Load trajectory

This modifier loads time-dependent atomic positions and other properties from a separate molecular dynamics trajectory file and combines them with static topology data (e.g. bonds and atom type information) from another 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 code at the beginning of the simulation. The MD code writes the computed trajectories to a separate file containing just the time-dependent coordinates and perhaps other varying properties like atomic energies (but no 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 as usual. Then apply the Load Trajectory modifier to the dataset and select the corresponding trajectory file. The modifier will replace the initial atomic positions from the topology file with the time-dependent positions loaded from the trajectory file. The same is done for the simulation cell geometry and also any other particle property that is present in the trajectory file.

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.

If particles in the topology and the trajectory file possess IDs, then the modifier uses them to determine the correct one-to-one mapping when the storage order of particles changes during the course of a simulation. If no particle IDs are available, then the modifier assumes that the storage order of particles in the topology and the trajectory file is the same.