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Warning: This is an important upgrade to ROMS biology models.

The light attenuation formulation for photosynthesis (PAR) in couple of biology models in ROMS were revisited. We are now using the averaged (finite volume) value of PAR at the center of the grid cell instead of the median value. It turns out that the old fomulation understimates primary productivity. See the following forum ​post for details. I only correted BIO_FENNEL and NPZD_POWELL. I still need to fix this problem in the NEMURO model, which has in addition a photoinhibition (Platt et al., 1980) formulation.

Many thanks to Mark Baird for bringing this problem to our attention and to Bronwying Cahill for testing this upgrade.

I am also releasing a new NPZD model with iron limitation (Fiechter et al., 2009). This model is similar to the Powell et al. (2006) formulation but it includes iron limitation on phytoplankton growth. This new model is activated with the NPZD_IRON option. To activate the iron limitation on phytoplankton growth, use in addition IRON_LIMIT option. In addition, use IRON_RELAX to simulate the sources of dissolved iron in coastal areas where the bathymetry h(i,j) <= FeHmin (See input script npzd_iron.in for details).

This new NPZD model (npzd_iron.h) also has a tangent linear, representer, and adjoint model version which we are still testing. Many thanks to Jerome Fiechter and Andy Moore for their help on developing this nee model.

Corrected a parallel bug in random_ic.F which is used to estimate the 4DVAR posterior error analysis covariance matrix. The calls the the white_noise2d_bry and white_noise3d_bry need to be outside of a parallel conditional to avoid parallel hang-up.

Many thanks to Andy Moore for reporting this problem.

The makefile was updated so the COMPILERS definition may be specified in either the build.sh or build.bach scripts. This allows the user to specify a customized version (different path) of the configuration files (*.mk) that are distributed in Compilers subdirectory. The makefile has now the following statement to facilitate such operation:

  COMPILERS ?= $(CURDIR)/Compilers

MAKE_MACROS := $(COMPILERS)/make_macros.mk

so we can set the COMPILERS definition with an environmental variable in build.sh:

 setenv COMPILERS            ${MY_ROMS_SRC}/Compilers

or you may use a copy of Linux-ifort.mk, for example, in your project directory:

 setenv COMPILERS            ${MY_PROJECT_DIR}

If you are using this strategy, make sure that you keep the make configuration scripts up-to-date.

I also modified Compilers/Linux-ifort.mk and Compilers/Darwin-ifort.mk files to use precise (IEEE) floating-point operations: -fp-model precise

           FFLAGS := -heap-arrays -fp-model precise

I was completely surprised with the -ip option in ifort which triggers a less precise operation to speed the computation during optimization. I even get different results when I ran the same executable again and again. This must be a bug in ifort 11. Also, I was not longer to check for parallel bugs by comparing output NetCDF files in serial and parallel. I have a lot of roundoff in all fields everywhere. This is very annoying...