Motivated by the work of Candelas et al. (Calabi–Yau manifolds over finite fields, I. arXiv:hep-th/0012233 , 2000) on counting points for quintic family we study relations among Hasse–Witt matrices, unit-root part zeta functions and period integrals Calabi–Yau hypersurfaces in both toric varieties flag varieties. We prove a conjecture Vlasenko (Higher matrices. Indag Math 29(5):1411–1424, 2018)...