Load trajectory

This modifier is used to load time-dependent atomic positions from a separate molecular dynamics trajectory file.

Some MD codes work with separate topology and a trajectory files. The former contain the initial atomic positions and other definitions like atom types, bonds, etc. which are constant throughout the simulation and which are read in by the MD simulation code. The MD code writes the computed trajectories to a separate file containing just the time-dependent coordinates (but no other static information like the bonds).

One typical example is the code LAMMPS, which relies on the data input file format for defining the bonds between atoms and the dump output file format to store the computed trajectories.

To load such a pair of topology/trajectory files in OVITO, first import the topology file. Then apply the Load Trajectory modifier to the loaded dataset and select the trajectory file on disk. The modifier will replace the initial atomic positions loaded from the topology file with the time-dependent positions loaded from the trajectory file. The same is done for the simulation cell geometry.

The modifier tries to fix bonds of particles whose trajectories cross a periodic simulation cell boundary. If the atomic trajectories are stored in wrapped coordinates, then the PBC shift vectors of bonds need to be readjusted to ensure a correct display. The method used by the modifier is based on the minimum image convention, which prevents bonds from spanning more than half of the simulation box size.