ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
pre_write_attach(function, interval=1, *args, **kwargs)
Attach a function to be called before writing begins.
function: The function or callable object to be called.
interval: How often the function is called. Default: every time (1).
All other arguments are stored, and passed to the function.
set_atoms(atoms=None)
Associate an Atoms object with the trajectory.
Mostly for internal use.
write(atoms=None)
Write the atoms to the file.
If the atoms argument is not given, the atoms object specified when creating the trajectory object is
used.
Note that there is apparently no methods for reading the trajectory. Reading is instead done by indexing the
trajectory, or by iterating over the trajectory: traj[0] and traj[-1] return the first and last Atoms object in
the trajectory.
Examples
Reading a configuration:
from ase.io.trajectory import PickleTrajectory
traj = PickleTrajectory("example.traj")
atoms = traj[-1]
Reading all configurations:
traj = PickleTrajectory("example.traj")
for atoms in traj:
# Analyze atoms
Writing every 100th time step in a molecular dynamics simulation:
# dyn is the dynamics (e.g. VelocityVerlet, Langevin or similar)
traj = PickleTrajectory("example.traj", "w", atoms)
dyn.attach(traj.write, interval=100)
dyn.run(10000)
traj.close()
7.25.2 BundleTrajectory
The BundleTrajectory has the interface
class ase.io.bundletrajectory.BundleTrajectory(filename, mode=’r’, atoms=None,
backup=True)
Reads and writes atoms into a .bundle directory.
The BundleTrajectory is an alternative way of storing trajectories, intended for large-scale molecular dynamics
simulations, where a single flat file becomes unwieldy. Instead, the data is stored in directory, a
‘bundle’ (the name bundle is inspired from bundles in Mac OS, which are really just directories the user is
supposed to think of as a single file-like unit).
Parameters:
filename: The name of the directory. Preferably ending in .bundle.
170 Chapter 7. Documentation for modules in ASE