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Simulating with PacIOOS ROMS as input

I am working on my masters thesis involving population genetics of coral in Hawaii and I realized that researching the genetic structure of the population means little without accounting for oceanographic conditions. I am completely new to both ocean modelling and to larval simulation, so please forgive me if my questions are a bit silly or obvious.
The Pacific Island Ocean Observing System (PacIOOS) has a 100m resolution ROMS model for Kaneohe Bay (my study area) that I was hoping to input (either with OpenDAP or as a file) into Ichthyop to simulate dispersal over the coral spawning period. However, the model outputs are not like any other ROMS output I have seen. The output does not contain many of the fields that Ichthyop requests and only contains:

  • mask (1) = field mask = sea_binary_mask
  • salt (1e-3) = salinity = sea_water_salinity
  • temp (Celsius) = potential temperature = sea_water_potential_temperature
  • u (meter second-1) = u-velocity component = eastward_sea_water_velocity
  • v (meter second-1) = v-velocity component = northward_sea_water_velocity
  • zeta (meter) = free-surface = sea_surface_height

Is it possible to utilize such data in Ichthyop? Here is a bit more about the model if needed: http://www.pacioos.hawaii.edu/currents/model-kaneohe/#about
Thank you,

Ichthyop version: 
Ichthyop 3.3alpha
Hydrodynamic dataset: 
Java version: 
Java SE 8
Operating system: 

Hi Nicolas

Can you tell me more about your domain? Is it a regular grid (i.e. 1D longitude or latitude)? Are the vertical levels in sigma or in z? Are data 2D or 3D?

If it is on a regular grid but in sigma, I think the best option is to reconstruct the "scale factors" (i.e. the pm and pn variables) from the longitudes/latitudes.

If it is on a regular grid in z, maybe it is better to adapt the Oscar configuration file.