PHILEX IOP09 February/March 2009 Exercise - MSEAS Home Page

2 February - 24 March

This web page presents the output from a coupled biogeochemical/physical free surface simulation in our archipelago domain. This is the latest re-analysis (issued on 9 June 2009).

The simulation is forced with a combination of COAMPS (wind stress) and NOGAPS (heat-flux, E-P) atmospheric forcing. It is initialized using a February climatology from the World Ocean Atlas, created using our Fast-Marching-Method Objective Analysis scheme to account for the complex geometries and the disconnected seas at depth. Large-scale open boundary conditions are weakly forced by HYCOM fields, provided by Joseph Metzger, Ole Martin Smedstad and Harley Hurlburt (NRL-SSC). The bathymetry used is that of Smith and Sandwell. All simulations are forced with our Generalized Inverse High-Resolution Barotropic Tides. Plots of the COAMPS winds can be found here.

Remotely-sensed Sea Surface Height anomalies and Sea Surface Temperature are the only synoptic data utilized for initialization and assimilation. No hydrographic data are currently available.

The min/max values under each plot are for the plotted field, while the plot values are indicated by the colorbar. The velocity vectors are scaled by the vector seen on the plot. The colorbars are consistent for each variable and location, but differ from variable to variable.

2 February - 24 March: Snapshot Time-Series of the Estimated Ocean State (every 6 hours)
3km Archipelago Domain
  Chlorophyll Nitrate Ammonium Zooplankton Detritus
20m X X X X X
60m X X X X X
120m X X X X X

Vertical Sections
  Chlorophyll Nitrate Ammonium Zooplankton Detritus
Northern Mindoro Strait X X X X X
Southern Mindoro Strait X X X X X
Sulu Sea X X X X X
Bohol Sea X X X X X
San Bernadino Strait X X X X X

Plots for the physical variables are located here.

Biological parameter initialization:

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NetCDF files with Simulation Field Estimates

The following files contain our MIT field estimates in time and 3D space, for the following variables: temperature, salinity, surface pressure, total velocity, vertical velocity, and concentrations of nitrate, ammonium, zooplankton, phytoplankton, chlorophyll and detritus. To create horizontal maps at given depth or sections at given lat/lon, don't hesitate to contact us.

NetCDF files
Along Grid MIT_bio_reanal_20090609_20090202_20090325_06h.nc.gz
Geographic MIT_bio_reanal_geo_20090609_20090202_20090325_06h.nc.gz

To help extract data from these files in Matlab, we include the function readhopspe.m. To use this function, you'll also need to download

  1. The appropriate mexnc for your system
  2. the NetCDF ToolBox
Then you need to edit your MATLABPATH to include the necessary directories. In the below example, both mexnc and the NetCDF ToolBox were installed in the directory /matlab/toolbox/local 

        /matlab/toolbox/local/mexnc
        /matlab/toolbox/local/netcdf_toolbox/netcdf
        /matlab/toolbox/local/netcdf_toolbox/netcdf/ncutility
        /matlab/toolbox/local/netcdf_toolbox/netcdf/nctype
Notice that you have to include to additional subdirectories that are part of the NetCDF ToolBox.

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