Fix for biofuel emissions

In removing passive tracers, the code that wrote the biofuel emissions
was inadvertently commented out. This restores biofuel emissions.

Signed-off-by: Jenny Fisher <jennyf@uow.edu.au>
Fixes to GLYX, MGLY uptake

Add IDT checks so that STT array is not being accessed for indices that
don't exist. Checks are separate for IDTGLYX & IDTMGLY vs IDTSOAG & IDTSOAM
so that gas-phase uptake can be computed and used in non-SOA simulations
IFF GLYX and MGLY are included in the simulation as tracers (and therefore
with a value in STT). Otherwise there is no point in including these
routines as neither aerosol nor gas phase species will be updated!

Also cleaned this up a little and commented out some print statements.

Signed-off-by: Jenny Fisher <jennyf@uow.edu.au>
Reduce memory footprint in GeosCore/strat_chem_mod.F90

    The following arrays in GeosCore/strat_chem_mod.F90 can be declared
    as REAL*4 instead of REAL*8:

    (1) PROD(:,:,:,:)
    (2) LOSS(:,:,:,:)
    (3) STRAT_OH(:,:,:)
    (4) MINIT(:,:,:)
    (5) SCHEM_TEND(:,:,:,:)

    For the most part, these arrays hold values that are read from netCDF
    files as REAL*4 data, or are computed from REAL*4 data.  This change
    now allows us to run the 2x25 model in the smp8 computational queue at
    Harvard.  (Previously, the 2x25 model would exit with a seg fault in
    this queue.)

    This update also required a modification to transfer_mod.F.  We now had
    to split routine TRANSFER_3D into two routines: TRANSFER_3D_R4 (with
    an output argument of REAL*4) and TRANSFER_3D_R8 (with an output
    argument of REAL*8).  These routines are overloaded with a module
    interface.  This allows us to use TRANSFER_3D on the PROD, LOSS,
    and STRAT_OH arrays in strat_chem_mod.F90, because these are now
    REAL*4 instead of REAL*8.

    Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Comment out print statements

Comment out print statements in aerosol_mod.F to make log file cleaner and
smaller.

Signed-off-by: Jenny Fisher <jennyf@uow.edu.au>
Facilitate CSPEC debugging

When there is a mismatch while reading the CSPEC restart, now print the
names of both the species expected and the species read.

Signed-off-by: Jenny Fisher <jennyf@uow.edu.au>
Dry dep bug fixes:

1. Duplicate entries for PMNN, PPN removed
2. ISN1 was being treated as PAN not HNO3
3. MP had wrong entry for NDVZIND
4. Deposition like HNO3 missing for ISNP, ISOPNB/ISOPND, MVKN/MACRN, ETHLN,
   PROPNN

Signed-off-by: Jenny Fisher <jennyf@uow.edu.au>
Add IDTIMAE to tracerid_mod.F

Although these are not used here, they are referenced in the new
AEROSOL_UPTAKE code, so defining them here avoids rewriting that code.


Signed-off-by: Jenny Fisher <jennyf@uow.edu.au>