Hello Jason,
As told a few times in other posts, if a segmentation fault or a NaN (Not a Number) occurs, you should use a debug configuration with debug options to investigate.
See e.g. the S11.gfortran.debug configuration in the $HOMETEL/configs/systel.edf.cfg configuration file, in particular the flag fflags_debug_gfo for gfortran compiler.
fflags_debug_gfo: -g -Wall -fcheck=all -fbacktrace -fbounds-check -finit-integer=-1 -finit-real=nan -ffpe-trap=invalid,zero,overflow
It will show in which subroutine the issue/nan/segfault occurs, the first suspicious line and may help you to change something in your computation.
Anyway, can you also provide your steering files + potention Fortran files?
Do you have dry areas in your domain? That may explain this issue. I am not sure the coupling TELEMAC-3D with AED2 works correctly with dry areas.
What about the results of your TELEMAC-3D model without coupling with AED2, does it work?
If yes, does it work coupling with WAQTEL/THERMIC (WATER QUALITY PROCESS = 11)? Does it work with ATMOSPHERE-WATER EXCHANGE MODEL = 2 and/or 1? You may get errors with option 2 as it does work well with dry areas (if you have some).
Hope this helps,
Chi-Tuan