Custom Query (986 matches)

The red tide model (RED_TIDE) was updated to include a Q10 mortality rate equation, as a function of temperature. It includes new input parameters in red_tide.in:

! Mortality rate Q10 equation parameters, as a function of temperature:
!
!   M_rate = Mor_a * Mor_Q10^[(temperature-MOR_To)/10] + Mor_b

         MOR_a == 0.04d0                         ! amplitude, 1/day

         MOR_b == 0.03d0                         ! intercept, 1/day

       MOR_Q10 == 10.0d0                         ! reaction rate base

        MOR_T0 == 15.0d0                         ! background temperature (C)

A couple of input parameters are also adjusted in red_tide.in for the Gulf of Maine:

! Maximum growth rate at optimal temperature and salinity [1/day]

          Gmax == 1.05d0                        ! Gmax

! Germination depth [cm]

            Dg == 0.18d0                         ! Dg

The BIO_TOY example gives the following Alexandrium Fundyense concentration:

Notice that I am plotting the LOG of the concentration.

Many thanks to Yizhen Li for the testing and update of the Red Tide Model.

In ROMS/Include/globaldefs.h at lines 765-768 the effect of the following lines...

#if (!defined BIO_FENNEL  && defined DIAGNOSTICS_BIO) || \
    (!defined HYPOXIA_SRM && defined DIAGNOSTICS_BIO)
#  undef DIAGNOSTICS_BIO
#endif

...is to undefine DIAGNOSTICS_BIO unless both BIO_FENNEL and HYPOXIA_SRM are defined.

I suggest...

#if defined DIAGNOSTICS_BIO && !(defined BIO_FENNEL || HYPOXIA_SRM)
#  undef DIAGNOSTICS_BIO
#endif

...or its syllogistic equivalent.

Oops, the defined is missing before HYPOXIA_SRM. We need to have instead:

#if defined DIAGNOSTICS_BIO && \
  !(defined BIO_FENNEL      || defined HYPOXIA_SRM)
#  undef DIAGNOSTICS_BIO
#endif

I think, in lines 626 and 701 of def_diags.F the pre-processor conditions should read as:

#if defined DIAGNOSTICS_BIO && defined BIO_FENNEL

Currently, they only read as:

#ifdef BIO_FENNEL

This can cause "undefined variable" errors for iDbio2 and iDbio3 during compilation when other diagnostics but not DIAGNOSTICS_BIO are enabled in combination with BIO_FENNEL.

Yes, thank you for bringing this problem to my attention. I cleaned the logic in def_diags.F, set_diags.F, and wrt_diags.F. I also added the 2D biological diagnotics for HYPOXIA_SRM. It was not included in the above files.

Also removed apostrophes in fennel.h documentation to suppress the warnings from ifort during compilation. I also cleaned a DIAGNOSTIC_BIO bug in hypoxia_srm.h. We don't need the 3D diagnostics arrays in this simple model.

Fixed OMP directives in initial.F, ad_initial.F, rp_initial.F, and tl_initial.F when the 4D-Var algorithms are activated. This bug is of no consequence since we cannot run any of the adjoint-based algorithms in shared-memory (OpenMP).