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Several files were modified to allow customization of biology/ecosystem model header files (ecosim.h, fasham.h, nemuro.h, npzd_Franks.h, and npzd_Powell.h). Now it is possible to shadow released version of these header files with a user-customized version. This is similar to the analytical functionals in ROMS/Functionals. For more information, please check the following ​forum posting.

• The makefile was modified to allow shadowing of released header files. This shadowing occurs during C-preprocessing.
• The make configuration files (Compilers/*.mk) were modified to allowfree-format in biology.o for the long-string path of the header file.
• The biology/ecology header file is saved in output NetCDF files so solutions can be reproduced in the future. This required a new routine netcdf_close in mod_netcdf.F to process the global attribute bio_file before closing the file. The variable BIONAME values are not known when the NetCDF files are created.
• Corrected a bug in fasham.h and renamed TALK_PROGNOSTIC to TALK_NONCONSERV.

• Corrected a shared memory bug in the ana_*.h routines when ANANAME is assigned. Recall that only one tile is allowed to assign global variables.

There is distributed-memory bug in routine ana_nudgcoef.h when setting the passive/active coefficient used in the nudging terms for open boundary conditions. We need to use mp_collect instead mp_bcastf. This is a global reduction opearation instead a broadcast communication. See the following ​forum post for more details.

Many thanks to Francesco Nencioli for reporting this problem.

The W4DPSAS weak-constraint data assimilation algorithm was redesigned to follow closely Courtier's (1997) dual formulation paper. This upgrade includes:

• Added spectral and Ritz preconditioning to W4DPSAS similar to that coded for W4DVAR.
• Added hot start for subsequent outer loop in W4DPSAS and W4DVAR. This can be activated by turning new input parameter LhotStart in s4dvar.in.
• Added all the variables necessary for the observation sensitivity driver in output NetCDF MODname. We are currently working on this new driver which is the adjoint of the W4DPSAS and W4DVAR system.
• Removed obsolete routine impulse.F.

Now both weak-constraint data assimilation driver are working very nicely. Many thanks to Andy Moore for his help coding and testing these algorithms.