DIFy\_TH  & $K.Pa.m^2/s   $ & Nr
           &\begin{minipage}[t]{3in}
-           {Net clearsky Shortwave heating rate for each level}
+           {Meridional Diffusive Flux of Pot.Temperature}
           \end{minipage}\\
-& OSR      &   $Watts/m^2$  &    1
+  DFrI\_TH  & $K.Pa.m^2/s   $ & Nr
           &\begin{minipage}[t]{3in}
-           {Net downward Shortwave flux at the top of the model}
+           {Vertical Diffusive Flux of Pot.Temperature (Implicit part)}
           \end{minipage}\\
-& OSRCLR   &   $Watts/m^2$  &    1
+  ADVr\_SLT & $g/kg.Pa.m^2/s$ & Nr
           &\begin{minipage}[t]{3in}
-           {Net downward clearsky Shortwave flux at the top of the model}
+           {Vertical   Advective Flux of Water-Vapor}
           \end{minipage}\\
-& CLDMAS   &   $kg / m^2$  &    Nrphys
+  ADVx\_SLT & $g/kg.Pa.m^2/s$ & Nr
           &\begin{minipage}[t]{3in}
-           {Convective cloud mass flux}
+           {Zonal      Advective Flux of Water-Vapor}
           \end{minipage}\\
-& UAVE     &   $m/sec$  &    Nrphys
+  ADVy\_SLT & $g/kg.Pa.m^2/s$ & Nr
           &\begin{minipage}[t]{3in}
-           {Time-averaged $u-Wind$}
+           {Meridional Advective Flux of Water-Vapor}
           \end{minipage}\\
  \end{tabular}
+ \vspace{1.5in}
  \vfill
  \newpage
  \vspace*{\fill}
- \begin{tabular}{lllll}
+ \begin{tabular}{llll}
  \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
+  NAME & UNITS & LEVELS & DESCRIPTION \\
  \hline
  &\\
-& VAVE     &   $m/sec$  &    Nrphys
+  DFrE\_SLT & $g/kg.Pa.m^2/s$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Time-averaged $v-Wind$}
-          \end{minipage}\\
-& TAVE     &   $deg$  &    Nrphys
           &\begin{minipage}[t]{3in}
-           {Time-averaged $Temperature$}
+           {Vertical Diffusive Flux of Water-Vapor (Explicit part)}
           \end{minipage}\\
-& QAVE     &   $g/g$  &    Nrphys
+  DIFx\_SLT & $g/kg.Pa.m^2/s$ & Nr
           &\begin{minipage}[t]{3in}
-           {Time-averaged $Specific \, \, Humidity$}
+           {Zonal      Diffusive Flux of Water-Vapor}
           \end{minipage}\\
-& RFT      &    $deg/day$ &  Nrphys
+  DIFy\_SLT & $g/kg.Pa.m^2/s$ & Nr
           &\begin{minipage}[t]{3in}
-           {Temperature tendency due Rayleigh Friction}
+           {Meridional Diffusive Flux of Water-Vapor}
           \end{minipage}\\
-& PS       &   $mb$  &    1
+  DFrI\_SLT & $g/kg.Pa.m^2/s$ & Nr
           &\begin{minipage}[t]{3in}
-           {Surface Pressure}
+           {Vertical Diffusive Flux of Water-Vapor (Implicit part)}
-          \end{minipage}\\
-& QQAVE    &   $(m/sec)^2$  &    Nrphys
-          &\begin{minipage}[t]{3in}
-           {Time-averaged $Turbulent Kinetic Energy$}
-          \end{minipage}\\
-& SWGCLR   &   $Watts/m^2$  &    1
-          &\begin{minipage}[t]{3in}
-           {Net downward clearsky Shortwave flux at the ground}
-          \end{minipage}\\
-& PAVE     &   $mb$  &    1
-          &\begin{minipage}[t]{3in}
-           {Time-averaged Surface Pressure}
-          \end{minipage}\\
-& 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}\\
-& DIABU    & $m/sec/day$ &    Nrphys
-          &\begin{minipage}[t]{3in}
-           {Total Diabatic forcing on $u-Wind$}
-          \end{minipage}\\
-& DIABV    & $m/sec/day$ &    Nrphys
-          &\begin{minipage}[t]{3in}
-           {Total Diabatic forcing on $v-Wind$}
-          \end{minipage}\\
-& DIABT    & $deg/day$ &    Nrphys
-          &\begin{minipage}[t]{3in}
-           {Total Diabatic forcing on $Temperature$}
-          \end{minipage}\\
-& DIABQ    & $g/kg/day$ &    Nrphys
-          &\begin{minipage}[t]{3in}
-           {Total Diabatic forcing on $Specific \, \, Humidity$}
-          \end{minipage}\\
-& RFU      &    $m/sec/day$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {U-Wind tendency due to Rayleigh Friction}
-          \end{minipage}\\
-& RFV      &    $m/sec/day$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {V-Wind tendency due to Rayleigh Friction}
-          \end{minipage}\\
-& GWDU     &    $m/sec/day$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {U-Wind tendency due to Gravity Wave Drag}
-          \end{minipage}\\
-& GWDU     &    $m/sec/day$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {V-Wind tendency due to Gravity Wave Drag}
-          \end{minipage}\\
-& GWDUS    &    $N/m^2$ &  1
-          &\begin{minipage}[t]{3in}
-           {U-Wind Gravity Wave Drag Stress at Surface}
-          \end{minipage}\\
-& GWDVS    &    $N/m^2$ &  1
-          &\begin{minipage}[t]{3in}
-           {V-Wind Gravity Wave Drag Stress at Surface}
-          \end{minipage}\\
-& GWDUT    &    $N/m^2$ &  1
-          &\begin{minipage}[t]{3in}
-           {U-Wind Gravity Wave Drag Stress at Top}
-          \end{minipage}\\
-& GWDVT    &    $N/m^2$ &  1
-          &\begin{minipage}[t]{3in}
-           {V-Wind Gravity Wave Drag Stress at Top}
-          \end{minipage}\\
-& LZRAD    &    $mg/kg$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {Estimated Cloud Liquid Water used in Radiation}
-          \end{minipage}\\
- \end{tabular}
- \vfill
- \newpage
- \vspace*{\fill}
- \begin{tabular}{lllll}
- \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
- \hline
- &\\
-& SLP      &   $mb$  &    1
-          &\begin{minipage}[t]{3in}
-           {Time-averaged Sea-level Pressure}
-          \end{minipage}\\
-& NOT USED &    $$ &
-          &\begin{minipage}[t]{3in}
-           {}
-          \end{minipage}\\
-& NOT USED &    $$ &
-          &\begin{minipage}[t]{3in}
-           {}
-          \end{minipage}\\
-& NOT USED &    $$ &
-          &\begin{minipage}[t]{3in}
-           {}
-          \end{minipage}\\
-& NOT USED &    $$ &
-          &\begin{minipage}[t]{3in}
-           {}
-          \end{minipage}\\
-& CLDFRC  & $0-1$ &    1
-          &\begin{minipage}[t]{3in}
-           {Total Cloud Fraction}
-          \end{minipage}\\
-& TPW     & $gm/cm^2$ &    1
-          &\begin{minipage}[t]{3in}
-           {Precipitable water}
-          \end{minipage}\\
-& U2M     & $m/sec$ &    1
-          &\begin{minipage}[t]{3in}
-           {U-Wind at 2 meters}
-          \end{minipage}\\
-& V2M     & $m/sec$ &    1
-          &\begin{minipage}[t]{3in}
-           {V-Wind at 2 meters}
-          \end{minipage}\\
-& T2M     & $deg$ &    1
-          &\begin{minipage}[t]{3in}
-           {Temperature at 2 meters}
-          \end{minipage}\\
-& Q2M     & $g/kg$ &    1
-          &\begin{minipage}[t]{3in}
-           {Specific Humidity at 2 meters}
-          \end{minipage}\\
-& U10M    & $m/sec$ &    1
-          &\begin{minipage}[t]{3in}
-           {U-Wind at 10 meters}
-          \end{minipage}\\
-& V10M    & $m/sec$ &    1
-          &\begin{minipage}[t]{3in}
-           {V-Wind at 10 meters}
-          \end{minipage}\\
-& T10M    & $deg$ &    1
-          &\begin{minipage}[t]{3in}
-           {Temperature at 10 meters}
-          \end{minipage}\\
-& Q10M    & $g/kg$ &    1
-          &\begin{minipage}[t]{3in}
-           {Specific Humidity at 10 meters}
-          \end{minipage}\\
-& DTRAIN  & $kg/m^2$ &    Nrphys
-          &\begin{minipage}[t]{3in}
-           {Detrainment Cloud Mass Flux}
-          \end{minipage}\\
-& QFILL   & $g/kg/day$ &    Nrphys
-          &\begin{minipage}[t]{3in}
-           {Filling of negative specific humidity}
-          \end{minipage}\\
-& NOT USED &    $$ &
-          &\begin{minipage}[t]{3in}
-           {}
-          \end{minipage}\\
-& NOT USED &    $$ &
-          &\begin{minipage}[t]{3in}
-           {}
-          \end{minipage}\\
-& SHAPU    &    $m/sec/day$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {U-Wind tendency due to Shapiro Filter}
-          \end{minipage}\\
-& SHAPV    &    $m/sec/day$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {V-Wind tendency due to Shapiro Filter}
-          \end{minipage}\\
-& SHAPT    &    $deg/day$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {Temperature tendency due Shapiro Filter}
-          \end{minipage}\\
-& SHAPQ    &    $g/kg/day$ &  Nrphys
-          &\begin{minipage}[t]{3in}
-           {Specific Humidity tendency due to Shapiro Filter}
-          \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}\\
- \end{tabular}
- \vspace{1.5in}
- \vfill
- \newpage
- \vspace*{\fill}
- \begin{tabular}{lllll}
- \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
- \hline
- &\\
-& 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}\\
  \end{tabular}
  \vspace{1.5in}
  \vfill
  \newpage
- \vspace*{\fill}
- \begin{tabular}{lllll}
- \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
- \hline
- &\\
+ \subsubsection{Diagnostic Description}
-& 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}\\
-& THETA    & $deg K$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Potential Temperature}
-          \end{minipage}\\
-& SALT     & $g/kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Salt (or Water Vapor Mixing Ratio)}
-          \end{minipage}\\
-& UVEL     & $m/sec$ & Nr
-          &\begin{minipage}[t]{3in}
-           {U-Velocity}
-          \end{minipage}\\
-& VVEL     & $m/sec$ & Nr
-          &\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}\\
-& 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}\\
-& UVELVVEL & $m^2/sec^2$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Meridional Transport of Zonal Momentum}
-          \end{minipage}\\
- \end{tabular}
- \vspace{1.5in}
- \vfill
- \newpage
+ In this section we list and describe the diagnostic quantities available within the
- \vspace*{\fill}
+ GCM.  The diagnostics are listed in the order that they appear in the
- \begin{tabular}{lllll}
+ Diagnostic Menu, Section \ref{sec:diagnostics:menu}.
- \hline\hline
+ In all cases, each diagnostic as currently archived on the output datasets
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
+ is time-averaged over its diagnostic output frequency:
- \hline
- &\\
-& 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}\\
-& UTRAC1   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Zonal Transp of Tracer 1}
-          \end{minipage}\\
-& VTRAC1   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Meridional Transp of Tracer 1}
-          \end{minipage}\\
-& WTRAC1   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Vertical Transp of Tracer 1}
-          \end{minipage}\\
-& UTRAC2   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Zonal Transp of Tracer 2}
-          \end{minipage}\\
-& VTRAC2   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Meridional Transp of Tracer 2}
-          \end{minipage}\\
-& WTRAC2   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Vertical Transp of Tracer 2}
-          \end{minipage}\\
-& UTRAC3   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Zonal Transp of Tracer 3}
-          \end{minipage}\\
-& VTRAC3   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Meridional Transp of Tracer 3}
-          \end{minipage}\\
-& WTRAC3   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Vertical Transp of Tracer 3}
-          \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}\\
- \end{tabular}
- \vspace{1.5in}
- \vfill
- \newpage
- \vspace*{\fill}
- \begin{tabular}{lllll}
- \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
- \hline
- &\\
-& UTRAC4   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Zonal Transp of Tracer 4}
-          \end{minipage}\\
-& VTRAC4   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Meridional Transp of Tracer 4}
-          \end{minipage}\\
-& WTRAC4   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Vertical Transp of Tracer 4}
-          \end{minipage}\\
-& UTRAC5   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Zonal Transp of Tracer 5}
-          \end{minipage}\\
-& VTRAC5   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Meridional Transp of Tracer 5}
-          \end{minipage}\\
-& WTRAC5   & $m-kg/sec-kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Vertical Transp of Tracer 5}
-          \end{minipage}\\
-& TRAC1    & $kg/kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Mass-Weight Tracer 1}
-          \end{minipage}\\
-& TRAC2    & $kg/kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Mass-Weight Tracer 2}
-          \end{minipage}\\
-& TRAC3    & $kg/kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Mass-Weight Tracer 3}
-          \end{minipage}\\
-& TRAC4    & $kg/kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Mass-Weight Tracer 4}
-          \end{minipage}\\
-& TRAC5    & $kg/kg$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Mass-Weight Tracer 5}
-          \end{minipage}\\
-& DICBIOA  & $mol/m3/s$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Biological Productivity}
-          \end{minipage}\\
-& DICCARB  & $mol eq/m3/s$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Carbonate chg-biol prod and remin}
-          \end{minipage}\\
-& DICTFLX  & $mol/m3/s$ & 1
-          &\begin{minipage}[t]{3in}
-           {Tendency of DIC due to air-sea exch}
-          \end{minipage}\\
-& DICOFLX  & $mol/m3/s$ & 1
-          &\begin{minipage}[t]{3in}
-           {Tendency of O2 due to air-sea exch}
-          \end{minipage}\\
-& DICCFLX  & $mol/m2/s$ & 1
-          &\begin{minipage}[t]{3in}
-           {Flux of CO2 - air-sea exch}
-          \end{minipage}\\
-& DICPCO2  & $atm$ & 1
-          &\begin{minipage}[t]{3in}
-           {Partial Pressure of CO2}
-          \end{minipage}\\
-& DICPHAV  & $dimensionless$ & 1
-          &\begin{minipage}[t]{3in}
-           {Average pH}
-          \end{minipage}\\
-& DTCONV   & $deg/sec$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Temp Change due to Convection}
-          \end{minipage}\\
-& DQCONV   & $g/kg/sec$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Specific Humidity Change due to Convection}
-          \end{minipage}\\
-& RELHUM   & $percent$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Relative Humidity}
-          \end{minipage}\\
-& PRECLS   & $g/m^2/sec$ & 1
-          &\begin{minipage}[t]{3in}
-           {Large Scale Precipitation}
-          \end{minipage}\\
-& ENPREC   & $J/g$ & 1
-          &\begin{minipage}[t]{3in}
-           {Energy of Precipitation (snow, rain Temp)}
-          \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}\\
-& DRHODR   & $kg/m^3/{r-unit}$ & Nr
-          &\begin{minipage}[t]{3in}
-           {Stratification: d.Sigma/dr}
-          \end{minipage}\\
- \end{tabular}
- \vspace{1.5in}
- \vfill
- \newpage
- \vspace*{\fill}
- \begin{tabular}{lllll}
- \hline\hline
- N & NAME & UNITS & LEVELS & DESCRIPTION \\
- \hline
- &\\
-& DETADT2  & ${r-unit}^2/s^2$ & 1
-          &\begin{minipage}[t]{3in}
-           {Square of Eta (Surf.P,SSH) Tendency}
-          \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)
-Line 1223 
 where $TTOT = {{\bf NQDIAG} \over \Delta
+Line 823 
 where $TTOT = {{\bf NQDIAG} \over \Delta
  output frequency of the diagnostic, and $\Delta t$ is
  the timestep over which the diagnostic is updated.
- {\bf 1)  \underline {UFLUX} Surface Zonal Wind Stress on the Atmosphere ($Newton/m^2$) }
- The zonal wind stress is the turbulent flux of zonal momentum from
- the surface. See section 3.3 for a description of the surface layer parameterization.
- \[
- {\bf UFLUX} =  - \rho C_D W_s u \hspace{1cm}where: \hspace{.2cm}C_D = C^2_u
- \]
- where $\rho$ = the atmospheric density at the surface, $C_{D}$ is the surface
- drag coefficient, $C_u$ is the dimensionless surface exchange coefficient for momentum
- (see diagnostic number 10), $W_s$ is the magnitude of the surface layer wind, and $u$ is
- the zonal wind in the lowest model layer.
- \\
- {\bf 2)  \underline {VFLUX} Surface Meridional Wind Stress on the Atmosphere ($Newton/m^2$) }
- The meridional wind stress is the turbulent flux of meridional momentum from
- the surface. See section 3.3 for a description of the surface layer parameterization.
- \[
- {\bf VFLUX} =  - \rho C_D W_s v \hspace{1cm}where: \hspace{.2cm}C_D = C^2_u
- \]
- where $\rho$ = the atmospheric density at the surface, $C_{D}$ is the surface
- drag coefficient, $C_u$ is the dimensionless surface exchange coefficient for momentum
- (see diagnostic number 10), $W_s$ is the magnitude of the surface layer wind, and $v$ is
- the meridional wind in the lowest model layer.
- \\
- {\bf 3)  \underline {HFLUX} Surface Flux of Sensible Heat ($Watts/m^2$) }
- The turbulent flux of sensible heat from the surface to the atmosphere is a function of the
- gradient of virtual potential temperature and the eddy exchange coefficient:
- \[
- {\bf HFLUX} =  P^{\kappa}\rho c_{p} C_{H} W_s (\theta_{surface} - \theta_{Nrphys})
- \hspace{1cm}where: \hspace{.2cm}C_H = C_u C_t
- \]
- where $\rho$ = the atmospheric density at the surface, $c_{p}$ is the specific
- heat of air, $C_{H}$ is the dimensionless surface heat transfer coefficient, $W_s$ is the
- magnitude of the surface layer wind, $C_u$ is the dimensionless surface exchange coefficient
- for momentum (see diagnostic number 10), $C_t$ is the dimensionless surface exchange coefficient
- for heat and moisture (see diagnostic number 9), and $\theta$ is the potential temperature
- at the surface and at the bottom model level.
- \\
- {\bf 4)  \underline {EFLUX} Surface Flux of Latent Heat ($Watts/m^2$) }
- The turbulent flux of latent heat from the surface to the atmosphere is a function of the
- gradient of moisture, the potential evapotranspiration fraction and the eddy exchange coefficient:
- \[
- {\bf EFLUX} =  \rho \beta L C_{H} W_s (q_{surface} - q_{Nrphys})
- \hspace{1cm}where: \hspace{.2cm}C_H = C_u C_t
- \]
- where $\rho$ = the atmospheric density at the surface, $\beta$ is the fraction of
- the potential evapotranspiration actually evaporated, L is the latent
- heat of evaporation, $C_{H}$ is the dimensionless surface heat transfer coefficient, $W_s$ is the
- magnitude of the surface layer wind, $C_u$ is the dimensionless surface exchange coefficient
- for momentum (see diagnostic number 10), $C_t$ is the dimensionless surface exchange coefficient
- for heat and moisture (see diagnostic number 9), and $q_{surface}$ and $q_{Nrphys}$ are the specific
- humidity at the surface and at the bottom model level, respectively.
- \\
- {\bf 5)  \underline {QICE} Heat Conduction Through Sea Ice ($Watts/m^2$) }
- Over sea ice there is an additional source of energy at the surface due to the heat
- conduction from the relatively warm ocean through the sea ice. The heat conduction
- through sea ice represents an additional energy source term for the ground temperature equation.
- \[
- {\bf QICE} = {C_{ti} \over {H_i}} (T_i-T_g)
- \]
- where $C_{ti}$ is the thermal conductivity of ice, $H_i$ is the ice thickness, assumed to
- be $3 \hspace{.1cm} m$ where sea ice is present, $T_i$ is 273 degrees Kelvin, and
- $T_g$ is the temperature of the sea ice.
- NOTE: QICE is not available through model version 5.3, but is available in subsequent versions.
- \\
- {\bf 6) \underline {RADLWG} Net upward Longwave Flux at the surface ($Watts/m^2$)}
- \begin{eqnarray*}
- {\bf RADLWG} & =  & F_{LW,Nrphys+1}^{Net} \\
-              & =  & F_{LW,Nrphys+1}^\uparrow - F_{LW,Nrphys+1}^\downarrow
- \end{eqnarray*}
- \\
- where Nrphys+1 indicates the lowest model edge-level, or $p = p_{surf}$.
- $F_{LW}^\uparrow$ is
- the upward Longwave flux and $F_{LW}^\downarrow$ is the downward Longwave flux.
- \\
- {\bf 7) \underline {RADSWG} Net downard shortwave Flux at the surface ($Watts/m^2$)}
- \begin{eqnarray*}
- {\bf RADSWG} & =  & F_{SW,Nrphys+1}^{Net} \\
-              & =  & F_{SW,Nrphys+1}^\downarrow - F_{SW,Nrphys+1}^\uparrow
- \end{eqnarray*}
- \\
- where Nrphys+1 indicates the lowest model edge-level, or $p = p_{surf}$.
- $F_{SW}^\downarrow$ is
- the downward Shortwave flux and $F_{SW}^\uparrow$ is the upward Shortwave flux.
- \\
- \noindent
- {\bf 8)  \underline {RI} Richardson Number} ($dimensionless$)
- \noindent
- The non-dimensional stability indicator is the ratio of the buoyancy to the shear:
- \[
- {\bf RI} = { { {g \over \theta_v} \pp {\theta_v}{z} } \over { (\pp{u}{z})^2 + (\pp{v}{z})^2 } }
-  =  {  {c_p \pp{\theta_v}{z} \pp{P^ \kappa}{z} } \over { (\pp{u}{z})^2 + (\pp{v}{z})^2 } }
- \]
- \\
- where we used the hydrostatic equation:
- \[
- {\pp{\Phi}{P^ \kappa}} = c_p \theta_v
- \]
- Negative values indicate unstable buoyancy {\bf{AND}} shear, small positive values ($<0.4$)
- indicate dominantly unstable shear, and large positive values indicate dominantly stable
- stratification.
- \\
- \noindent
- {\bf 9)  \underline {CT}  Surface Exchange Coefficient for Temperature and Moisture ($dimensionless$) }
- \noindent
- The surface exchange coefficient is obtained from the similarity functions for the stability
-  dependant flux profile relationships:
- \[
- {\bf CT} = -{( {\overline{w^{\prime}\theta^{\prime}}}) \over {u_* \Delta \theta }} =
- -{( {\overline{w^{\prime}q^{\prime}}}) \over {u_* \Delta q }} =
- { k \over { (\psi_{h} + \psi_{g}) } }
- \]
- where $\psi_h$ is the surface layer non-dimensional temperature change and $\psi_g$ is the
- viscous sublayer non-dimensional temperature or moisture change:
- \[
- \psi_{h} = {\int_{\zeta_{0}}^{\zeta} {\phi_{h} \over \zeta} d \zeta} \hspace{1cm} and
- \hspace{1cm} \psi_{g} = { 0.55 (Pr^{2/3} - 0.2) \over \nu^{1/2} }
- (h_{0}u_{*} - h_{0_{ref}}u_{*_{ref}})^{1/2}
- \]
- and:
- $h_{0} = 30z_{0}$ with a maximum value over land of 0.01
- \noindent
- $\phi_h$ is the similarity function of $\zeta$, which expresses the stability dependance of
- the temperature and moisture gradients, specified differently for stable and unstable
- layers according to Helfand and Schubert, 1993. k is the Von Karman constant, $\zeta$ is the
- non-dimensional stability parameter, Pr is the Prandtl number for air, $\nu$ is the molecular
- viscosity, $z_{0}$ is the surface roughness length, $u_*$ is the surface stress velocity
- (see diagnostic number 67), and the subscript ref refers to a reference value.
- \\
- \noindent
- {\bf 10)  \underline {CU}  Surface Exchange Coefficient for Momentum ($dimensionless$) }
- \noindent
- The surface exchange coefficient is obtained from the similarity functions for the stability
-  dependant flux profile relationships:
- \[
- {\bf CU} = {u_* \over W_s} = { k \over \psi_{m} }
- \]
- where $\psi_m$ is the surface layer non-dimensional wind shear:
- \[
- \psi_{m} = {\int_{\zeta_{0}}^{\zeta} {\phi_{m} \over \zeta} d \zeta}
- \]
- \noindent
- $\phi_m$ is the similarity function of $\zeta$, which expresses the stability dependance of
- the temperature and moisture gradients, specified differently for stable and unstable layers
- according to Helfand and Schubert, 1993. k is the Von Karman constant, $\zeta$ is the
- non-dimensional stability parameter, $u_*$ is the surface stress velocity
- (see diagnostic number 67), and $W_s$ is the magnitude of the surface layer wind.
- \\
- \noindent
- {\bf 11)  \underline {ET}  Diffusivity Coefficient for Temperature and Moisture ($m^2/sec$) }
- \noindent
- In the level 2.5 version of the Mellor-Yamada (1974) hierarchy, the turbulent heat or
- moisture flux for the atmosphere above the surface layer can be expressed as a turbulent
- diffusion coefficient $K_h$ times the negative of the gradient of potential temperature
- or moisture. In the Helfand and Labraga (1988) adaptation of this closure, $K_h$
- takes the form:
- \[
- {\bf ET} = K_h = -{( {\overline{w^{\prime}\theta_v^{\prime}}}) \over {\pp{\theta_v}{z}} }
-  = \left\{ \begin{array}{l@{\quad\mbox{for}\quad}l} q \, \ell \, S_H(G_M,G_H) & \mbox{decaying turbulence}
- \\ { q^2 \over {q_e} } \, \ell \, S_{H}(G_{M_e},G_{H_e}) & \mbox{growing turbulence} \end{array} \right.
- \]
- where $q$ is the turbulent velocity, or $\sqrt{2*turbulent \hspace{.2cm} kinetic \hspace{.2cm}
- energy}$, $q_e$ is the turbulence velocity derived from the more simple level 2.0 model,
- which describes equilibrium turbulence, $\ell$ is the master length scale related to the layer
- depth,
- $S_H$ is a function of $G_H$ and $G_M$, the dimensionless buoyancy and
- wind shear parameters, respectively, or a function of $G_{H_e}$ and $G_{M_e}$, the equilibrium
- dimensionless buoyancy and wind shear
- parameters.   Both $G_H$ and $G_M$, and their equilibrium values $G_{H_e}$ and $G_{M_e}$,
- are functions of the Richardson number.
- \noindent
- For the detailed equations and derivations of the modified level 2.5 closure scheme,
- see Helfand and Labraga, 1988.
- \noindent
- In the surface layer, ${\bf {ET}}$ is the exchange coefficient for heat and moisture,
- in units of $m/sec$, given by:
- \[
- {\bf ET_{Nrphys}} =  C_t * u_* = C_H W_s
- \]
- \noindent
- where $C_t$ is the dimensionless exchange coefficient for heat and moisture from the
- surface layer similarity functions (see diagnostic number 9), $u_*$ is the surface
- friction velocity (see diagnostic number 67), $C_H$ is the heat transfer coefficient,
- and $W_s$ is the magnitude of the surface layer wind.
- \\
- \noindent
- {\bf 12)  \underline {EU}  Diffusivity Coefficient for Momentum ($m^2/sec$) }
- \noindent
- In the level 2.5 version of the Mellor-Yamada (1974) hierarchy, the turbulent heat
- momentum flux for the atmosphere above the surface layer can be expressed as a turbulent
- diffusion coefficient $K_m$ times the negative of the gradient of the u-wind.
- In the Helfand and Labraga (1988) adaptation of this closure, $K_m$
- takes the form:
- \[
- {\bf EU} = K_m = -{( {\overline{u^{\prime}w^{\prime}}}) \over {\pp{U}{z}} }
-  = \left\{ \begin{array}{l@{\quad\mbox{for}\quad}l} q \, \ell \, S_M(G_M,G_H) & \mbox{decaying turbulence}
- \\ { q^2 \over {q_e} } \, \ell \, S_{M}(G_{M_e},G_{H_e}) & \mbox{growing turbulence} \end{array} \right.
- \]
- \noindent
- where $q$ is the turbulent velocity, or $\sqrt{2*turbulent \hspace{.2cm} kinetic \hspace{.2cm}
- energy}$, $q_e$ is the turbulence velocity derived from the more simple level 2.0 model,
- which describes equilibrium turbulence, $\ell$ is the master length scale related to the layer
- depth,
- $S_M$ is a function of $G_H$ and $G_M$, the dimensionless buoyancy and
- wind shear parameters, respectively, or a function of $G_{H_e}$ and $G_{M_e}$, the equilibrium
- dimensionless buoyancy and wind shear
- parameters.   Both $G_H$ and $G_M$, and their equilibrium values $G_{H_e}$ and $G_{M_e}$,
- are functions of the Richardson number.
- \noindent
- For the detailed equations and derivations of the modified level 2.5 closure scheme,
- see Helfand and Labraga, 1988.
- \noindent
- In the surface layer, ${\bf {EU}}$ is the exchange coefficient for momentum,
- in units of $m/sec$, given by:
- \[
- {\bf EU_{Nrphys}} = C_u * u_* = C_D W_s
- \]
- \noindent
- where $C_u$ is the dimensionless exchange coefficient for momentum from the surface layer
- similarity functions (see diagnostic number 10), $u_*$ is the surface friction velocity
- (see diagnostic number 67), $C_D$ is the surface drag coefficient, and $W_s$ is the
- magnitude of the surface layer wind.
- \\
- \noindent
- {\bf 13)  \underline {TURBU}  Zonal U-Momentum changes due to Turbulence ($m/sec/day$) }
- \noindent
- The tendency of U-Momentum due to turbulence is written:
- \[
- {\bf TURBU} = {\pp{u}{t}}_{turb} = {\pp{}{z} }{(- \overline{u^{\prime}w^{\prime}})}
-  = {\pp{}{z} }{(K_m \pp{u}{z})}
- \]
- \noindent
- The Helfand and Labraga level 2.5 scheme models the turbulent
- flux of u-momentum in terms of $K_m$, and the equation has the form of a diffusion
- equation.
- \noindent
- {\bf 14)  \underline {TURBV}  Meridional V-Momentum changes due to Turbulence ($m/sec/day$) }
- \noindent
- The tendency of V-Momentum due to turbulence is written:
- \[
- {\bf TURBV} = {\pp{v}{t}}_{turb} = {\pp{}{z} }{(- \overline{v^{\prime}w^{\prime}})}
-  = {\pp{}{z} }{(K_m \pp{v}{z})}
- \]
- \noindent
- The Helfand and Labraga level 2.5 scheme models the turbulent
- flux of v-momentum in terms of $K_m$, and the equation has the form of a diffusion
- equation.
- \\
- \noindent
- {\bf 15)  \underline {TURBT}  Temperature changes due to Turbulence ($deg/day$) }
- \noindent
- The tendency of temperature due to turbulence is written:
- \[
- {\bf TURBT} = {\pp{T}{t}} = P^{\kappa}{\pp{\theta}{t}}_{turb} =
- P^{\kappa}{\pp{}{z} }{(- \overline{w^{\prime}\theta^{\prime}})}
-  = P^{\kappa}{\pp{}{z} }{(K_h \pp{\theta_v}{z})}
- \]
- \noindent
- The Helfand and Labraga level 2.5 scheme models the turbulent
- flux of temperature in terms of $K_h$, and the equation has the form of a diffusion
- equation.
- \\
- \noindent
- {\bf 16)  \underline {TURBQ}  Specific Humidity changes due to Turbulence ($g/kg/day$) }
- \noindent
- The tendency of specific humidity due to turbulence is written:
- \[
- {\bf TURBQ} = {\pp{q}{t}}_{turb} = {\pp{}{z} }{(- \overline{w^{\prime}q^{\prime}})}
-  = {\pp{}{z} }{(K_h \pp{q}{z})}
- \]
- \noindent
- The Helfand and Labraga level 2.5 scheme models the turbulent
- flux of temperature in terms of $K_h$, and the equation has the form of a diffusion
- equation.
- \\
- \noindent
- {\bf 17)  \underline {MOISTT} Temperature Changes Due to Moist Processes ($deg/day$) }
- \noindent
- \[
- {\bf MOISTT} = \left. {\pp{T}{t}}\right|_{c} + \left. {\pp{T}{t}} \right|_{ls}
- \]
- where:
- \[
- \left.{\pp{T}{t}}\right|_{c} = R \sum_i \left( \alpha { m_B \over c_p} \Gamma_s \right)_i
- \hspace{.4cm} and
- \hspace{.4cm} \left.{\pp{T}{t}}\right|_{ls} = {L \over c_p } (q^*-q)
- \]
- and
- \[
- \Gamma_s = g \eta \pp{s}{p}
- \]
- \noindent
- The subscript $c$ refers to convective processes, while the subscript $ls$ refers to large scale
- precipitation processes, or supersaturation rain.
- The summation refers to contributions from each cloud type called by RAS.
- The dry static energy is given
- as $s$, the convective cloud base mass flux is given as $m_B$, and the cloud entrainment is
- given as $\eta$, which are explicitly defined in Section \ref{sec:fizhi:mc},
- the description of the convective parameterization.  The fractional adjustment, or relaxation
- parameter, for each cloud type is given as $\alpha$, while
- $R$ is the rain re-evaporation adjustment.
- \\
- \noindent
- {\bf 18)  \underline {MOISTQ} Specific Humidity Changes Due to Moist Processes ($g/kg/day$) }
- \noindent
- \[
- {\bf MOISTQ} = \left. {\pp{q}{t}}\right|_{c} + \left. {\pp{q}{t}} \right|_{ls}
- \]
- where:
- \[
- \left.{\pp{q}{t}}\right|_{c} = R \sum_i \left( \alpha { m_B \over {L}}(\Gamma_h-\Gamma_s) \right)_i
- \hspace{.4cm} and
- \hspace{.4cm} \left.{\pp{q}{t}}\right|_{ls} = (q^*-q)
- \]
- and
- \[
- \Gamma_s = g \eta \pp{s}{p}\hspace{.4cm} and \hspace{.4cm}\Gamma_h = g \eta \pp{h}{p}
- \]
- \noindent
- The subscript $c$ refers to convective processes, while the subscript $ls$ refers to large scale
- precipitation processes, or supersaturation rain.
- The summation refers to contributions from each cloud type called by RAS.
- The dry static energy is given as $s$,
- the moist static energy is given as $h$,
- the convective cloud base mass flux is given as $m_B$, and the cloud entrainment is
- given as $\eta$, which are explicitly defined in Section \ref{sec:fizhi:mc},
- the description of the convective parameterization.  The fractional adjustment, or relaxation
- parameter, for each cloud type is given as $\alpha$, while
- $R$ is the rain re-evaporation adjustment.
- \\
- \noindent
- {\bf 19)  \underline {RADLW} Heating Rate due to Longwave Radiation ($deg/day$) }
- \noindent
- The net longwave heating rate is calculated as the vertical divergence of the
- net terrestrial radiative fluxes.
- Both the clear-sky and cloudy-sky longwave fluxes are computed within the
- longwave routine.
- The subroutine calculates the clear-sky flux, $F^{clearsky}_{LW}$, first.
- For a given cloud fraction,
- the clear line-of-sight probability $C(p,p^{\prime})$ is computed from the current level pressure $p$
- to the model top pressure, $p^{\prime} = p_{top}$, and the model surface pressure, $p^{\prime} = p_{surf}$,
- for the upward and downward radiative fluxes.
- (see Section \ref{sec:fizhi:radcloud}).
- The cloudy-sky flux is then obtained as:
- \noindent
- \[
- F_{LW} = C(p,p') \cdot F^{clearsky}_{LW},
- \]
- \noindent
- Finally, the net longwave heating rate is calculated as the vertical divergence of the
- net terrestrial radiative fluxes:
- \[
- \pp{\rho c_p T}{t} = - {\partial \over \partial z} F_{LW}^{NET} ,
- \]
- or
- \[
- {\bf RADLW} = \frac{g}{c_p \pi} {\partial \over \partial \sigma} F_{LW}^{NET} .
- \]
- \noindent
- where $g$ is the accelation due to gravity,
- $c_p$ is the heat capacity of air at constant pressure,
- and
- \[
- F_{LW}^{NET} = F_{LW}^\uparrow - F_{LW}^\downarrow
- \]
- \\
- \noindent
- {\bf 20)  \underline {RADSW} Heating Rate due to Shortwave Radiation ($deg/day$) }
- \noindent
- The net Shortwave heating rate is calculated as the vertical divergence of the
- net solar radiative fluxes.
- The clear-sky and cloudy-sky shortwave fluxes are calculated separately.
- For the clear-sky case, the shortwave fluxes and heating rates are computed with
- both CLMO (maximum overlap cloud fraction) and
- CLRO (random overlap cloud fraction) set to zero (see Section \ref{sec:fizhi:radcloud}).
- The shortwave routine is then called a second time, for the cloudy-sky case, with the
- true time-averaged cloud fractions CLMO
- and CLRO being used.  In all cases, a normalized incident shortwave flux is used as
- input at the top of the atmosphere.
- \noindent
- The heating rate due to Shortwave Radiation under cloudy skies is defined as:
- \[
- \pp{\rho c_p T}{t} = - {\partial \over \partial z} F(cloudy)_{SW}^{NET} \cdot {\rm RADSWT},
- \]
- or
- \[
- {\bf RADSW} = \frac{g}{c_p \pi} {\partial \over \partial \sigma} F(cloudy)_{SW}^{NET}\cdot {\rm RADSWT} .
- \]
- \noindent
- where $g$ is the accelation due to gravity,
- $c_p$ is the heat capacity of air at constant pressure, RADSWT is the true incident
- shortwave radiation at the top of the atmosphere (See Diagnostic \#48), and
- \[
- F(cloudy)_{SW}^{Net} = F(cloudy)_{SW}^\uparrow - F(cloudy)_{SW}^\downarrow
- \]
- \\
- \noindent
- {\bf 21)  \underline {PREACC} Total (Large-scale + Convective) Accumulated Precipition ($mm/day$) }
- \noindent
- For a change in specific humidity due to moist processes, $\Delta q_{moist}$,
- the vertical integral or total precipitable amount is given by:
- \[
- {\bf PREACC} = \int_{surf}^{top} \rho \Delta q_{moist} dz = - \int_{surf}^{top} \Delta  q_{moist}
- {dp \over g} = {1 \over g} \int_0^1 \Delta q_{moist} dp
- \]
- \\
- \noindent
- A precipitation rate is defined as the vertically integrated moisture adjustment per Moist Processes
- time step, scaled to $mm/day$.
- \\
- \noindent
- {\bf 22)  \underline {PRECON} Convective Precipition ($mm/day$) }
- \noindent
- For a change in specific humidity due to sub-grid scale cumulus convective processes, $\Delta q_{cum}$,
- the vertical integral or total precipitable amount is given by:
- \[
- {\bf PRECON} = \int_{surf}^{top} \rho \Delta q_{cum} dz = - \int_{surf}^{top} \Delta  q_{cum}
- {dp \over g} = {1 \over g} \int_0^1 \Delta q_{cum} dp
- \]
- \\
- \noindent
- A precipitation rate is defined as the vertically integrated moisture adjustment per Moist Processes
- time step, scaled to $mm/day$.
- \\
- \noindent
- {\bf 23)  \underline {TUFLUX}  Turbulent Flux of U-Momentum ($Newton/m^2$) }
- \noindent
- The turbulent flux of u-momentum is calculated for $diagnostic \hspace{.2cm} purposes
-  \hspace{.2cm} only$ from the eddy coefficient for momentum:
- \[
- {\bf TUFLUX} =  {\rho } {(\overline{u^{\prime}w^{\prime}})} =
- {\rho } {(- K_m \pp{U}{z})}
- \]
- \noindent
- where $\rho$ is the air density, and $K_m$ is the eddy coefficient.
- \\
- \noindent
- {\bf 24)  \underline {TVFLUX}  Turbulent Flux of V-Momentum ($Newton/m^2$) }
- \noindent
- The turbulent flux of v-momentum is calculated for $diagnostic \hspace{.2cm} purposes
- \hspace{.2cm} only$ from the eddy coefficient for momentum:
- \[
- {\bf TVFLUX} =  {\rho } {(\overline{v^{\prime}w^{\prime}})} =
-  {\rho } {(- K_m \pp{V}{z})}
- \]
- \noindent
- where $\rho$ is the air density, and $K_m$ is the eddy coefficient.
- \\
- \noindent
- {\bf 25)  \underline {TTFLUX}  Turbulent Flux of Sensible Heat ($Watts/m^2$) }
- \noindent
- The turbulent flux of sensible heat is calculated for $diagnostic \hspace{.2cm} purposes
- \hspace{.2cm} only$ from the eddy coefficient for heat and moisture:
- \noindent
- \[
- {\bf TTFLUX} = c_p {\rho }
- P^{\kappa}{(\overline{w^{\prime}\theta^{\prime}})}
-  = c_p  {\rho } P^{\kappa}{(- K_h \pp{\theta_v}{z})}
- \]
- \noindent
- where $\rho$ is the air density, and $K_h$ is the eddy coefficient.
- \\
- \noindent
- {\bf 26)  \underline {TQFLUX}  Turbulent Flux of Latent Heat ($Watts/m^2$) }
- \noindent
- The turbulent flux of latent heat is calculated for $diagnostic \hspace{.2cm} purposes
- \hspace{.2cm} only$ from the eddy coefficient for heat and moisture:
- \noindent
- \[
- {\bf TQFLUX} = {L {\rho } (\overline{w^{\prime}q^{\prime}})} =
- {L {\rho }(- K_h \pp{q}{z})}
- \]
- \noindent
- where $\rho$ is the air density, and $K_h$ is the eddy coefficient.
- \\
- \noindent
- {\bf 27)  \underline {CN}  Neutral Drag Coefficient ($dimensionless$) }
- \noindent
- The drag coefficient for momentum obtained by assuming a neutrally stable surface layer:
- \[
- {\bf CN} = { k \over { \ln({h \over {z_0}})} }
- \]
- \noindent
- where $k$ is the Von Karman constant, $h$ is the height of the surface layer, and
- $z_0$ is the surface roughness.
- \noindent
- NOTE: CN is not available through model version 5.3, but is available in subsequent
- versions.
- \\
- \noindent
- {\bf 28)  \underline {WINDS}  Surface Wind Speed ($meter/sec$) }
- \noindent
- The surface wind speed is calculated for the last internal turbulence time step:
- \[
- {\bf WINDS} = \sqrt{u_{Nrphys}^2 + v_{Nrphys}^2}
- \]
- \noindent
- where the subscript $Nrphys$ refers to the lowest model level.
- \\
- \noindent
- {\bf 29)  \underline {DTSRF}  Air/Surface Virtual Temperature Difference ($deg \hspace{.1cm} K$) }
- \noindent
- The air/surface virtual temperature difference measures the stability of the surface layer:
- \[
- {\bf DTSRF} = (\theta_{v{Nrphys+1}} - \theta{v_{Nrphys}}) P^{\kappa}_{surf}
- \]
- \noindent
- where
- \[
- \theta_{v{Nrphys+1}} = { T_g \over {P^{\kappa}_{surf}} } (1 + .609 q_{Nrphys+1}) \hspace{1cm}
- and \hspace{1cm} q_{Nrphys+1} = q_{Nrphys} + \beta(q^*(T_g,P_s) - q_{Nrphys})
- \]
- \noindent
- $\beta$ is the surface potential evapotranspiration coefficient ($\beta=1$ over oceans),
- $q^*(T_g,P_s)$ is the saturation specific humidity at the ground temperature
- and surface pressure, level $Nrphys$ refers to the lowest model level and level $Nrphys+1$
- refers to the surface.
- \\
- \noindent
- {\bf 30)  \underline {TG}  Ground Temperature ($deg \hspace{.1cm} K$) }
- \noindent
- The ground temperature equation is solved as part of the turbulence package
- using a backward implicit time differencing scheme:
- \[
- {\bf TG} \hspace{.1cm} is \hspace{.1cm} obtained \hspace{.1cm} from: \hspace{.1cm}
- C_g\pp{T_g}{t} = R_{sw} - R_{lw} + Q_{ice} - H - LE
- \]
- \noindent
- where $R_{sw}$ is the net surface downward shortwave radiative flux, $R_{lw}$ is the
- net surface upward longwave radiative flux, $Q_{ice}$ is the heat conduction through
- sea ice, $H$ is the upward sensible heat flux, $LE$ is the upward latent heat
- flux, and $C_g$ is the total heat capacity of the ground.
- $C_g$ is obtained by solving a heat diffusion equation
- for the penetration of the diurnal cycle into the ground (Blackadar, 1977), and is given by:
- \[
- C_g = \sqrt{ {\lambda C_s \over {2 \omega} } } = \sqrt{(0.386 + 0.536W + 0.15W^2)2x10^{-3}
- { 86400. \over {2 \pi} } } \, \, .
- \]
- \noindent
- Here, the thermal conductivity, $\lambda$, is equal to $2x10^{-3}$ ${ly\over{ sec}}
- {cm \over {^oK}}$,
- the angular velocity of the earth, $\omega$, is written as $86400$ $sec/day$ divided
- by $2 \pi$ $radians/
- day$, and the expression for $C_s$, the heat capacity per unit volume at the surface,
- is a function of the ground wetness, $W$.
- \\
- \noindent
- {\bf 31)  \underline {TS}  Surface Temperature ($deg \hspace{.1cm} K$) }
- \noindent
- The surface temperature estimate is made by assuming that the model's lowest
- layer is well-mixed, and therefore that $\theta$ is constant in that layer.
- The surface temperature is therefore:
- \[
- {\bf TS} = \theta_{Nrphys} P^{\kappa}_{surf}
- \]
- \\
- \noindent
- {\bf 32)  \underline {DTG}  Surface Temperature Adjustment ($deg \hspace{.1cm} K$) }
- \noindent
- The change in surface temperature from one turbulence time step to the next, solved
- using the Ground Temperature Equation (see diagnostic number 30) is calculated:
- \[
- {\bf DTG} = {T_g}^{n} - {T_g}^{n-1}
- \]
- \noindent
- where superscript $n$ refers to the new, updated time level, and the superscript $n-1$
- refers to the value at the previous turbulence time level.
- \\
- \noindent
- {\bf 33)  \underline {QG}  Ground Specific Humidity ($g/kg$) }
- \noindent
- The ground specific humidity is obtained by interpolating between the specific
- humidity at the lowest model level and the specific humidity of a saturated ground.
- The interpolation is performed using the potential evapotranspiration function:
- \[
- {\bf QG} = q_{Nrphys+1} = q_{Nrphys} + \beta(q^*(T_g,P_s) - q_{Nrphys})
- \]
- \noindent
- where $\beta$ is the surface potential evapotranspiration coefficient ($\beta=1$ over oceans),
- and $q^*(T_g,P_s)$ is the saturation specific humidity at the ground temperature and surface
- pressure.
- \\
- \noindent
- {\bf 34)  \underline {QS}  Saturation Surface Specific Humidity ($g/kg$) }
- \noindent
- The surface saturation specific humidity is the saturation specific humidity at
- the ground temprature and surface pressure:
- \[
- {\bf QS} = q^*(T_g,P_s)
- \]
- \\
- \noindent
- {\bf 35)  \underline {TGRLW} Instantaneous ground temperature used as input to the Longwave
-  radiation subroutine (deg)}
- \[
- {\bf TGRLW}  = T_g(\lambda , \phi ,n)
- \]
- \noindent
- where $T_g$ is the model ground temperature at the current time step $n$.
- \\
- \noindent
- {\bf 36)  \underline {ST4} Upward Longwave flux at the surface ($Watts/m^2$) }
- \[
- {\bf ST4} = \sigma T^4
- \]
- \noindent
- where $\sigma$ is the Stefan-Boltzmann constant and T is the temperature.
- \\
- \noindent
- {\bf 37)  \underline {OLR} Net upward Longwave flux at $p=p_{top}$ ($Watts/m^2$) }
- \[
- {\bf OLR}  =  F_{LW,top}^{NET}
- \]
- \noindent
- where top indicates the top of the first model layer.
- In the GCM, $p_{top}$ = 0.0 mb.
- \\
- \noindent
- {\bf 38)  \underline {OLRCLR} Net upward clearsky Longwave flux at $p=p_{top}$ ($Watts/m^2$) }
- \[
- {\bf OLRCLR}  =  F(clearsky)_{LW,top}^{NET}
- \]
- \noindent
- where top indicates the top of the first model layer.
- In the GCM, $p_{top}$ = 0.0 mb.
- \\
- \noindent
- {\bf 39)  \underline {LWGCLR} Net upward clearsky Longwave flux at the surface ($Watts/m^2$) }
- \noindent
- \begin{eqnarray*}
- {\bf LWGCLR} & =  & F(clearsky)_{LW,Nrphys+1}^{Net} \\
-              & =  & F(clearsky)_{LW,Nrphys+1}^\uparrow - F(clearsky)_{LW,Nrphys+1}^\downarrow
- \end{eqnarray*}
- where Nrphys+1 indicates the lowest model edge-level, or $p = p_{surf}$.
- $F(clearsky)_{LW}^\uparrow$ is
- the upward clearsky Longwave flux and the $F(clearsky)_{LW}^\downarrow$ is the downward clearsky Longwave flux.
- \\
- \noindent
- {\bf 40)  \underline {LWCLR} Heating Rate due to Clearsky Longwave Radiation ($deg/day$) }
- \noindent
- The net longwave heating rate is calculated as the vertical divergence of the
- net terrestrial radiative fluxes.
- Both the clear-sky and cloudy-sky longwave fluxes are computed within the
- longwave routine.
- The subroutine calculates the clear-sky flux, $F^{clearsky}_{LW}$, first.
- For a given cloud fraction,
- the clear line-of-sight probability $C(p,p^{\prime})$ is computed from the current level pressure $p$
- to the model top pressure, $p^{\prime} = p_{top}$, and the model surface pressure, $p^{\prime} = p_{surf}$,
- for the upward and downward radiative fluxes.
- (see Section \ref{sec:fizhi:radcloud}).
- The cloudy-sky flux is then obtained as:
- \noindent
- \[
- F_{LW} = C(p,p') \cdot F^{clearsky}_{LW},
- \]
- \noindent
- Thus, {\bf LWCLR} is defined as the net longwave heating rate due to the
- vertical divergence of the
- clear-sky longwave radiative flux:
- \[
- \pp{\rho c_p T}{t}_{clearsky} = - {\partial \over \partial z} F(clearsky)_{LW}^{NET} ,
- \]
- or
- \[
- {\bf LWCLR} = \frac{g}{c_p \pi} {\partial \over \partial \sigma} F(clearsky)_{LW}^{NET} .
- \]
- \noindent
- where $g$ is the accelation due to gravity,
- $c_p$ is the heat capacity of air at constant pressure,
- and
- \[
- F(clearsky)_{LW}^{Net} = F(clearsky)_{LW}^\uparrow - F(clearsky)_{LW}^\downarrow
- \]
- \\
- \noindent
- {\bf 41)  \underline {TLW} Instantaneous temperature used as input to the Longwave
-  radiation subroutine (deg)}
- \[
- {\bf TLW}  = T(\lambda , \phi ,level, n)
- \]
- \noindent
- where $T$ is the model temperature at the current time step $n$.
- \\
- \noindent
- {\bf 42)  \underline {SHLW} Instantaneous specific humidity used as input to
-  the Longwave radiation subroutine (kg/kg)}
- \[
- {\bf SHLW}  = q(\lambda , \phi , level , n)
- \]
- \noindent
- where $q$ is the model specific humidity at the current time step $n$.
- \\
- \noindent
- {\bf 43)  \underline {OZLW} Instantaneous ozone used as input to
-  the Longwave radiation subroutine (kg/kg)}
- \[
- {\bf OZLW}  = {\rm OZ}(\lambda , \phi , level , n)
- \]
- \noindent
- where $\rm OZ$ is the interpolated ozone data set from the climatological monthly
- mean zonally averaged ozone data set.
- \\
- \noindent
- {\bf 44) \underline {CLMOLW} Maximum Overlap cloud fraction used in LW Radiation ($0-1$) }
- \noindent
- {\bf CLMOLW} is the time-averaged maximum overlap cloud fraction that has been filled by the Relaxed
- Arakawa/Schubert Convection scheme and will be used in the Longwave Radiation algorithm.  These are
- convective clouds whose radiative characteristics are assumed to be correlated in the vertical.
- For a complete description of cloud/radiative interactions, see Section \ref{sec:fizhi:radcloud}.
- \[
- {\bf CLMOLW} = CLMO_{RAS,LW}(\lambda, \phi,  level )
- \]
- \\
- {\bf 45) \underline {CLDTOT} Total cloud fraction used in LW and SW Radiation ($0-1$) }
- {\bf CLDTOT} is the time-averaged total cloud fraction that has been filled by the Relaxed
- Arakawa/Schubert and Large-scale Convection schemes and will be used in the Longwave and Shortwave
- Radiation packages.
- For a complete description of cloud/radiative interactions, see Section \ref{sec:fizhi:radcloud}.
- \[
- {\bf CLDTOT} = F_{RAS} + F_{LS}
- \]
- \\
- where $F_{RAS}$ is the time-averaged cloud fraction due to sub-grid scale convection, and $F_{LS}$ is the
- time-averaged cloud fraction due to precipitating and non-precipitating large-scale moist processes.
- \\
- \noindent
- {\bf 46) \underline {CLMOSW} Maximum Overlap cloud fraction used in SW Radiation ($0-1$) }
- \noindent
- {\bf CLMOSW} is the time-averaged maximum overlap cloud fraction that has been filled by the Relaxed
- Arakawa/Schubert Convection scheme and will be used in the Shortwave Radiation algorithm.  These are
- convective clouds whose radiative characteristics are assumed to be correlated in the vertical.
- For a complete description of cloud/radiative interactions, see Section \ref{sec:fizhi:radcloud}.
- \[
- {\bf CLMOSW} = CLMO_{RAS,SW}(\lambda, \phi,  level )
- \]
- \\
- \noindent
- {\bf 47) \underline {CLROSW} Random Overlap cloud fraction used in SW Radiation ($0-1$) }
- \noindent
- {\bf CLROSW} is the time-averaged random overlap cloud fraction that has been filled by the Relaxed
- Arakawa/Schubert and Large-scale Convection schemes and will be used in the Shortwave
- Radiation algorithm.  These are
- convective and large-scale clouds whose radiative characteristics are not
- assumed to be correlated in the vertical.
- For a complete description of cloud/radiative interactions, see Section \ref{sec:fizhi:radcloud}.
- \[
- {\bf CLROSW} = CLRO_{RAS,Large Scale,SW}(\lambda, \phi,  level )
- \]
- \\
- \noindent
- {\bf 48)  \underline {RADSWT} Incident Shortwave radiation at the top of the atmosphere ($Watts/m^2$) }
- \[
- {\bf RADSWT} = {\frac{S_0}{R_a^2}} \cdot cos \phi_z
- \]
- \noindent
- where $S_0$, is the extra-terrestial solar contant,
- $R_a$ is the earth-sun distance in Astronomical Units,
- and $cos \phi_z$ is the cosine of the zenith angle.
- It should be noted that {\bf RADSWT}, as well as
- {\bf OSR} and {\bf OSRCLR},
- are calculated at the top of the atmosphere (p=0 mb).  However, the
- {\bf OLR} and {\bf OLRCLR} diagnostics are currently
- calculated at $p= p_{top}$ (0.0 mb for the GCM).
- \\
- \noindent
- {\bf 49)  \underline {EVAP}  Surface Evaporation ($mm/day$) }
- \noindent
- The surface evaporation is a function of the gradient of moisture, the potential
- evapotranspiration fraction and the eddy exchange coefficient:
- \[
- {\bf EVAP} =  \rho \beta K_{h} (q_{surface} - q_{Nrphys})
- \]
- where $\rho$ = the atmospheric density at the surface, $\beta$ is the fraction of
- the potential evapotranspiration actually evaporated ($\beta=1$ over oceans), $K_{h}$ is the
- turbulent eddy exchange coefficient for heat and moisture at the surface in $m/sec$ and
- $q{surface}$ and $q_{Nrphys}$ are the specific humidity at the surface (see diagnostic
- number 34) and at the bottom model level, respectively.
- \\
- \noindent
- {\bf 50)  \underline {DUDT} Total Zonal U-Wind Tendency  ($m/sec/day$) }
- \noindent
- {\bf DUDT} is the total time-tendency of the Zonal U-Wind due to Hydrodynamic, Diabatic,
- and Analysis forcing.
- \[
- {\bf DUDT} = \pp{u}{t}_{Dynamics} + \pp{u}{t}_{Moist} + \pp{u}{t}_{Turbulence} + \pp{u}{t}_{Analysis}
- \]
- \\
- \noindent
- {\bf 51)  \underline {DVDT} Total Zonal V-Wind Tendency  ($m/sec/day$) }
- \noindent
- {\bf DVDT} is the total time-tendency of the Meridional V-Wind due to Hydrodynamic, Diabatic,
- and Analysis forcing.
- \[
- {\bf DVDT} = \pp{v}{t}_{Dynamics} + \pp{v}{t}_{Moist} + \pp{v}{t}_{Turbulence} + \pp{v}{t}_{Analysis}
- \]
- \\
- \noindent
- {\bf 52)  \underline {DTDT} Total Temperature Tendency  ($deg/day$) }
- \noindent
- {\bf DTDT} is the total time-tendency of Temperature due to Hydrodynamic, Diabatic,
- and Analysis forcing.
- \begin{eqnarray*}
- {\bf DTDT} & = & \pp{T}{t}_{Dynamics} + \pp{T}{t}_{Moist Processes} + \pp{T}{t}_{Shortwave Radiation} \\
-            & + & \pp{T}{t}_{Longwave Radiation} + \pp{T}{t}_{Turbulence} + \pp{T}{t}_{Analysis}
- \end{eqnarray*}
- \\
- \noindent
- {\bf 53)  \underline {DQDT} Total Specific Humidity Tendency  ($g/kg/day$) }
- \noindent
- {\bf DQDT} is the total time-tendency of Specific Humidity due to Hydrodynamic, Diabatic,
- and Analysis forcing.
- \[
- {\bf DQDT} = \pp{q}{t}_{Dynamics} + \pp{q}{t}_{Moist Processes}
- + \pp{q}{t}_{Turbulence} + \pp{q}{t}_{Analysis}
- \]
- \\
- \noindent
- {\bf 54)  \underline {USTAR}  Surface-Stress Velocity ($m/sec$) }
- \noindent
- The surface stress velocity, or the friction velocity, is the wind speed at
- the surface layer top impeded by the surface drag:
- \[
- {\bf USTAR} = C_uW_s \hspace{1cm}where: \hspace{.2cm}
- C_u = {k \over {\psi_m} }
- \]
- \noindent
- $C_u$ is the non-dimensional surface drag coefficient (see diagnostic
- number 10), and $W_s$ is the surface wind speed (see diagnostic number 28).
- \noindent
- {\bf 55)  \underline {Z0}  Surface Roughness Length ($m$) }
- \noindent
- Over the land surface, the surface roughness length is interpolated to the local
- time from the monthly mean data of Dorman and Sellers (1989). Over the ocean,
- the roughness length is a function of the surface-stress velocity, $u_*$.
- \[
- {\bf Z0} = c_1u^3_* + c_2u^2_* + c_3u_* + c_4 + {c_5 \over {u_*}}
- \]
- \noindent
- where the constants are chosen to interpolate between the reciprocal relation of
- Kondo(1975) for weak winds, and the piecewise linear relation of Large and Pond(1981)
- for moderate to large winds.
- \\
- \noindent
- {\bf 56)  \underline {FRQTRB}  Frequency of Turbulence ($0-1$) }
- \noindent
- The fraction of time when turbulence is present is defined as the fraction of
- time when the turbulent kinetic energy exceeds some minimum value, defined here
- to be $0.005 \hspace{.1cm}m^2/sec^2$. When this criterion is met, a counter is
- incremented. The fraction over the averaging interval is reported.
- \\
- \noindent
- {\bf 57)  \underline {PBL}  Planetary Boundary Layer Depth ($mb$) }
- \noindent
- The depth of the PBL is defined by the turbulence parameterization to be the
- depth at which the turbulent kinetic energy reduces to ten percent of its surface
- value.
- \[
- {\bf PBL} = P_{PBL} - P_{surface}
- \]
- \noindent
- where $P_{PBL}$ is the pressure in $mb$ at which the turbulent kinetic energy
- reaches one tenth of its surface value, and $P_s$ is the surface pressure.
- \\
- \noindent
- {\bf 58)  \underline {SWCLR} Clear sky Heating Rate due to Shortwave Radiation ($deg/day$) }
- \noindent
- The net Shortwave heating rate is calculated as the vertical divergence of the
- net solar radiative fluxes.
- The clear-sky and cloudy-sky shortwave fluxes are calculated separately.
- For the clear-sky case, the shortwave fluxes and heating rates are computed with
- both CLMO (maximum overlap cloud fraction) and
- CLRO (random overlap cloud fraction) set to zero (see Section \ref{sec:fizhi:radcloud}).
- The shortwave routine is then called a second time, for the cloudy-sky case, with the
- true time-averaged cloud fractions CLMO
- and CLRO being used.  In all cases, a normalized incident shortwave flux is used as
- input at the top of the atmosphere.
- \noindent
- The heating rate due to Shortwave Radiation under clear skies is defined as:
- \[
- \pp{\rho c_p T}{t} = - {\partial \over \partial z} F(clear)_{SW}^{NET} \cdot {\rm RADSWT},
- \]
- or
- \[
- {\bf SWCLR} = \frac{g}{c_p } {\partial \over \partial p} F(clear)_{SW}^{NET}\cdot {\rm RADSWT} .
- \]
- \noindent
- where $g$ is the accelation due to gravity,
- $c_p$ is the heat capacity of air at constant pressure, RADSWT is the true incident
- shortwave radiation at the top of the atmosphere (See Diagnostic \#48), and
- \[
- F(clear)_{SW}^{Net} = F(clear)_{SW}^\uparrow - F(clear)_{SW}^\downarrow
- \]
- \\
- \noindent
- {\bf 59)  \underline {OSR} Net upward Shortwave flux at the top of the model ($Watts/m^2$) }
- \[
- {\bf OSR}  =  F_{SW,top}^{NET}
- \]
- \noindent
- where top indicates the top of the first model layer used in the shortwave radiation
- routine.
- In the GCM, $p_{SW_{top}}$ = 0 mb.
- \\
- \noindent
- {\bf 60)  \underline {OSRCLR} Net upward clearsky Shortwave flux at the top of the model ($Watts/m^2$) }
- \[
- {\bf OSRCLR}  =  F(clearsky)_{SW,top}^{NET}
- \]
- \noindent
- where top indicates the top of the first model layer used in the shortwave radiation
- routine.
- In the GCM, $p_{SW_{top}}$ = 0 mb.
- \\
- \noindent
- {\bf 61)  \underline {CLDMAS} Convective Cloud Mass Flux ($kg/m^2$) }
- \noindent
- The amount of cloud mass moved per RAS timestep from all convective clouds is written:
- \[
- {\bf CLDMAS} = \eta m_B
- \]
- where $\eta$ is the entrainment, normalized by the cloud base mass flux, and $m_B$ is
- the cloud base mass flux. $m_B$ and $\eta$ are defined explicitly in Section \ref{sec:fizhi:mc}, the
- description of the convective parameterization.
- \\
- \noindent
- {\bf 62)  \underline {UAVE} Time-Averaged Zonal U-Wind ($m/sec$) }
- \noindent
- The diagnostic {\bf UAVE} is simply the time-averaged Zonal U-Wind over
- the {\bf NUAVE} output frequency.  This is contrasted to the instantaneous
- Zonal U-Wind which is archived on the Prognostic Output data stream.
- \[
- {\bf UAVE} = u(\lambda, \phi, level , t)
- \]
- \\
- Note, {\bf UAVE} is computed and stored on the staggered C-grid.
- \\
- \noindent
- {\bf 63)  \underline {VAVE} Time-Averaged Meridional V-Wind ($m/sec$) }
- \noindent
- The diagnostic {\bf VAVE} is simply the time-averaged Meridional V-Wind over
- the {\bf NVAVE} output frequency.  This is contrasted to the instantaneous
- Meridional V-Wind which is archived on the Prognostic Output data stream.
- \[
- {\bf VAVE} = v(\lambda, \phi, level , t)
- \]
- \\
- Note, {\bf VAVE} is computed and stored on the staggered C-grid.
- \\
- \noindent
- {\bf 64)  \underline {TAVE} Time-Averaged Temperature ($Kelvin$) }
- \noindent
- The diagnostic {\bf TAVE} is simply the time-averaged Temperature over
- the {\bf NTAVE} output frequency.  This is contrasted to the instantaneous
- Temperature which is archived on the Prognostic Output data stream.
- \[
- {\bf TAVE} = T(\lambda, \phi, level , t)
- \]
- \\
- \noindent
- {\bf 65)  \underline {QAVE} Time-Averaged Specific Humidity ($g/kg$) }
- \noindent
- The diagnostic {\bf QAVE} is simply the time-averaged Specific Humidity over
- the {\bf NQAVE} output frequency.  This is contrasted to the instantaneous
- Specific Humidity which is archived on the Prognostic Output data stream.
- \[
- {\bf QAVE} = q(\lambda, \phi, level , t)
- \]
- \\
- \noindent
- {\bf 66)  \underline {PAVE} Time-Averaged Surface Pressure - PTOP ($mb$) }
- \noindent
- The diagnostic {\bf PAVE} is simply the time-averaged Surface Pressure - PTOP over
- the {\bf NPAVE} output frequency.  This is contrasted to the instantaneous
- Surface Pressure - PTOP which is archived on the Prognostic Output data stream.
- \begin{eqnarray*}
- {\bf PAVE} & =  & \pi(\lambda, \phi, level , t) \\
-            & =  & p_s(\lambda, \phi, level , t) - p_T
- \end{eqnarray*}
- \\
- \noindent
- {\bf 67)  \underline {QQAVE} Time-Averaged Turbulent Kinetic Energy $(m/sec)^2$ }
- \noindent
- The diagnostic {\bf QQAVE} is simply the time-averaged prognostic Turbulent Kinetic Energy
- produced by the GCM Turbulence parameterization over
- the {\bf NQQAVE} output frequency.  This is contrasted to the instantaneous
- Turbulent Kinetic Energy which is archived on the Prognostic Output data stream.
- \[
- {\bf QQAVE} = qq(\lambda, \phi, level , t)
- \]
- \\
- Note, {\bf QQAVE} is computed and stored at the ``mass-point'' locations on the staggered C-grid.
- \\
- \noindent
- {\bf 68)  \underline {SWGCLR} Net downward clearsky Shortwave flux at the surface ($Watts/m^2$) }
- \noindent
- \begin{eqnarray*}
- {\bf SWGCLR} & =  & F(clearsky)_{SW,Nrphys+1}^{Net} \\
-              & =  & F(clearsky)_{SW,Nrphys+1}^\downarrow - F(clearsky)_{SW,Nrphys+1}^\uparrow
- \end{eqnarray*}
- \noindent
- \\
- where Nrphys+1 indicates the lowest model edge-level, or $p = p_{surf}$.
- $F(clearsky){SW}^\downarrow$ is
- the downward clearsky Shortwave flux and $F(clearsky)_{SW}^\uparrow$ is
- the upward clearsky Shortwave flux.
- \\
- \noindent
- {\bf 69)  \underline {SDIAG1} User-Defined Surface Diagnostic-1 }
- \noindent
- The GCM provides Users with a built-in mechanism for archiving user-defined
- diagnostics.  The generic diagnostic array QDIAG located in COMMON /DIAG/, and the associated
- diagnostic counters and pointers located in COMMON /DIAGP/,
- must be accessable in order to use the user-defined diagnostics (see Section \ref{sec:diagnostics:diagover}).
- A convenient method for incorporating all necessary COMMON files is to
- include the GCM {\em vstate.com} file in the routine which employs the
- user-defined diagnostics.
- \noindent
- In addition to enabling the user-defined diagnostic (ie., CALL SETDIAG(84)), the User must fill
- the QDIAG array with the desired quantity within the User's
- application program or within modified GCM subroutines, as well as increment
- the diagnostic counter at the time when the diagnostic is updated.
- The QDIAG location index for {\bf SDIAG1} and its corresponding counter is
- automatically defined as {\bf ISDIAG1} and {\bf NSDIAG1}, respectively, after the
- diagnostic has been enabled.
- The syntax for its use is given by
- \begin{verbatim}
-       do j=1,jm
-       do i=1,im
-       qdiag(i,j,ISDIAG1) = qdiag(i,j,ISDIAG1) + ...
-       enddo
-       enddo
-       NSDIAG1 = NSDIAG1 + 1
- \end{verbatim}
- The diagnostics defined in this manner will automatically be archived by the output routines.
- \\
- \noindent
- {\bf 70)  \underline {SDIAG2} User-Defined Surface Diagnostic-2 }
- \noindent
- The GCM provides Users with a built-in mechanism for archiving user-defined
- diagnostics.  For a complete description refer to Diagnostic \#84.
- The syntax for using the surface SDIAG2 diagnostic is given by
- \begin{verbatim}
-       do j=1,jm
-       do i=1,im
-       qdiag(i,j,ISDIAG2) = qdiag(i,j,ISDIAG2) + ...
-       enddo
-       enddo
-       NSDIAG2 = NSDIAG2 + 1
- \end{verbatim}
- The diagnostics defined in this manner will automatically be archived by the output routines.
- \\
- \noindent
- {\bf 71)  \underline {UDIAG1} User-Defined Upper-Air Diagnostic-1 }
- \noindent
- The GCM provides Users with a built-in mechanism for archiving user-defined
- diagnostics.  For a complete description refer to Diagnostic \#84.
- The syntax for using the upper-air UDIAG1 diagnostic is given by
- \begin{verbatim}
-       do L=1,Nrphys
-       do j=1,jm
-       do i=1,im
-       qdiag(i,j,IUDIAG1+L-1) = qdiag(i,j,IUDIAG1+L-1) + ...
-       enddo
-       enddo
-       enddo
-       NUDIAG1 = NUDIAG1 + 1
- \end{verbatim}
- The diagnostics defined in this manner will automatically be archived by the
- output programs.
- \\
- \noindent
- {\bf 72)  \underline {UDIAG2} User-Defined Upper-Air Diagnostic-2 }
- \noindent
- The GCM provides Users with a built-in mechanism for archiving user-defined
- diagnostics.  For a complete description refer to Diagnostic \#84.
- The syntax for using the upper-air UDIAG2 diagnostic is given by
- \begin{verbatim}
-       do L=1,Nrphys
-       do j=1,jm
-       do i=1,im
-       qdiag(i,j,IUDIAG2+L-1) = qdiag(i,j,IUDIAG2+L-1) + ...
-       enddo
-       enddo
-       enddo
-       NUDIAG2 = NUDIAG2 + 1
- \end{verbatim}
- The diagnostics defined in this manner will automatically be archived by the
- output programs.
- \\
- \noindent
- {\bf 73)  \underline {DIABU} Total Diabatic Zonal U-Wind Tendency  ($m/sec/day$) }
- \noindent
- {\bf DIABU} is the total time-tendency of the Zonal U-Wind due to Diabatic processes
- and the Analysis forcing.
- \[
- {\bf DIABU} = \pp{u}{t}_{Moist} + \pp{u}{t}_{Turbulence} + \pp{u}{t}_{Analysis}
- \]
- \\
- \noindent
- {\bf 74)  \underline {DIABV} Total Diabatic Meridional V-Wind Tendency  ($m/sec/day$) }
- \noindent
- {\bf DIABV} is the total time-tendency of the Meridional V-Wind due to Diabatic processes
- and the Analysis forcing.
- \[
- {\bf DIABV} = \pp{v}{t}_{Moist} + \pp{v}{t}_{Turbulence} + \pp{v}{t}_{Analysis}
- \]
- \\
- \noindent
- {\bf 75)  \underline {DIABT} Total Diabatic Temperature Tendency  ($deg/day$) }
- \noindent
- {\bf DIABT} is the total time-tendency of Temperature due to Diabatic processes
- and the Analysis forcing.
- \begin{eqnarray*}
- {\bf DIABT} & = & \pp{T}{t}_{Moist Processes} + \pp{T}{t}_{Shortwave Radiation} \\
-            & + & \pp{T}{t}_{Longwave Radiation} + \pp{T}{t}_{Turbulence} + \pp{T}{t}_{Analysis}
- \end{eqnarray*}
- \\
- If we define the time-tendency of Temperature due to Diabatic processes as
- \begin{eqnarray*}
- \pp{T}{t}_{Diabatic} & = & \pp{T}{t}_{Moist Processes} + \pp{T}{t}_{Shortwave Radiation} \\
-                      & + & \pp{T}{t}_{Longwave Radiation} + \pp{T}{t}_{Turbulence}
- \end{eqnarray*}
- then, since there are no surface pressure changes due to Diabatic processes, we may write
- \[
- \pp{T}{t}_{Diabatic} = {p^\kappa \over \pi }\pp{\pi \theta}{t}_{Diabatic}
- \]
- where $\theta = T/p^\kappa$.  Thus, {\bf DIABT} may be written as
- \[
- {\bf DIABT} = {p^\kappa \over \pi } \left( \pp{\pi \theta}{t}_{Diabatic} + \pp{\pi \theta}{t}_{Analysis} \right)
- \]
- \\
- \noindent
- {\bf 76)  \underline {DIABQ} Total Diabatic Specific Humidity Tendency  ($g/kg/day$) }
- \noindent
- {\bf DIABQ} is the total time-tendency of Specific Humidity due to Diabatic processes
- and the Analysis forcing.
- \[
- {\bf DIABQ} = \pp{q}{t}_{Moist Processes} + \pp{q}{t}_{Turbulence} + \pp{q}{t}_{Analysis}
- \]
- If we define the time-tendency of Specific Humidity due to Diabatic processes as
- \[
- \pp{q}{t}_{Diabatic} = \pp{q}{t}_{Moist Processes} + \pp{q}{t}_{Turbulence}
- \]
- then, since there are no surface pressure changes due to Diabatic processes, we may write
- \[
- \pp{q}{t}_{Diabatic} = {1 \over \pi }\pp{\pi q}{t}_{Diabatic}
- \]
- Thus, {\bf DIABQ} may be written as
- \[
- {\bf DIABQ} = {1 \over \pi } \left( \pp{\pi q}{t}_{Diabatic} + \pp{\pi q}{t}_{Analysis} \right)
- \]
- \\
- \noindent
- {\bf 77)  \underline {VINTUQ} Vertically Integrated Moisture Flux ($m/sec \cdot g/kg$) }
- \noindent
- The vertically integrated moisture flux due to the zonal u-wind is obtained by integrating
- $u q$ over the depth of the atmosphere at each model timestep,
- and dividing by the total mass of the column.
- \[
- {\bf VINTUQ} = \frac{ \int_{surf}^{top} u q \rho dz  } { \int_{surf}^{top} \rho dz  }
- \]
- Using $\rho \delta z = -{\delta p \over g} = - {1 \over g} \delta p$, we have
- \[
- {\bf VINTUQ} = { \int_0^1 u q dp  }
- \]
- \\
- \noindent
- {\bf 78)  \underline {VINTVQ} Vertically Integrated Moisture Flux ($m/sec \cdot g/kg$) }
- \noindent
- The vertically integrated moisture flux due to the meridional v-wind is obtained by integrating
- $v q$ over the depth of the atmosphere at each model timestep,
- and dividing by the total mass of the column.
- \[
- {\bf VINTVQ} = \frac{ \int_{surf}^{top} v q \rho dz  } { \int_{surf}^{top} \rho dz  }
- \]
- Using $\rho \delta z = -{\delta p \over g} = - {1 \over g} \delta p$, we have
- \[
- {\bf VINTVQ} = { \int_0^1 v q dp  }
- \]
- \\
- \noindent
- {\bf 79)  \underline {VINTUT} Vertically Integrated Heat Flux ($m/sec \cdot deg$) }
- \noindent
- The vertically integrated heat flux due to the zonal u-wind is obtained by integrating
- $u T$ over the depth of the atmosphere at each model timestep,
- and dividing by the total mass of the column.
- \[
- {\bf VINTUT} = \frac{ \int_{surf}^{top} u T \rho dz  } { \int_{surf}^{top} \rho dz  }
- \]
- Or,
- \[
- {\bf VINTUT} = { \int_0^1 u T dp  }
- \]
- \\
- \noindent
- {\bf 80)  \underline {VINTVT} Vertically Integrated Heat Flux ($m/sec \cdot deg$) }
- \noindent
- The vertically integrated heat flux due to the meridional v-wind is obtained by integrating
- $v T$ over the depth of the atmosphere at each model timestep,
- and dividing by the total mass of the column.
- \[
- {\bf VINTVT} = \frac{ \int_{surf}^{top} v T \rho dz  } { \int_{surf}^{top} \rho dz  }
- \]
- Using $\rho \delta z = -{\delta p \over g} $, we have
- \[
- {\bf VINTVT} = { \int_0^1 v T dp  }
- \]
- \\
- \noindent
- {\bf 81 \underline {CLDFRC} Total 2-Dimensional Cloud Fracton ($0-1$) }
- If we define the
- time-averaged random and maximum overlapped cloudiness as CLRO and
- CLMO respectively, then the probability of clear sky associated
- with random overlapped clouds at any level is (1-CLRO) while the probability of
- clear sky associated with maximum overlapped clouds at any level is (1-CLMO).
- The total clear sky probability is given by (1-CLRO)*(1-CLMO), thus
- the total cloud fraction at each  level may be obtained by
--(1-CLRO)*(1-CLMO).
- At any given level, we may define the clear line-of-site probability by
- appropriately accounting for the maximum and random overlap
- cloudiness.  The clear line-of-site probability is defined to be
- equal to the product of the clear line-of-site probabilities
- associated with random and maximum overlap cloudiness.  The clear
- line-of-site probability $C(p,p^{\prime})$ associated with maximum overlap clouds,
- from the current pressure $p$
- to the model top pressure, $p^{\prime} = p_{top}$, or the model surface pressure, $p^{\prime} = p_{surf}$,
- is simply 1.0 minus the largest maximum overlap cloud value along  the
- line-of-site, ie.
- $$1-MAX_p^{p^{\prime}} \left( CLMO_p \right)$$
- Thus, even in the time-averaged sense it is assumed that the
- maximum overlap clouds are correlated in the vertical.  The clear
- line-of-site probability associated with random overlap clouds is
- defined to be the product of the clear sky probabilities at each
- level along the line-of-site, ie.
- $$\prod_{p}^{p^{\prime}} \left( 1-CLRO_p \right)$$
- The total cloud fraction at a given level associated with a line-
- of-site calculation is given by
- $$1-\left( 1-MAX_p^{p^{\prime}} \left[ CLMO_p \right] \right)
-     \prod_p^{p^{\prime}} \left( 1-CLRO_p \right)$$
- \noindent
- The 2-dimensional net cloud fraction as seen from the top of the
- atmosphere is given by
- \[
- {\bf CLDFRC} = 1-\left( 1-MAX_{l=l_1}^{Nrphys} \left[ CLMO_l \right] \right)
-     \prod_{l=l_1}^{Nrphys} \left( 1-CLRO_l \right)
- \]
- \\
- For a complete description of cloud/radiative interactions, see Section \ref{sec:fizhi:radcloud}.
- \noindent
- {\bf 82)  \underline {QINT} Total Precipitable Water ($gm/cm^2$) }
- \noindent
- The Total Precipitable Water is defined as the vertical integral of the specific humidity,
- given by:
- \begin{eqnarray*}
- {\bf QINT} & = & \int_{surf}^{top} \rho q dz \\
-            & = & {\pi \over g} \int_0^1 q dp
- \end{eqnarray*}
- where we have used the hydrostatic relation
- $\rho \delta z = -{\delta p \over g} $.
- \\
- \noindent
- {\bf 83)  \underline {U2M}  Zonal U-Wind at 2 Meter Depth ($m/sec$) }
- \noindent
- The u-wind at the 2-meter depth is determined from the similarity theory:
- \[
- {\bf U2M} = {u_* \over k} \psi_{m_{2m}} {u_{sl} \over {W_s}} =
- { \psi_{m_{2m}} \over {\psi_{m_{sl}} }}u_{sl}
- \]
- \noindent
- where $\psi_m(2m)$ is the non-dimensional wind shear at two meters, and the subscript
- $sl$ refers to the height of the top of the surface layer. If the roughness height
- is above two meters, ${\bf U2M}$ is undefined.
- \\
- \noindent
- {\bf 84)  \underline {V2M}  Meridional V-Wind at 2 Meter Depth ($m/sec$) }
- \noindent
- The v-wind at the 2-meter depth is a determined from the similarity theory:
- \[
- {\bf V2M} = {u_* \over k} \psi_{m_{2m}} {v_{sl} \over {W_s}} =
- { \psi_{m_{2m}} \over {\psi_{m_{sl}} }}v_{sl}
- \]
- \noindent
- where $\psi_m(2m)$ is the non-dimensional wind shear at two meters, and the subscript
- $sl$ refers to the height of the top of the surface layer. If the roughness height
- is above two meters, ${\bf V2M}$ is undefined.
- \\
- \noindent
- {\bf 85)  \underline {T2M}  Temperature at 2 Meter Depth ($deg \hspace{.1cm} K$) }
- \noindent
- The temperature at the 2-meter depth is a determined from the similarity theory:
- \[
- {\bf T2M} = P^{\kappa} ({\theta* \over k} ({\psi_{h_{2m}}+\psi_g}) + \theta_{surf} ) =
- P^{\kappa}(\theta_{surf} + { {\psi_{h_{2m}}+\psi_g} \over {{\psi_{h_{sl}}+\psi_g}} }
- (\theta_{sl} - \theta_{surf}))
- \]
- where:
- \[
- \theta_* = - { (\overline{w^{\prime}\theta^{\prime}}) \over {u_*} }
- \]
- \noindent
- where $\psi_h(2m)$ is the non-dimensional temperature gradient at two meters, $\psi_g$ is
- the non-dimensional temperature gradient in the viscous sublayer, and the subscript
- $sl$ refers to the height of the top of the surface layer. If the roughness height
- is above two meters, ${\bf T2M}$ is undefined.
- \\
- \noindent
- {\bf 86)  \underline {Q2M}  Specific Humidity at 2 Meter Depth ($g/kg$) }
- \noindent
- The specific humidity at the 2-meter depth is determined from the similarity theory:
- \[
- {\bf Q2M} = P^{\kappa} ({q_* \over k} ({\psi_{h_{2m}}+\psi_g}) + q_{surf} ) =
- P^{\kappa}(q_{surf} + { {\psi_{h_{2m}}+\psi_g} \over {{\psi_{h_{sl}}+\psi_g}} }
- (q_{sl} - q_{surf}))
- \]
- where:
- \[
- q_* = - { (\overline{w^{\prime}q^{\prime}}) \over {u_*} }
- \]
- \noindent
- where $\psi_h(2m)$ is the non-dimensional temperature gradient at two meters, $\psi_g$ is
- the non-dimensional temperature gradient in the viscous sublayer, and the subscript
- $sl$ refers to the height of the top of the surface layer. If the roughness height
- is above two meters, ${\bf Q2M}$ is undefined.
- \\
- \noindent
- {\bf 87)  \underline {U10M}  Zonal U-Wind at 10 Meter Depth ($m/sec$) }
- \noindent
- The u-wind at the 10-meter depth is an interpolation between the surface wind
- and the model lowest level wind using the ratio of the non-dimensional wind shear
- at the two levels:
- \[
- {\bf U10M} = {u_* \over k} \psi_{m_{10m}} {u_{sl} \over {W_s}} =
- { \psi_{m_{10m}} \over {\psi_{m_{sl}} }}u_{sl}
- \]
- \noindent
- where $\psi_m(10m)$ is the non-dimensional wind shear at ten meters, and the subscript
- $sl$ refers to the height of the top of the surface layer.
- \\
- \noindent
- {\bf 88)  \underline {V10M}  Meridional V-Wind at 10 Meter Depth ($m/sec$) }
- \noindent
- The v-wind at the 10-meter depth is an interpolation between the surface wind
- and the model lowest level wind using the ratio of the non-dimensional wind shear
- at the two levels:
- \[
- {\bf V10M} = {u_* \over k} \psi_{m_{10m}} {v_{sl} \over {W_s}} =
- { \psi_{m_{10m}} \over {\psi_{m_{sl}} }}v_{sl}
- \]
- \noindent
- where $\psi_m(10m)$ is the non-dimensional wind shear at ten meters, and the subscript
- $sl$ refers to the height of the top of the surface layer.
- \\
- \noindent
- {\bf 89)  \underline {T10M}  Temperature at 10 Meter Depth ($deg \hspace{.1cm} K$) }
- \noindent
- The temperature at the 10-meter depth is an interpolation between the surface potential
- temperature and the model lowest level potential temperature using the ratio of the
- non-dimensional temperature gradient at the two levels:
- \[
- {\bf T10M} = P^{\kappa} ({\theta* \over k} ({\psi_{h_{10m}}+\psi_g}) + \theta_{surf} ) =
- P^{\kappa}(\theta_{surf} + { {\psi_{h_{10m}}+\psi_g} \over {{\psi_{h_{sl}}+\psi_g}} }
- (\theta_{sl} - \theta_{surf}))
- \]
- where:
- \[
- \theta_* = - { (\overline{w^{\prime}\theta^{\prime}}) \over {u_*} }
- \]
- \noindent
- where $\psi_h(10m)$ is the non-dimensional temperature gradient at two meters, $\psi_g$ is
- the non-dimensional temperature gradient in the viscous sublayer, and the subscript
- $sl$ refers to the height of the top of the surface layer.
- \\
- \noindent
- {\bf 90)  \underline {Q10M}  Specific Humidity at 10 Meter Depth ($g/kg$) }
- \noindent
- The specific humidity at the 10-meter depth is an interpolation between the surface specific
- humidity and the model lowest level specific humidity using the ratio of the
- non-dimensional temperature gradient at the two levels:
- \[
- {\bf Q10M} = P^{\kappa} ({q_* \over k} ({\psi_{h_{10m}}+\psi_g}) + q_{surf} ) =
- P^{\kappa}(q_{surf} + { {\psi_{h_{10m}}+\psi_g} \over {{\psi_{h_{sl}}+\psi_g}} }
- (q_{sl} - q_{surf}))
- \]
- where:
- \[
- q_* =  - { (\overline{w^{\prime}q^{\prime}}) \over {u_*} }
- \]
- \noindent
- where $\psi_h(10m)$ is the non-dimensional temperature gradient at two meters, $\psi_g$ is
- the non-dimensional temperature gradient in the viscous sublayer, and the subscript
- $sl$ refers to the height of the top of the surface layer.
- \\
- \noindent
- {\bf 91)  \underline {DTRAIN} Cloud Detrainment Mass Flux ($kg/m^2$) }
- The amount of cloud mass moved per RAS timestep at the cloud detrainment level is written:
- \[
- {\bf DTRAIN} = \eta_{r_D}m_B
- \]
- \noindent
- where $r_D$ is the detrainment level,
- $m_B$ is the cloud base mass flux, and $\eta$
- is the entrainment, defined in Section \ref{sec:fizhi:mc}.
- \\
- \noindent
- {\bf 92)  \underline {QFILL}  Filling of negative Specific Humidity ($g/kg/day$) }
- \noindent
- Due to computational errors associated with the numerical scheme used for
- the advection of moisture, negative values of specific humidity may be generated.  The
- specific humidity is checked for negative values after every dynamics timestep.  If negative
- values have been produced, a filling algorithm is invoked which redistributes moisture from
- below.  Diagnostic {\bf QFILL} is equal to the net filling needed
- to eliminate negative specific humidity, scaled to a per-day rate:
- \[
- {\bf QFILL} = q^{n+1}_{final} - q^{n+1}_{initial}
- \]
- where
- \[
- q^{n+1} = (\pi q)^{n+1} / \pi^{n+1}
- \]
  \subsection{Dos and Donts}
  \subsection{Diagnostics Reference}

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