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\subsection{Diagnostics--A Flexible Infrastructure} |
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\label{sec:pkg:diagnostics} |
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\begin{rawhtml} |
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<!-- CMIREDIR:package_diagnostics: --> |
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\end{rawhtml} |
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\subsubsection{Introduction} |
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\noindent |
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This section of the documentation describes the Diagnostics package available within |
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the GCM. A large selection of model diagnostics is available for output. |
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In addition to the diagnostic quantities pre-defined in the GCM, there exists |
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the option, in any experiment, to define a new diagnostic quantity and include it |
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as part of the diagnostic output with the addition of a single subroutine call in the |
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routine where the field is computed. As a matter of philosophy, no diagnostic is enabled |
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as default, thus each user must specify the exact diagnostic information required for an |
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experiment. This is accomplished by enabling the specific diagnostic of interest cataloged |
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in the Diagnostic Menu (see Section \ref{sec:diagnostics:menu}). Instructions for enabling |
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diagnostic output and defining new diagnostic quantities are found in Section |
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\ref{sec:diagnostics:usersguide} of this document. |
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\noindent |
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The Diagnostic Menu in this section of the manual is a listing of diagnostic quantities available |
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within the main (dynamics) part of the GCM. Additional diagnostic quantities, defined within the |
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different GCM packages, are available and are listed in the diagnostic menu subsection of |
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the manual section associated with each relevant package. Once a diagnostic is enabled, the |
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GCM will continually increment an array specifically allocated for that diagnostic whenever the |
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appropriate quantity is computed. A counter is defined which records how many times each diagnostic |
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quantity has been incremented. Several special diagnostics are included in the menu. Quantities |
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refered to as ``Counter Diagnostics'', are defined for selected diagnostics which record the |
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frequency at which a diagnostic is incremented separately for each model grid location. |
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Quantitied refered to as ``User Diagnostics'' are included in the menu to facilitate |
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defining new diagnostics for a particular experiment. |
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\subsubsection{Equations} |
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Not relevant. |
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\subsubsection{Key Subroutines and Parameters} |
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\label{sec:diagnostics:diagover} |
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\noindent |
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There are several utilities within the GCM available to users to enable, disable, |
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clear, write and retrieve model diagnostics, and may be called from any routine. |
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The available utilities and the CALL sequences are listed below. |
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\noindent |
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{\bf diagnostics\_fill}: This is the main user interface routine to the diagnostics |
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package. This routine will increment the specified diagnostic quantity with a field |
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sent through the argument list. |
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> call diagnostics\_fill (arrayin, chardiag, levflg, nlevs, \\ |
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\> bibjflg, bi, bj, myThid) \\ |
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\\ |
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where \> arrayin \>= Field to increment diagnostics array \\ |
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\> chardiag \>= Character *8 expression for diag to fill \\ |
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\> levflg \>= Integer flag for vertical levels: \\ |
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\> \>= 0 indicates multiple (nlevs) levels incremented \\ |
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\> \>= -1 indicates multiple (nlevs) levels incremented, \\ |
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\> \> but in reverse vertical order \\ |
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\> \> positive integer - WHICH single level to increment. \\ |
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\> nlevs \>= indicates Number of levels to be filled (1 if levflg gt 0) \\ |
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\> bibjflg \>= Integer flag to indicate instructions for bi bj loop \\ |
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\> \>= 0 indicates that the bi-bj loop must be done here \\ |
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\> \>= 1 indicates that the bi-bj loop is done OUTSIDE \\ |
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\> \>= 2 indicates that the bi-bj loop is done OUTSIDE \\ |
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\> \> AND that we have been sent a local array \\ |
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\> \> AND that the array has the shadow regions \\ |
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\> \>= 3 indicates that the bi-bj loop is done OUTSIDE \\ |
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\> \> AND that we have been sent a local array \\ |
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\> \> AND that the array has no shadow regions \\ |
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\> bi \>= X-direction process(or) number - used for bibjflg=1-3 \\ |
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\> bj \>= Y-direction process(or) number - used for bibjflg=1-3 \\ |
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\> myThid \>= Current Thread number \\ |
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\end{tabbing} |
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\noindent |
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{\bf diagnostics\_scale\_fill}: This is a possible alternative routine to |
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diagnostics\_fill which performs the same functions and has an additional option |
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to scale the field before filling or raise the field to a power before filling. |
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> call diagnostics\_scale\_fill (arrayin, scalefactor, power, chardiag, \\ |
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\> levflg, nlevs, bibjflg, bi, bj, myThid) \\ |
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\\ |
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where \> All the arguments are the same as for diagnostics\_fill with the addition of: \\ |
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\> scalefactor \>= Factor to scale field \\ |
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\> power \>= Integer power to which to raise the input field \\ |
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\end{tabbing} |
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\noindent |
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{\bf diagnostics\_is\_on}: Function call to inquire whether a diagnostic is active |
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and can be incremented. Useful when there is a computation that must be done locally |
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before a call to diagnostics\_fill. The call sequence: |
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> flag = diagnostics\_is\_on( diagName, myThid ) |
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\\ |
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where \> diagName \>= Character *8 expression for diagnostic \\ |
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\> myThid \>= Current Thread number \\ |
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\end{tabbing} |
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\noindent |
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{\bf diagnostics\_get\_pointers}: This subroutine retrieves the value of a the diagnostics |
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pointers that other routines require as input - can be useful if the diagnostics common |
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blocks are not local to a routine. |
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> call diagnostics\_get\_pointers( diagName, ipoint, jpoint, myThid ) |
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\\ |
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where \> diagName \>= Character *8 expression of diagnostic \\ |
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\> ipoint \>= Pointer into qdiag array - from idiag array in common \\ |
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\> jpoint \>= Pointer into diagnostics menu - from jdiag array in common \\ |
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\> myThid \>= Current Thread number \\ |
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\end{tabbing} |
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\noindent |
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{\bf getdiag}: This subroutine retrieves the value of a model diagnostic. This routine |
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is particulary useful when called from a user output routine, although it can be called |
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from any routine. This routine returns the time-averaged value of the diagnostic by |
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dividing the current accumulated diagnostic value by its corresponding counter. This |
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routine does not change the value of the diagnostic itself, that is, it does not replace |
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the diagnostic with its time-average. The calling sequence for this routine is givin by: |
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> call getdiag (lev, undef, qtmp, ipoint, mate, bi, bj, myThid) \\ |
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\\ |
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where \> lev \>= Model Level at which the diagnostic is desired \\ |
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\> undef \>= Fill value to be used when diagnostic is undefined \\ |
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\> qtmp \>= Time-Averaged Diagnostic Output \\ |
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\> ipoint \>= Pointer into qdiag array - from idiag array in common \\ |
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\> mate \>= Diagnostic mate pointer number \\ |
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\> bi \>= X-direction process(or) number \\ |
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\> bj \>= Y-direction process(or) number \\ |
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\> myThid \>= Current Thread number \\ |
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\end{tabbing} |
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\noindent |
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{\bf diagnostics\_add2list}: This subroutine enables a diagnostic from the Diagnostic Menu, meaning |
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that space is allocated for the diagnostic and the model routines will increment the |
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diagnostic value during execution. This routine is the underlying interface routine |
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for defining a new permanent diagnostic in the main model or in a package. The calling sequence is: |
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> call diagnostics\_add2list( diagNum,diagName, diagCode, \\ |
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\> diagUnits, diagTitle, myThid ) \\ |
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\\ |
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where \> diagNum \>=Diagnostic number - Output from routine \\ |
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\> diagName \>=character*8 diagnostic name \\ |
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\> diagCode \>=character*16 parsing code (see description of gdiag below) \\ |
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\> diagUnits \>=Diagnostic units (character*16) \\ |
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\> diagTitle \>=Diagnostic title or long name (up to character*80) \\ |
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\> myThid \>=Current Thread number \\ |
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\end{tabbing} |
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\noindent |
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{\bf clrdiag}: This subroutine initializes the values of model diagnostics to zero, and is |
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particularly useful when called from user output routines to re-initialize diagnostics |
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during the run. The calling sequence is: |
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> call diagnostics\_clrdiag (jpoint, ipoint, myThid) \\ |
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\\ |
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where \> jpoint \>= Diagnostic number from menu - from jdiag array \\ |
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ipoint \>= Pointer number into qdiag array - from idiag array \\ |
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\> myThid \>=Current Thread number \\ |
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\end{tabbing} |
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\noindent |
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The diagnostics are computed at various times and places within the GCM. Because the |
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MIT GCM may employ a staggered grid, diagnostics may be computed at grid box centers, |
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corners, or edges, and at the middle or edge in the vertical. Some diagnostics are scalars, |
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while others are components of vectors. An internal array is defined which contains |
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information concerning various grid attributes of each diagnostic. The GDIAG |
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array (in common block \\diagnostics in file DIAGNOSTICS.h) is internally defined as a |
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character*8 variable, and is equivalenced to a character*1 "parse" array in output in |
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order to extract the grid-attribute information. The GDIAG array is described in |
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Table \ref{tab:diagnostics:gdiag.tabl}. |
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\begin{table} |
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\caption{Diagnostic Parsing Array} |
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\label{tab:diagnostics:gdiag.tabl} |
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\begin{center} |
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\begin{tabular}{ |c|c|l| } |
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\hline |
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\multicolumn{3}{|c|}{\bf Diagnostic Parsing Array} \\ |
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\hline |
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\hline |
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Array & Value & Description \\ |
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\hline |
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parse(1) & $\rightarrow$ S & Scalar Diagnostic \\ |
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& $\rightarrow$ U & U-vector component Diagnostic \\ |
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& $\rightarrow$ V & V-vector component Diagnostic \\ \hline |
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parse(2) & $\rightarrow$ U & C-Grid U-Point \\ |
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& $\rightarrow$ V & C-Grid V-Point \\ |
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& $\rightarrow$ M & C-Grid Mass Point \\ |
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& $\rightarrow$ Z & C-Grid Vorticity (Corner) Point \\ \hline |
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parse(3) & $\rightarrow$ R & Not Currently in Use \\ \hline |
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parse(4) & $\rightarrow$ P & Positive Definite Diagnostic \\ \hline |
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parse(5) & $\rightarrow$ C & Counter Diagnostic \\ |
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& $\rightarrow$ D & Disabled Diagnostic for output \\ \hline |
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parse(6-8) & $\rightarrow$ C & 3-digit integer corresponding to \\ |
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& & vector or counter component mate \\ \hline |
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\end{tabular} |
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\addcontentsline{lot}{section}{Table 3: Diagnostic Parsing Array} |
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\end{center} |
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\end{table} |
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\noindent |
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As an example, consider a diagnostic whose associated GDIAG parameter is equal |
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to ``UU 002''. From GDIAG we can determine that this diagnostic is a |
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U-vector component located at the C-grid U-point. |
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Its corresponding V-component diagnostic is located in Diagnostic \# 002. |
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\noindent |
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In this way, each Diagnostic in the model has its attributes (ie. vector or scalar, |
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C-grid location, etc.) defined internally. The Output routines use this information |
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in order to determine what type of transformations need to be performed. Any |
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interpolations are done at the time of output rather than during each model step. |
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In this way the User has flexibility in determining the type of gridded data which |
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is output. |
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\subsubsection{Usage Notes} |
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\label{sec:diagnostics:usersguide} |
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\noindent |
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To use the diagnostics package, other than enabling it in packages.conf |
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and turning the usediagnostics flag in data.pkg to .TRUE., there are two |
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further steps the user must take to enable the diagnostics package for |
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output of quantities that are already defined in the GCM under an experiment's |
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configuration of packages. A namelist must be supplied in the run directory |
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called data.diagnostics, and the file DIAGNOSTICS\_SIZE.h must be included in the |
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code directory. The steps for defining a new (permanent or experiment-specific |
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temporary) diagnostic quantity will be outlined later. |
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\noindent The namelist will activate a user-defined list of diagnostics quantities |
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to be computed, specify the frequency and type of output, the number of levels, and |
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the name of all the separate output files. A sample data.diagnostics namelist file: |
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\noindent |
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$\#$ Diagnostic Package Choices \\ |
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$\&$diagnostics\_list \\ |
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frequency(1) = 86400., \ \\ |
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levels(1,1) = 1., \ \\ |
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fields(1,1) = 'RSURF ', \ \\ |
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filename(1) = 'surface', \ \\ |
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frequency(2) = 86400., \ \\ |
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levels(1,2) = 1.,2.,3.,4.,5., \ \\ |
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fields(1,2) = 'UVEL ','VVEL ', \ \\ |
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filename(2) = 'diagout1', \ \\ |
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frequency(3) = 3600., \ \\ |
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fields(1,3) = 'UVEL ','VVEL ','PRESSURE', \ \\ |
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filename(3) = 'diagout2', \ \\ |
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fileflags(3) = ' P1 ', \ \\ |
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$\&$end \ \\ |
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\noindent |
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In this example, there are two output files that will be generated |
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for each tile and for each output time. The first set of output files |
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has the prefix diagout1, does time averaging every 86400. seconds, |
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(frequency is 86400.), and will write fields which are multiple-level |
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fields at output levels 1-5. The names of diagnostics quantities are |
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UVEL and VVEL. The second set of output files |
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has the prefix diagout2, does time averaging every 3600. seconds, |
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includes fields which are multiple-level fields, levels output are 1-5, |
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and the names of diagnostics quantities are THETA and SALT. |
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\noindent |
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The user must assure that enough computer memory is allocated for the diagnostics |
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and the output streams selected for a particular experiment. This is acomplished by |
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modifying the file DIAGNOSTICS\_SIZE.h and including it in the experiment code directory. |
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The parameters that should be checked are called numdiags, numlists, numperlist, and |
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diagSt\_size. |
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\noindent numdiags (and diagSt\_size): \\ |
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\noindent All GCM diagnostic quantities are stored in the single diagnostic array QDIAG |
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which is located in the file \\ \filelink{pkg/diagnostics/DIAGNOSTICS.h}{pkg-diagnostics-DIAGNOSTICS.h}.\\ |
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and has the form:\\ |
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common /diagnostics/ qdiag(1-Olx,sNx+Olx,1-Olx,sNx+Olx,numdiags,Nsx,Nsy) \\ |
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\noindent |
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The first two-dimensions of qdiag correspond to the horizontal dimension of a given diagnostic, |
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and the third dimension of qdiag is used to identify diagnostic fields and levels combined. In |
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order to minimize the memory requirement of the model for diagnostics, the default GCM |
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executable is compiled with room for only one horizontal diagnostic array, or with |
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numdiags set to Nr. In order for the User to enable more than 1 three-dimensional diagnostic, |
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the size of the diagnostics common must be expanded to accomodate the desired diagnostics. |
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This can be accomplished by manually changing the parameter numdiags in the |
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file \filelink{pkg/diagnostics/DIAGNOSTICS\_SIZE.h}{pkg-diagnostics-DIAGNOSTICS\_SIZE.h}. |
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numdiags should be set greater than or equal to the sum of all the diagnostics activated |
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for output each multiplied by the number of levels defined for that diagnostic quantity. |
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For the above example, there are 4 multiple level fields, which the diagnostics menu |
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(see below) indicates are defined at the GCM vertical resolution, Nr. The value of |
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numdiag in DIAGNOSTICS\_SIZE.h would therefore be equal to 4*Nr, or, say 40 if $Nr=10$. |
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\noindent numlists and numperlist: \\ |
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\noindent The parameter numlists must be set greater than or equal to the number of |
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separate output streams that the user specifies in the namelist file data.diagnostics. |
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The parameter numperlist corresponds to the number of diagnostics requested in each |
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output stream. |
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\noindent |
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In order to define and include as part of the diagnostic output any field |
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that is desired for a particular experiment, two steps must be taken. The |
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first is to enable the ``User Diagnostic'' in data.diagnostics. This is |
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accomplished by adding one of the ``User Diagnostic'' field names (UDIAG1 through |
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UDIAG10, for multi-level fields, or SDIAG1 through SDIAG10 for single level |
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fields) to the data.diagnostics namelist in one of the output streams. These |
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fields are listed in the diagnostics menu. The second step is to |
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add a call to diagnostics\_fill from the subroutine in which the quantity |
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desired for diagnostic output is computed. |
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\noindent |
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In order to add a new diagnostic to the permanent set of diagnostics that the |
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main model or any package contains as part of its diagnostics menu, the subroutine |
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diagnostics\_add2list should be called during the initialization phase of the |
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main model or package. For the main model, the call should be made from |
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subroutine diagnostics\_main\_init, and for a package, the call should probably |
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be made from somewhere in the packages\_init\_fixed sequence (probaby from inside |
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the particular package's init\_fixed routine). A typical code sequence to set the |
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input arguments to diagnostics\_add2list would look like: |
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> diagName = 'THETA ' \\ |
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\> diagTitle = 'Potential Temperature (degC,K)' \\ |
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\> diagUnits = 'Degrees K ' \\ |
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\> diagCode = 'SM MR ' \\ |
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\> CALL DIAGNOSTICS\_ADD2LIST( diagNum, \\ |
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\> I diagName, diagCode, diagUnits, diagTitle, myThid ) \\ |
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\\ |
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\end{tabbing} |
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\noindent If the new diagnostic quantity is associated with either a vector |
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pair or a diagnostic counter, the diagCode argument must be filled with the |
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proper index for the ``mate''. The output argument from diagnostics\_add2list |
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that is called diagNum here contains a running total of the number of diagnostics |
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defined in the code up to any point during the run. The sequence number for the |
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next two diagnostics defined (the two components of the vector pair, for instance) |
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will be diagNum+1 and diagNum+2. The definition of the first component of the vector |
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pair must fill the ``mate'' segment of the diagCode as diagnostic number diagNum+2. |
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Since the subroutine increments diagNum, the definition of the second component of |
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the vector fills the ``mate'' part of diagCode with diagNum. A code sequence for |
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this case would look like: |
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|
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\noindent |
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\begin{tabbing} |
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XXXXXXXXX\=XXXXXX\= \kill |
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\> diagName = 'UVEL ' \\ |
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\> diagTitle = 'Zonal Velocity ' \\ |
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\> diagUnits = 'm / sec ' \\ |
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\> diagCode = 'SM MR ' \\ |
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\> write(diagCode,'(A,I3.3,A)') 'VV ', diagNum+2 ,'MR ' \\ |
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\> call diagnostics\_add2list( diagNum, \\ |
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\> I diagName, diagCode, diagUnits, diagTitle, myThid ) \\ |
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\> diagName = 'VVEL ' \\ |
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\> diagTitle = 'Meridional Velocity ' \\ |
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\> diagUnits = 'm / sec ' \\ |
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\> diagCode = 'SM MR ' \\ |
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\> write(diagCode,'(A,I3.3,A)') 'VV ', diagNum ,'MR ' \\ |
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\> call diagnostics\_add2list( diagNum, \\ |
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\> I diagName, diagCode, diagUnits, diagTitle, myThid ) \\ |
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\\ |
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\end{tabbing} |
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\input{part7/diagnostics-menu.tex} |
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\newpage |
| 384 |
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\noindent For a list of the diagnostic fields available in the |
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different MITgcm packages, follow the link to the diagnostics menu |
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in the manual section describing the package: |
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|
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\filelink{part6/fizhi-diagnostics-menu.tex}{pkg-fizhi-fizhi-diagnostics-menu.tex} |
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\subsubsection{Dos and Donts} |
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|
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\subsubsection{Diagnostics Reference} |
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