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Added the Copyright scripts copyright.sh and copyright.bash in the ROMS/Bin subdirectory. These scripts updates copyright information on ROMS sources files. I also updates the copyright svn property. Either of these scripts must be executed fron the top level of the ROMS directory tree:

Usage:

     ./ROMS/Bin/copyright.bash

Options:

      -nosvn      skip updating of the svn properties.
      -verbose    list files that are modified.

Many thanks to David Robertson for coding these nice scripts.

Added new drivers to compute singular vectors and stochastic optimals:

• hessian_op_ocean.h: Hessian singular vectors driver. Use HESSIAN_SV to activate.
• hessian_so_ocean.h: Hessian stochastic optimals driver. Use STOCHASTIC_OPT and HESSIAN_SO to activate.
• so_ocean.h: Full stochastic optimals driver. Use STOCHASTIC_OPT to activate.

The associated propagators are:

• propagator_hop.h: Hessian singular vectors propagator.
• propagator_hso.h: Hessian stochastic optimals propagator
• propagator_so.h: Full stochastic optimals propagator.

The Hessian algorithms require the Lanczos vectors generated by any of the 4D-Var algorithms, which is stored in the adjoint output file. That is, we need to run any of the 4D-Var algorithms first. All these algorithms will be described in a publication in the near future. They are complex and requires a lot of expertise.

Many thanks to Andy Moore for helping us to design and code these algorithms. They are released now because of substantial changes and corrections to the GST drivers. Currently, we are testing these algorithms and tracking couple of parallel issues with the Hessian Stochastic Optimals algorithm.

Added the Red Tide Ecosystem Model for Alexandrium fundyense. It can be activated with CPP option RED_TIDE. This model is primarily designed for the Gulf of Maine.

As code it, the user needs to provide the bottom cyst concentration (cyst_bottom; cell/m2; 2D array) and the observed dissolved inorganic nutrient (DIN; micromoles; 3D array). The cyst_bottom and DIN fields can be provided in a separated forcing NetCDF file. See varinfo.dat for the metadata for these input variables.

Many thanks to Dennis McGillicudy and Ruoying He for providing us their code. This model was rewritten from scratch.

Also, many thanks to Sasha Shchepetkin for providing us his updated semi-Lagrangian code sinking and ascending used for vertical swimming.

References:

Stock, C.A., D.J. McGillicudy, A.R. Solow, and D.M. Anderson, 2005: Evaluating hypotheses for the initiation and development of Alexandrium fundyense blooms in the western Gulf of Maine using a couple physical-biological model, Deep-Sea Research II, 52, 2715-2744.

He, R., D.J. McGillicuddy, B.A. Keafer, and D.M. Anderson, 2008: Historic 2005 toxic bloom of Alexandrium fundyence in the western Gulf of Maine: 2, Coupled biophysical modeling, J. Geophys. Res., 113, C07040, doi:10.1029/2007JC004602