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Theory and implementation

It is often of interest to restrict attention to motions in a specific frequency interval, both for quantitative analysis and for visualization by animated display. This is particularly useful to study low-frequency motions without being distracted by the high frequency "noise". nMOLDYN can create Pass-Band Filtered Trajectory (PBFT) by applying a frequency pass-band filter to the atomic trajectories, either on the whole system or on an user-defined subset. The result is stored in a new trajectory file that contains only motions in the chosen interval. Frequency filtering uses a straightforward algorithm:

- take the discrete Fourier transform of each particle trajectory,
- set the Fourier coefficients outside the filtering interval to zero,
- and transform back to the time domain.

This corresponds to applying a rectangular window in the frequency domain.