Trajectory Submodule

Experimental trajectory submodule adds support for trajectory structures that are subtypes of AbstractVector{AbstractSystem}. These are more optimized than simply storing systems in a vector.

The optimizations come from the fact that data structures are only allocated once for the trajectory not for each frame.

Trajectory types

The basic principle is same as with systems. The structures are layered with additional properties.

• SimpleTrajectory - species and position only
• SimpleVelocityTrajectory - species, position and velocity
• ConstantVolumeTrajectory - constant cell trajectory
• VariableVolumeTrajectory - cell can change for each frame

All trajectory types expect that number of atoms and species are constants.

Examples

You can create trajectories by giving vector of systems as and input

using AtomsBase
using AtomsSystems
using AtomsSystems.AtomsTrajectories

first_frame = generic_system"""
    H 0 0 0
    O 1 0 0
"""

second_frame = generic_system"""
    H 0   0 0
    O 1.1 0 0
"""

traj = VariableVolumeTrajectory([first_frame, second_frame])

SimpleTrajectory with 2 frames, each with 2 atoms

or by creating trajectory by giving first frame and then pushing to the system

traj = VariableVolumeTrajectory(first_frame)

push!(traj, second_frame)

SimpleTrajectory with 2 frames, each with 2 atoms

To use you can just index it

traj[2]