Unwrap trajectories


Replaces "wrapped" particle coordinates with "unwrapped" coordinates to make the trajectories of particles continuous.

The modifier can be applied to a series of simulation frames to "unwrap" the time-dependent positions of the particles. To do this, the modifier needs to step through all simulation frames to detect crossings of particles through the boundaries of the periodic simulation cell, which are associated with jumps (discontinuities) in the input trajectories. The modifier will then dynamically adjust the coordinates of particles that have crossed a periodic boundary to "unfold" their trajectories and make them continuous.

The modifier uses the minimum image principle to detect transitions of a particle through a periodic boundary of the simulation cell from one frame to the next, i.e. in an incremental fashion. After unfolding, the continuous trajectories can span distances larger than the cell dimensions.

In the current program version, you must press the Update button of the modifier to manually trigger an analysis of the input particle trajectories. The modifier will step through the entire sequence of simulation frames and detect and record all crossings of the periodic cell boundaries. Subsequently, it will use this information to unfold the trajectories and replace particle coordinates with unwrapped versions.

The unwrapping of trajectories is only performed along those directions for which periodic boundary conditions (PBC) are enabled for the simulation cell. The PBC flags are read from the input simulation file if available and can be manually set in the Simulation cell panel.

If the Periodic Image particle property is present, which some MD simulation codes store in the trajectory file, then the modifier will directly use this information to unwrap the particle positions. In this case you don't have to use the Update button, because a detection of the particles crossing through the cell boundaries is not necessary.