Unwrap trajectories — OVITO User Manual 3.5.4 documentation

# Unwrap trajectories

This modifier “unwraps” particle coordinates to make the particle trajectories continuous. It reverses the effect of periodic boundary conditions, i.e. the folding of particle positions back into the primary simulation cell, which is typically performed by molecular dynamics codes.

Input

Output

The modifier can do the unwrapping of particle trajectories in two different ways: If available, it uses the information stored in the `Periodic Image` particle property to map particles from the primary periodic cell image to their actual positions. The `Periodic Image` particle property consists of a triplet of integers, \((i_x, i_y, i_z)\), specifying for each particle which periodic image of the cell it is currently in. Some MD simulation codes write this information to their output trajectory file, and OVITO will make use of it if available.

If the `Periodic Image` particle property is not present, the modifier automatically uses a heuristic to unwrap the particle trajectories. It steps through all simulation frames to detect jumps (discontinuities) in the input trajectories. Such jumps usually occur with every transition of a particle from one periodic cell image to another. After the modifier has scanned the input trajectories and recorded all particle jumps, it subsequently modifies the coordinates of particles which have crossed a periodic boundary to “unfold” their trajectories.

The modifier uses the minimum image principle to detect the transition of a particle through a periodic cell boundary from one frame to the next.

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

See also

`ovito.modifiers.UnwrapTrajectoriesModifier` (Python API)