[mpas-developers] specifying tracers

[Michael Duda]

Hi, Mark.

The parser in the registry code is pretty basic, and is sensitive to
whitespace before and after the parentheses. Adding a space after the
'(' should fix the error you're seeing. Specifically, the new entries
should look like:

var real    temperature ( nVertLevels nCells Time ) iro temperature tracers dynamics
var real    salinity ( nVertLevels nCells Time ) iro salinity tracers dynamics

Cheers,
Michael


On Tue, Mar 23, 2010 at 04:54:00PM -0600, Mark Petersen wrote:
> Michael,
> 
> Specifying tracer names within super-arrays and classes is perfect.  When 
> I do the following to registry:
> 
> < var real    tracers ( nTracers nVertLevels nCells Time ) iro tracers - -
> ---
> >var real    temperature (nVertLevels nCells Time ) iro temperature tracers 
> >dynamics
> >var real    salinity (nVertLevels nCells Time ) iro salinity tracers 
> >dynamics
> 
> I get the following error during compile:
> 
> fortcom: Error: module_io_input.f90, line 2473: An explicit-shape-spec in 
> an ALLOCATE statement is incorrect.   [SUPER_REAL1D]
>       allocate(super_real1d())
> ---------------^
> fortcom: Error: module_io_input.f90, line 2494: An explicit-shape-spec in 
> an ALLOCATE statement is incorrect.   [SUPER_REAL1D]
>       allocate(super_real1d())
> ---------------^
> 
> Which is from lines that set up these new variables:
> 
>       allocate(super_real1d())
> 
>       real1d % ioinfo % fieldName = 'temperature'
>       call io_input_field_time(input_obj, real1d)
>       call dmpar_alltoall_field(dminfo, &
>                                 real1d % array, super_real1d, &
>                                 readCellsCount, block % mesh % nCells, &
>                                 sendCellsList, recvCellsList)
> 
> Is the lack of argument on allocate(super_real1d()) a text parsing issue? 
> Could you advise me on how to proceed?
> 
> Thanks,
> Mark
> 
> 
> On Mon, 22 Mar 2010, Michael Duda wrote:
> 
> >Mark,
> >
> >there is actually a capability in the registry to do what you've
> >described. You'll notice that the last two words in an entry for a
> >variable in the registry generally are '-' and '-'; these can be
> >changed to the name of a so-called super-array and a class,
> >respectively.
> >
> >Here's a description of how the capability works:
> >
> >  Two additional columns must now be specified for all variables in the
> >  Registry file. The first new column specifies the name of the
> >  'super-array' that a field belongs to in the code (or "-" if the field
> >  is to be kept as a separate array); the second new column specifies
> >  the class within the super-array that the field is associated with.
> >  For example:
> >
> >  var real    qi ( nVertLevels nCells Time ) iro qi scalars moist
> >  var real    qc ( nVertLevels nCells Time ) iro qc scalars moist
> >  var real    qr ( nVertLevels nCells Time ) iro qr scalars moist
> >  var real    o3 ( nVertLevels nCells Time ) iro o3 scalars chem
> >  var real    no2 ( nVertLevels nCells Time ) iro no2 scalars chem
> >
> >  For each field belonging to a super-array, an index into the
> >  inner-most dimension of the super-array is automatically defined and
> >  made available through the grid_types module. This index is named
> >  xyz_INDEX, where xyz is the name-in-code name specified in the third
> >  from the last column in the Registry file; this index may then be
> >  used to access a particular field in its super-array; for example:
> >
> >  scalars(qi_INDEX, k, iCell) = temp_qi
> >
> >  Also, for each class, all fields belonging to that class will be
> >  located contiguously in the super-array, regardless of their order in
> >  the Registry file, and they can be accessed collectively through
> >  automatically-generated indices ccc_start and ccc_end, where ccc is
> >  the name of the class; for example:
> >
> >  sum_species = sum(scalars(moist_start:moist_end, k, iCell))
> >
> >  Finally, the total number of members of a super-array is defined by an
> >  automatically-generated variable num_sss, where sss is the name of the
> >  super-array; for example:
> >
> >  do i=1,num_scalars
> >     tracer_edge(i) = 0.5*(scalars(i,k,cell1) + scalars(i,k,cell2))
> >  end do
> >
> >This description (from the commit for r87) is inaccurate in that
> >the indices are named index_ccc rather than ccc_index, I think,
> >but otherwise, it summarizes the capability correctly. We've made
> >use of this capability in the hydrostatic atmosphere model for
> >managing tracers; essentially, we now specify
> >
> >var real    qv ( nVertLevels nCells Time ) iro qv scalars moist
> >var real    qc ( nVertLevels nCells Time ) iro qc scalars moist
> >var real    qr ( nVertLevels nCells Time ) iro qr scalars moist
> >
> >rather than
> >
> >var real    tracers ( nTracers nVertLevels nCells Time ) iro tracers - -
> >
> >in the Registry file src/core_hyd_atmos/Registry to create a
> >scalars array (we decided to call the array 'scalars' rather than
> >'tracers') with three members, qv, qc, and qr, which are
> >accessible as scalars(index_qv,:,:), etc.
> >
> >Cheers,
> >Michael
> >
> >
> >On Mon, Mar 22, 2010 at 01:59:47PM -0600, Mark Petersen wrote:
> >>Michael,
> >>
> >>I need to assign an index number to temperature and salinity within the
> >>tracer array.  Eventually we will have numerous tracers that will need a
> >>corresponding tracer index.
> >>
> >>The easiest idea is to have integer variables
> >>iTemperature=1
> >>iSalinity=2
> >>But that requires manual manipulation and reordering as we add tracers.
> >>
> >>A more advanced method is to have an unnumbered list of tracers, perhaps
> >>in the Registry, and some function like
> >>   ind = getTracerIndex('temperature')
> >>so that the numbering is automatic and hidden.
> >>
> >>Have you given this any thought?  Perhaps mpas already has some indexing
> >>capabilities?
> >>
> >>Thanks,
> >>Mark
> >>
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