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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

In read_phypar.F, lines 2736 through 2750 check the point source methodologies

!
!  Check if both point sources methodologies are activated.  Only one
!  method is allowed for a particular grid.  Otherwise, the point
!  source will be applies twice.
!
       IF (LuvSrc(ng).and.LwSrc(ng)) THEN
         IF (Master) THEN
           WRITE (out,260) 'LuvSrc', LuvSrc(ng),                        &
     &           'Because LwSrc  is also ON; only one method is legal.'
           WRITE (out,260) 'LwSrc', LwSrc(ng),                          &
     &           'Because LuvSrc is also ON; only one method is legal.'
           exit_flag=4
           RETURN
         END IF
       END IF

This needs to be enclosed in a loop over ng:

      DO ng=1,Ngrids
       IF (LuvSrc(ng).and.LwSrc(ng)) THEN
      ...
       END IF
      END DO

Otherwise, ng has the value it acquired on exit from the previous such loop, which leads to an out-of-bound access in LuvSrc(ng) and LwSrc(ng).

Updated the ROMS/TOMS Copyright to all algorithms:

  Copyright (c) 2002-2016 The ROMS/TOMS Group
     Licensed under a MIT/X style license
     See License_ROMS.txt

In case that you were wondering, the Copyright for the ROMS repositories is updated with the either of ROMS/Bin/copyright.sh or ROMS/Bin/copyright.bash by executing the script from the root of the repository:

ROMS/Bin/copyright.sh -verbose

For example, notice than in copyright.sh there are two sections that are used to update all files:

set search = "2002-2015 The ROMS/TOMS"
set replace = "2002-2016 The ROMS/TOMS"

and

if ( $setsvn == 1 ) then
  svn propset -R copyright '(c) 2002-2016 The ROMS/TOMS Group' Compilers
  svn propset -R copyright '(c) 2002-2016 The ROMS/TOMS Group' Data
  svn propset -R copyright '(c) 2002-2016 The ROMS/TOMS Group' Master
  svn propset -R copyright '(c) 2002-2016 The ROMS/TOMS Group' ROMS
  svn propset -R copyright '(c) 2002-2016 The ROMS/TOMS Group' User
  svn propset copyright '(c) 2002-2016 The ROMS/TOMS Group' . makefile
  svn propset copyright '(c) 2002-2016 The ROMS/TOMS Group' Waves/SWAN/Src/Module.mk
  svn propset copyright '(c) 2002-2016 The ROMS/TOMS Group' Waves/SWAN/Src/waves_coupler.F
else
  echo ""
  echo "Not updating svn properties."
  echo ""
endif

Notice that the svn properties for all the files and directories are also updated.

If this is done annually, the replacement is trivial. Otherwise, the search string needs to be modified accordingly.

Finally, this is required by our institutions to keep the Open Source license of ROMS.