We consider almost periodic stationary nonlinear Schr\"odinger equations in dimension $1$. Under certain assumptions we prove the existence of nontrivial finite energy solutions in the strongly indefinite case. The proof is based on a carefull analysis of the energy functional restricted to the so-called generalized Nehari manifold, and the existence and fine properties of special Palais-Smale sequences. As an application, we show that certain one dimensional almost periodic photonic crystals possess gap solitons for all prohibited frequencies.
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