Hello.Why the values of this command is nagative but it shoud be positive.are the values of c_flux are complex?!
please one help me.

fix JJ all ave/correlate 1 1000 1000 c_flux[1] c_flux[2] c_flux[3] type auto file ar

I’m not sure why you think the correlation values have to be positive: they can certainly be negative, even without complex data. Even autocorrelations can be negative.