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3D dispersión using HYCOM model outputs

Dear colleagues:
I was wondering if it is possible using the HYCOM model outputs in order to carry out a 3-D simulation in Ichthyop.
In fact, I was able to adapt these HYCOM outputs for a 2-D simulation, based on the structure of the MARS model outputs (file: mars-iroise.nc, downloaded along Ichthyop 3.3), since both outputs are similar.
Now, in order to adapt these HYCOM outputs for a 3-D simulation, I have noticed that there are basically the same variables than MARS, which are (at left is indicated the HYCOM variable name; at right the MARS variable name):

  • Depth (in meters)  vs  level (not units indicated).
  • Batimetry (in meters)  vs  h0 (in meters).
  • ssh (in meters)  vs  xe (in meters).
  • u (m s-1)  vs  uz (m s-1)
  • v (m s-1)  vs  vz (m s-1)

However, when trying to carry out a 3-D simulation using these HYCOM outputs adapted (and using a template configuration file generated by Icthyop for a MARS-3d simulation), the simulation simply gets stuck in the second time step (I am attaching the output file generated by Ichthyop).
Finally, I should mention that in order to do not modify the variable names in the configuration file, I simply rename the HYCOM variable names as the ones of MARS.
I thank you in advance for any possible guidance.

Ichthyop version: 
Ichthyop 3.3alpha
Hydrodynamic dataset: 
Java version: 
Java SE 8
Operating system: 
Windows 7

Hi Miguel

Could you please send me a sample 3D Hycom file and your configuration file, so that I can try to reproduce your run?

One difference between Mars and Hycom is that depth is the depth (in meters), while level is the index of the vertical levels (ranging from 0 to Nz). It might be the cause of your problem (but it should be investigated though).


Hi Nocolas,
I really appreciate your goodwill. Since the file size is more than 64 MB, I am sharing the HYCOM adapted file in this One Drive public link (please notice that contains the bathymetry and the sea surface height):
This HYCOM data has a resolution of 1 day; it starts on 2015/12/7 14:00 and ends on 2015/12/9 14:00.
I conducted a new run for two days with this HYCOM data, and the configuration file used and the output file are attached to this message.
So, If HYCOM and MARS outputs are in differente vertical coordinates, it is possible to adapt/transform the HYCOM data into a MARS's like vertical system in order to be used in Ichthyop?
Thanks for any possible guidance,
All the best.

Hi Miguel

I have run your code, I had no problems. However, I would not trust the results.

Indeed, in your input file, the level variable is the depth (in m), while in Mars, the level variable is the sigma coordinate. As a consequence, you cannot apply Mars settings to Hycom model outputs in 3D, only
in 2D.