We applied the harmonic inversion technique to extract vibrational eigenvalues from the semiclassical initial value representation (SC-IVR) propagator of molecular systems described by explicit potential surfaces. The cross-correlation filter-diagonalization (CCFD) method is used for the inversion problem instead of the Fourier transformation, which allows much shorter propagation time and is thus capable of avoiding numerical divergence issues while getting rid of approximations like the separable one to the pre-exponential factor. We also used the "Divide-and-Conquer" technique to control the total dimensions under consideration, which helps to further enhance the numerical behavior of SC-IVR calculations and the stability of harmonic inversion methods. The technique is tested on small molecules and water trimer to justify its applicability and reliability. Results show that the CCFD method can effectively extract the vibrational eigenvalues from short trajectories and reproduce the original spectra conventionally obtained from long-time ones, with no loss on accuracy while the numerical behavior is much better. This work demonstrates the possibility to apply the combined method of CCFD and SC-IVR to real molecular potential surfaces, which might be a new way to overcome the numerical instabilities caused by the increase of dimensions.
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