Custom Query (964 matches)

Since the _FillValue has been introduced to mark land points in the ocean_his output files, one can not use them directly to restart the model (assuming the ocean_his files containing all relevant data). Since grid points' values located on land are set to _FillValue, ROMS stops during initialization by reporting unreasonable input values.

Setting the _FillValues to zero (like in the old case) resolves the problem but might be not intended. Therefore I would suggest, if the checking of unreasonable values might be improved and is restricted only on ocean points by using the existing masks.

Thanks in advance

Renamed cpp option BIO_FASHAM to BIO_FENNEL to avoid some confusions. It seems that there are some users publishing results with this model. The version in ROMS is very loosely based on Fasham et al. (1990) model. Users should cite the Fennel et al. (2006) reference to be more accurate. This version of the model have evolved substantially over the last few years and became a quite different model with a lot of options.

The routine fasham.h was also renamed to fennel.h. The following information was added to fennel.h to provide a better information about this ecosystem model:

!  This routine computes the  biological sources and sinks for the
!  Fennel et at. (2006) ecosystem model. Then, it adds those terms
!  to the global biological fields.
!
!  This model is loosly based on the model by Fasham et al. (1990)
!  but it differs in many respects.  The detailed equations of the
!  nitrogen cycling component  are given in  Fennel et al. (2006).
!  Nitrogen is the  fundamental elemental  currency in this model.
!  This model was adapted from a code written originally  by  John
!  Moisan and Emanule DiLorenzo.
!
!  It is recommended to activate always the  "BIO_SEDIMENT" option
!  to ensure conservation of mass by converting the organic matter
!  that is sinking out of the bottom most grid cell into inorganic
!  nutrients (i.e.,  instantanaous remineralization  at the water-
!  sediment interface). Additionally, the "DENITRIFICATION" option
!  can be activated.  Hence, a fraction of the instantenous bottom
!  remineralization is  assumed to  occur  through  the  anearobic
!  (denitrification)  pathway  and  thus  lost  from the  pool  of
!  biologically availalbe fixed nitrogen. See Fennel et al. (2006)
!  for details.
!
!  Additional  options can be  activated to  enable  simulation of
!  inorganic carbon and dissolved oxygen.  Accounting of inorganic
!  carbon is activated by the "CARBON" option,  and results in two
!  additional  biological  tracer  variables:  DIC and alkalinity.
!  See Fennel et al. (2008) for details.
!
!  If the "pCO2_RZ" options is activated, in addition to "CARBON",
!  the carbonate system  routines by Zeebe and Wolf-Gladrow (2001)
!  are used,  while the  OCMIP  standard routines are the default.
!  There are two different ways of treating alkalinity.  It can be
!  treated diagnostically (default),  in this case alkalinity acts
!  like a passive tracer  that is  not affected  by changes in the
!  concentration of  nitrate or ammonium.  However,  if the option
!  "TALK_NONCONSERV" is used,  the alkalinity  will be affected by
!  sources and sinks in nitrate. See Fennel et al. (2008) for more
!  details.
!
!  If the "OXYGEN" option is activated,  one additional biological
!  tracer variable for dissolved oxygen. "OXYGEN" can be activated
!  independently of the  "CARBON"  option. If "OCMIP_OXYGEN_SC" is
!  used, in addition to "OXYGEN",  the Schmidt number of oxygen in
!  seawater will be  computed  using the  formulation  proposed by
!  Keeling et al. (1998, Global Biogeochem. Cycles,  12, 141-163).
!  Otherwise, the Wanninkhof's (1992) formula will be used.
!
!  References:
!
!    Fennel, K., Wilkin, J., Levin, J., Moisan, J., O'Reilly, J.,
!      Haidvogel, D., 2006: Nitrogen cycling in the Mid Atlantic
!      Bight and implications for the North Atlantic nitrogen
!      budget: Results from a three-dimensional model.  Global
!      Biogeochemical Cycles 20, GB3007, doi:10.1029/2005GB002456.
!
!    Fennel, K., Wilkin, J., Previdi, M., Najjar, R. 2008:
!      Denitrification effects on air-sea CO2 flux in the coastal
!      ocean: Simulations for the Northwest North Atlantic.
!      Geophys. Res. Letters 35, L24608, doi:10.1029/2008GL036147.
!

When ROMS (the Nonlinear model) cannot find an input file, it exits, but before it does, CHECKDEFS reports an Illegal model configuration, eg:

 READ_PHYPAR - could not find input file:  stations.in

 Elapsed CPU time (seconds):

 Thread #  0 CPU:       0.063
 Total:                 0.063

 Nonlinear model elapsed time profile:

                                              Total:         0.000    0.0000

 All percentages are with respect to total time =            0.063

 ROMS/TOMS - Output NetCDF summary for Grid 01:

 ROMS/TOMS - Configuration error ..... exit_flag:   5


 ERROR: CHECKDEFS - Illegal model configuration.

When the missing file is supplied, it runs normally.

The Illegal model configuration message seems a bit misleading, and I think this behaviour is new. Is it intentional?