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Release/Recruitment zone

Hi dear all,
I am a beginner user with Ichthyop and I am trying to run Ichthyop with hourly outputs from ROMS Rutgers in the 3D configuration of Ichthyop 3.3 version.
 
I am setting up my experiments and I have 9 release and recrutiment zones, that are actually the same, therefore,  the release zones have the same latitudes and longitudes as the recrutiment zones. From those 9 zones, 5 of them are in the continental shelf and 4 of them are oceanic islands. Ichtyop undertands perfectly the the continental shelf zones.
 
However, it is not working with the oceanic islands zones, it does not release any particles in them. So I tried to run each oceanic island individually it reports the follwing error for the 4 of them:
 
ichthyop[info] ===== Simulation started =====
ichthyop[info] [Simulation] Run 1 / 1
ichthyop[info] [Simulation] Initialising...
ichthyop[info] {Dataset} Open /home/clarissa/Results/swa12ext_I02/swa12ext_Ichthy_avg_2008_jan.nc
ichthyop[info] Release manager setup [OK]
ichthyop[info] Time manager setup [OK]
ichthyop[info] Instantiated action "Advanced/Biology/Lethal temperature"
ichthyop[info] Instantiated action "Advanced/Biology/Recruitment/In zones"
ichthyop[info] Instantiated action "Advanced/Transport/Vertical migration"
ichthyop[info] Instantiated action "Advanced/Transport/Advection"
ichthyop[info] Instantiated action "Advanced/Transport/Buoyancy"
ichthyop[info] Instantiated system action "org.previmer.ichthyop.action.SysActionAgeMonitoring"
ichthyop[info] Instantiated system action "org.previmer.ichthyop.action.SysActionMove"
ichthyop[info] Action manager setup [OK]
ichthyop[info] Output manager setup [OK]
ichthyop[info] {Dataset} Open /home/clarissa/Results/swa12ext_I02/swa12ext_Ichthy_avg_2008_jan.nc
ichthyop[info] Reading NetCDF variables...
ichthyop[info] Release manager initialization [OK]
ichthyop[info] Time manager initialization [OK]
ichthyop[info] Zone manager initialization [OK]
ichthyop[info] Created output file /home/clarissa/Ichthyop/ichthyop-3.3/output/roms3d_I02_ichthyop-run201711281437.nc.part
ichthyop[info] Output manager initialization [OK]
ichthyop[info] [Simulation] Initialisation [OK]
ichthyop[info] Reading NetCDF variables...
ichthyop[severe] Unable to release particle in release zone 0. Check out the zone definitions. | java.lang.NullPointerException: Unable to release particle in release zone 0. Check out the zone definitions.
ichthyop[severe] [Simulation] Initialisation failed
 
In the attatchments is the grid (swa12ext_grd.nc) and the confiruation files (2017_11_17_roms3d_Ichthy04.xml) , as well as the zone file with all the zones enabled (swa12ext_allzones_coord2711_5.xml) and the file with only one of the oceanic island enabled (swa12ext_allzones_coord2711_AtolRocas.xml).
Any suggestions on what maybe happening?
Thanks in advance,
Clarissa
 

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

Hi Clarissa,

Can you see all 9 zones in the Preview?

Christophe

Hi Cristophe,
Thank you for your answer.
I can only see the 5 zones that are in the continental shelf. The 4 zones that are close to the oceanic islands are not visible, but I am thinking that this maybe relatead to the setting of the line offshore (which was set to 500m in my zone file) on the bathimetric mask.
 
I have some doubts about this. Is the bathimetric mask extracted from the grid file provided? If it is, do I still need to activate this feature and set up the line inshore and the line offshore ? If I do need to activate it, what does this feature consider?
 
Thank you,
Clarissa

Yes, desactivate the bathymetric mask and chek if you then see the missing zones.

Hi Cristophe,
Thank you very much! It seems to be working now.
All the best,
Clarissa