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Hi Pierre,
You can extract the total flow across one or multiple interfaces between two (or multiples of two) material types at all the "calibration" times specified in the >> TIMES block of the iTOUGH2 input file (but not for each TOUGH2 time, as block COFT does). Here is an example iTOUGH2 input file that does the trick:
> OBSERVATION >> TIMES: 100 EQUALLY spaced in DAYs between 1.0 100.0 >> FLOW >>> MATERIAL: RESER CAPRK RESER FAULT >>>> ANNOTATION: leakage from reservoir >>>> NO DATA <<<< <<< << <
Good luck!
Stefan