We study how Gromov-Witten invariants of projective 3-folds transform under a standard flop and a small extremal transition in the algebro-geometric setting from the recent development of algebraic relative Gromov-Witten theory and its applications. This gives an algebro-geometric account of Witten's wall-crossing formula for correlation functions of the descendant nonlinear sigma model in adjacent geometric phases of a gauge linear sigma model and of the symplectic approach in an earlier work of An-Min Li and Yongbin Ruan on the same problem. A terse account from the stringy and the symplectic viewpoint is given in the appendix to complement and compare to the discussion in the main text.

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Let k be the algebraic closure of a finite field of odd characteristic p, and X a smooth projective scheme over the Witt ring W (k) which is geometrically connected in characteristic zero. We introduce the notion of Higgs-de Rham flow1 and prove that the category of periodic Higgs-de Rham flows over X/W(k) is equivalent to the category of Fontaine modules, hence further equivalent to the category of crystalline representations of the e ́tale fundamental group π_1(X_K ) of the generic fiber of X, after Fontaine-Laffaille and Faltings, where K is the fraction field of W(k). Moreover, we prove that every semistable Higgs bundle over the special fiber X_k of X of rank ≤ p initiates a semistable Higgs–de Rham flow and thus those of rank ≤ p − 1 with trivial Chern classes induce k-representations of π_1(X_K ). A fundamental construction in this paper is the inverse Cartier transform over a truncated Witt ring. In characteristic p, it was constructed by Ogus–Vologodsky in the nonabelian Hodge theory in positive characteristic; in the affine local case, our construction is related to the local Ogus–Vologodsky correspondence of Shiho.

In this paper, it is proved that the Hodge metric completion of the moduli space of polarized and marked Calabi-Yau manifolds, ie the Torelli space, is a complex affine manifold. As applications we prove that the period map from the Torelli space and the extended period map from its completion space, both are injective into the period domain, and that the completion space is a bounded domain of holomorphy with a complete Khler-Einstein metric. As a corollary we show that the period map from the moduli space of polarized Calabi-Yau manifolds with level m structure is also injective.

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