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edhill |
1.2 |
\section{Diagnostics--A Flexible Infrastructure} |
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molod |
1.1 |
\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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edhill |
1.2 |
\subsection{Introduction} |
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\noindent |
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edhill |
1.2 |
This section of the documentation describes the Diagnostics package |
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available within the GCM. A large selection of model diagnostics is |
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available for output. In addition to the diagnostic quantities |
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pre-defined in the GCM, there exists the option, in any experiment, to |
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define a new diagnostic quantity and include it as part of the |
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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 |
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diagnostic is enabled as default, thus each user must specify the |
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exact diagnostic information required for an experiment. This is |
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accomplished by enabling the specific diagnostic of interest cataloged |
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in the Diagnostic Menu (see Section \ref{sec:diagnostics:menu}). |
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Instructions for enabling diagnostic output and defining new |
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diagnostic quantities are found in Section |
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1.1 |
\ref{sec:diagnostics:usersguide} of this document. |
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\noindent |
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edhill |
1.2 |
The Diagnostic Menu in this section of the manual is a listing of |
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diagnostic quantities available within the main (dynamics) part of the |
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GCM. Additional diagnostic quantities, defined within the different |
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GCM packages, are available and are listed in the diagnostic menu |
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subsection of the manual section associated with each relevant |
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package. Once a diagnostic is enabled, the GCM will continually |
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increment an array specifically allocated for that diagnostic whenever |
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the appropriate quantity is computed. A counter is defined which |
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records how many times each diagnostic quantity has been incremented. |
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Several special diagnostics are included in the menu. Quantities |
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refered to as ``Counter Diagnostics'', are defined for selected |
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diagnostics which record the frequency at which a diagnostic is |
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incremented separately for each model grid location. Quantitied |
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refered to as ``User Diagnostics'' are included in the menu to |
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facilitate defining new diagnostics for a particular experiment. |
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1.1 |
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edhill |
1.2 |
\subsection{Equations} |
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molod |
1.1 |
Not relevant. |
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edhill |
1.2 |
\subsection{Key Subroutines and Parameters} |
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1.1 |
\label{sec:diagnostics:diagover} |
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\noindent |
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edhill |
1.2 |
There are several utilities within the GCM available to users to |
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enable, disable, clear, write and retrieve model diagnostics, and may |
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be called from any routine. The available utilities and the CALL |
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sequences are listed below. |
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\noindent |
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{\bf diagnostics\_fill}: This is the main user interface routine to |
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the diagnostics package. This routine will increment the specified |
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diagnostic quantity with a field sent through the argument list. |
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\begin{verbatim} |
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call diagnostics_fill( |
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& arrayin, chardiag, levflg, nlevs, |
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& bibjflg, bi, bj, myThid ) |
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where: |
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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{verbatim} |
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molod |
1.1 |
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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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edhill |
1.2 |
\begin{verbatim} |
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call diagnostics_scale_fill( |
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& arrayin, scalefactor, power, chardiag, |
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& levflg, nlevs, bibjflg, bi, bj, myThid ) |
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where all the arguments are the same as for diagnostics_fill with |
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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{verbatim} |
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\noindent |
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{\bf diagnostics\_is\_on}: Function call to inquire whether a |
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diagnostic is active and can be incremented. Useful when there is a |
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computation that must be done locally before a call to |
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diagnostics\_fill. The call sequence: |
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\begin{verbatim} |
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flag = diagnostics_is_on( diagName, myThid ) |
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where: |
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diagName = Character *8 expression for diagnostic |
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myThid = Current Thread number |
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\end{verbatim} |
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\noindent |
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{\bf diagnostics\_get\_pointers}: This subroutine retrieves the value |
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of a the diagnostics pointers that other routines require as input - |
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can be useful if the diagnostics common blocks are not local to a |
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routine. |
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\begin{verbatim} |
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call diagnostics_get_pointers( diagName, ipoint, jpoint, myThid ) |
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where: |
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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{verbatim} |
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\noindent |
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{\bf getdiag}: This subroutine retrieves the value of a model |
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diagnostic. This routine is particulary useful when called from a |
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user output routine, although it can be called from any routine. This |
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routine returns the time-averaged value of the diagnostic by dividing |
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the current accumulated diagnostic value by its corresponding counter. |
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This routine does not change the value of the diagnostic itself, that |
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is, it does not replace the diagnostic with its time-average. The |
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calling sequence for this routine is givin by: |
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\begin{verbatim} |
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call getdiag (lev, undef, qtmp, ipoint, mate, bi, bj, myThid) |
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where: |
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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{verbatim} |
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\noindent |
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{\bf diagnostics\_add2list}: This subroutine enables a diagnostic from |
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the Diagnostic Menu, meaning that space is allocated for the |
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diagnostic and the model routines will increment the diagnostic value |
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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 |
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package. The calling sequence is: |
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\begin{verbatim} |
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call diagnostics_add2list( diagNum,diagName, diagCode, |
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diagUnits, diagTitle, myThid ) |
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where: |
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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{verbatim} |
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\noindent |
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{\bf clrdiag}: This subroutine initializes the values of model |
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diagnostics to zero, and is particularly useful when called from user |
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output routines to re-initialize diagnostics during the run. The |
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calling sequence is: |
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\begin{verbatim} |
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call diagnostics_clrdiag (jpoint, ipoint, myThid) |
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where: |
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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{verbatim} |
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\noindent |
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The diagnostics are computed at various times and places within the |
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GCM. Because MITgcm may employ a staggered grid, diagnostics may be |
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computed at grid box centers, corners, or edges, and at the middle or |
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edge in the vertical. Some diagnostics are scalars, while others are |
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components of vectors. An internal array is defined which contains |
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information concerning various grid attributes of each diagnostic. The |
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GDIAG array (in common block {\tt diagnostics} in file {\tt |
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DIAGNOSTICS.h}) is internally defined as a character*8 variable, and |
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is equivalenced to a character*1 "parse" array in output in order to |
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extract the grid-attribute information. The GDIAG array is described |
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in Table \ref{tab:diagnostics:gdiag.tabl}. |
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molod |
1.1 |
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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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edhill |
1.2 |
\subsection{Usage Notes} |
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molod |
1.1 |
\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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edhill |
1.2 |
\begin{verbatim} |
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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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\end{verbatim} |
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\noindent |
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In this example, there are two output files that will be generated for |
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each tile and for each output time. The first set of output files has |
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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 has the prefix |
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diagout2, does time averaging every 3600. seconds, includes fields |
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which are multiple-level fields, levels output are 1-5, and the names |
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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 |
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diagnostics and the output streams selected for a particular |
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experiment. This is acomplished by modifying the file |
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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, |
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numperlist, and diagSt\_size. |
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molod |
1.1 |
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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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edhill |
1.2 |
\begin{verbatim} |
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common /diagnostics/ |
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& qdiag(1-Olx,sNx+Olx,1-Olx,sNx+Olx,numdiags,Nsx,Nsy) |
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\end{verbatim} |
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\noindent |
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The first two-dimensions of qdiag correspond to the horizontal |
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dimension of a given diagnostic, and the third dimension of qdiag is |
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used to identify diagnostic fields and levels combined. In order to |
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minimize the memory requirement of the model for diagnostics, the |
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default GCM executable is compiled with room for only one horizontal |
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diagnostic array, or with numdiags set to Nr. In order for the User to |
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enable more than 1 three-dimensional diagnostic, the size of the |
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diagnostics common must be expanded to accomodate the desired |
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diagnostics. This can be accomplished by manually changing the |
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parameter numdiags in the file |
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\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 |
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diagnostics activated for output each multiplied by the number of |
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levels defined for that diagnostic quantity. For the above example, |
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there are 4 multiple level fields, which the diagnostics menu (see |
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below) indicates are defined at the GCM vertical resolution, Nr. The |
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value of numdiag in DIAGNOSTICS\_SIZE.h would therefore be equal to |
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4*Nr, or, say 40 if $Nr=10$. |
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molod |
1.1 |
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\noindent numlists and numperlist: \\ |
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edhill |
1.2 |
\noindent The parameter numlists must be set greater than or equal to |
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the number of separate output streams that the user specifies in the |
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namelist file data.diagnostics. The parameter numperlist corresponds |
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to the number of diagnostics requested in each output stream. |
| 337 |
|
|
|
| 338 |
|
|
\noindent |
| 339 |
|
|
In order to define and include as part of the diagnostic output any |
| 340 |
|
|
field that is desired for a particular experiment, two steps must be |
| 341 |
|
|
taken. The first is to enable the ``User Diagnostic'' in |
| 342 |
|
|
data.diagnostics. This is accomplished by adding one of the ``User |
| 343 |
|
|
Diagnostic'' field names (UDIAG1 through UDIAG10, for multi-level |
| 344 |
|
|
fields, or SDIAG1 through SDIAG10 for single level fields) to the |
| 345 |
|
|
data.diagnostics namelist in one of the output streams. These fields |
| 346 |
|
|
are listed in the diagnostics menu. The second step is to add a call |
| 347 |
|
|
to diagnostics\_fill from the subroutine in which the quantity desired |
| 348 |
|
|
for diagnostic output is computed. |
| 349 |
|
|
|
| 350 |
|
|
\noindent |
| 351 |
|
|
In order to add a new diagnostic to the permanent set of diagnostics |
| 352 |
|
|
that the main model or any package contains as part of its diagnostics |
| 353 |
|
|
menu, the subroutine diagnostics\_add2list should be called during the |
| 354 |
|
|
initialization phase of the main model or package. For the main model, |
| 355 |
|
|
the call should be made from subroutine diagnostics\_main\_init, and |
| 356 |
|
|
for a package, the call should probably be made from somewhere in the |
| 357 |
|
|
packages\_init\_fixed sequence (probaby from inside the particular |
| 358 |
|
|
package's init\_fixed routine). A typical code sequence to set the |
| 359 |
molod |
1.1 |
input arguments to diagnostics\_add2list would look like: |
| 360 |
|
|
|
| 361 |
edhill |
1.2 |
\begin{verbatim} |
| 362 |
|
|
diagName = 'THETA ' |
| 363 |
|
|
diagTitle = 'Potential Temperature (degC,K)' |
| 364 |
|
|
diagUnits = 'Degrees K ' |
| 365 |
|
|
diagCode = 'SM MR ' |
| 366 |
|
|
CALL DIAGNOSTICS\_ADD2LIST( diagNum, |
| 367 |
|
|
I diagName, diagCode, diagUnits, diagTitle, myThid ) |
| 368 |
|
|
\end{verbatim} |
| 369 |
|
|
|
| 370 |
|
|
\noindent If the new diagnostic quantity is associated with either a |
| 371 |
|
|
vector pair or a diagnostic counter, the diagCode argument must be |
| 372 |
|
|
filled with the proper index for the ``mate''. The output argument |
| 373 |
|
|
from diagnostics\_add2list that is called diagNum here contains a |
| 374 |
|
|
running total of the number of diagnostics defined in the code up to |
| 375 |
|
|
any point during the run. The sequence number for the next two |
| 376 |
|
|
diagnostics defined (the two components of the vector pair, for |
| 377 |
|
|
instance) will be diagNum+1 and diagNum+2. The definition of the first |
| 378 |
|
|
component of the vector pair must fill the ``mate'' segment of the |
| 379 |
|
|
diagCode as diagnostic number diagNum+2. Since the subroutine |
| 380 |
|
|
increments diagNum, the definition of the second component of the |
| 381 |
|
|
vector fills the ``mate'' part of diagCode with diagNum. A code |
| 382 |
|
|
sequence for this case would look like: |
| 383 |
|
|
|
| 384 |
|
|
\begin{verbatim} |
| 385 |
|
|
diagName = 'UVEL ' |
| 386 |
|
|
diagTitle = 'Zonal Velocity ' |
| 387 |
|
|
diagUnits = 'm / sec ' |
| 388 |
|
|
diagCode = 'SM MR ' |
| 389 |
|
|
write(diagCode,'(A,I3.3,A)') 'VV ', diagNum+2 ,'MR ' |
| 390 |
|
|
call diagnostics\_add2list( diagNum, |
| 391 |
|
|
I diagName, diagCode, diagUnits, diagTitle, myThid ) |
| 392 |
|
|
diagName = 'VVEL ' |
| 393 |
|
|
diagTitle = 'Meridional Velocity ' |
| 394 |
|
|
diagUnits = 'm / sec ' |
| 395 |
|
|
diagCode = 'SM MR ' |
| 396 |
|
|
write(diagCode,'(A,I3.3,A)') 'VV ', diagNum ,'MR ' |
| 397 |
|
|
call diagnostics\_add2list( diagNum, |
| 398 |
|
|
I diagName, diagCode, diagUnits, diagTitle, myThid ) |
| 399 |
|
|
\end{verbatim} |
| 400 |
molod |
1.1 |
|
| 401 |
jmc |
1.8 |
\input{s_outp_pkgs/text/diagnostics-menu.tex} |
| 402 |
molod |
1.1 |
|
| 403 |
|
|
\newpage |
| 404 |
|
|
\noindent For a list of the diagnostic fields available in the |
| 405 |
|
|
different MITgcm packages, follow the link to the diagnostics menu |
| 406 |
|
|
in the manual section describing the package: |
| 407 |
|
|
|
| 408 |
edhill |
1.5 |
\begin{itemize} |
| 409 |
|
|
\item aim: \ref{sec:pkg:aim:diagnostics} |
| 410 |
|
|
\item exf: \ref{sec:pkg:exf:diagnostics} |
| 411 |
|
|
\item gchem: \ref{sec:pkg:gchem:diagnostics} |
| 412 |
molod |
1.6 |
\item generic\_advdiff: \ref{sec:pkg:gad:diagnostics} |
| 413 |
edhill |
1.5 |
\item gridalt: \ref{sec:pkg:gridalt:diagnostics} |
| 414 |
|
|
\item gmredi: \ref{sec:pkg:gmredi:diagnostics} |
| 415 |
|
|
\item fizhi: \ref{sec:pkg:fizhi:diagnostics} |
| 416 |
|
|
\item kpp: \ref{sec:pkg:kpp:diagnostics} |
| 417 |
|
|
\item land: \ref{sec:pkg:land:diagnostics} |
| 418 |
|
|
\item mom\_common: \ref{sec:pkg:mom_common:diagnostics} |
| 419 |
|
|
\item obcs: \ref{sec:pkg:obcs:diagnostics} |
| 420 |
|
|
\item thsice: \ref{sec:pkg:thsice:diagnostics} |
| 421 |
|
|
\item shap\_filt: \ref{sec:pkg:shap_filt:diagnostics} |
| 422 |
molod |
1.7 |
\item ptracers: \ref{sec:pkg:ptracers:diagnostics} |
| 423 |
edhill |
1.5 |
\end{itemize} |
| 424 |
molod |
1.1 |
|
| 425 |
edhill |
1.2 |
\subsection{Dos and Donts} |
| 426 |
molod |
1.1 |
|
| 427 |
edhill |
1.2 |
\subsection{Diagnostics Reference} |
| 428 |
molod |
1.1 |
|
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