1-D    physical-biological model of shelf sea primary production.

Background.
The original model (PHYTO_1D), described in Sharples, J., Progress in Oceanography, 1 Suppl. S, 3 - 38, 1999, was a DOS-based program, requiring the user to edit initialisation files prior to running the model. There was soon a clear need to rewrite the model code to produce a version capable of running within Windows, with parameter input controlled via more familiar-looking menus and dialogs. The shift to this new version was driven from two directions:

1. Involvement in the European Union research programme IMPRESS (Interactions between the Marine environment, PREdators and prey: implications for the Sustainable Sandeel fisheries) required the develoment of a more user-friendly model. The aim was to produce a tool for the investigation of interannual variability in spring bloom timing and primary production, and to assess water column characteristics during times when seabirds were observed to be foraging.
2. The development of my own teaching, primarily in a course on shelf sea and shelf edge dynamics, required the development of a version of the model that the students felt comfortable with, and on which I could base modelling practicals. The aims of these practicals were to allow the students to develop their understanding of the interaction between physics and primary production in shelf seas, and also to develop there own appreciation of what can and cannot be done with models.

Program Environment.
This new version of the model was written in Fortran 95 (Lahey LF95), with the Winteracter GUI toolset (Interactive Software Services) used to produce the Windows environment.
The model will run on pcs running Windows 9*, 2000, ME, NT and XP.

Changes to the original PHYTO_1D.
The model equations are generally as found in Sharples, 1999. The main changes between the old and new versions are:

• The model now uses the k-e turbulence scheme of Canuto et al., Journal of Physical Oceanography, 31, 1413-1426, 2001. The original version used a Mellor-Yamada closure scheme.
• There are now 3 different methods of including mixing by internal waves. The original version simply allowed the specification of a background diffusivity and viscosity.
• It is now possible to include a seasonal cycle in the grazing impact on the phytoplankton.
• The version of the model developed for the EU IMPRESS project includes the possibility of choosing one of several meteorological datafiles for the years 1974 to 2002.
• The version developed for teaching has fixed, smoothly-varying, seasonal meteorological forcing.

Versions available.
I have made two versions available here:

1. The EU-IMPRESS model: impress_v3.exe
This is a self-extracting executable containing the model executable, a Windows help file accessed by the model, and the meteorology data files. An initialisation file (marbank_init.txt) contains the information used to run the model for conditions at a mooring site occupied for the IMPRESS project (NE coast of Scotland). Note that the meteorology data has aligned the x-axis of the wind vector to lie along the major axis of the tidal currents observed by the mooring. This is something I intend to fix eventually, but for the moment I am struggling to get the general solution to the oscillating tidal slopes for any ellipse orientation.

2. The teaching model: OA311.exe
This is a self-extracting executable containing the model executable and a Windows help file accessed by the model.

For both versions, download the zip file and unzip all the contents into a directory on your pc. Run the model by double-clicking the executable (impress_model_v3.exe or oa311_biophy.exe). Hopefully the rest is self-explanatory, assuming the Instructions accessed from the Help on the main menu are any use.

Note: this software comes with no guarantees or support! I am happy to receive comments or suggestions about the model, and will do my best to answer any queries.....but can make no promises.

Still to be done.
There are still a few points that I need to work through. Obvious ones that I know about are:

• Fix the tidal ellipse orientation so that the major ellipse axis does not have to lie along the x-axis.
• Introduce a semi-implicit integration scheme for the equation of motion. The current explicit scheme produces over-enthusiastic inertial oscillations.
• Add an option that allows a user-specified meteorological data file to be used.

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