Hi Mojtaba, Polarization is a vector, so negative or positive just indicate its direction. So no worries about negative polarization. But in periodic boundary conditions you may still need to add (subtract) multiples of the polarization quantum in order to get the "reasonable" value of the spontaneous polarization of the material.
A favorite of mine which go over some of these difficulties is this paper: http://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.014113 Mostafa Youssef MIT
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