def test_append_bundle(images, bundletraj):
traj = BundleTrajectory(bundletraj, mode='a')
assert len(read(bundletraj, ':')) == 2
#write(bundletraj, images, append=True)
for atoms in images:
traj.write(atoms)
traj.close()
images1 = read(bundletraj, ':')
assert len(images1) == 4
# XXX Fix the magmoms/charges bug
assert_images_equal(images * 2, images1)
def read_from_trajectory(cls, trajectory, frame=-1, atoms=None):
"""Read dynamics and atoms from trajectory (Class method).
Simultaneously reads the atoms and the dynamics from a BundleTrajectory,
including the internal data of the NPT dynamics object (automatically
saved when attaching a BundleTrajectory to an NPT object).
Arguments:
trajectory
The filename or an open BundleTrajectory object.
frame (optional)
Which frame to read. Default: the last.
atoms (optional, internal use only)
Pre-read atoms. Do not use.
"""
if isinstance(trajectory, str):
if trajectory.endswith('/'):
trajectory = trajectory[:-1]
if trajectory.endswith('.bundle'):
from ase.io.bundletrajectory import BundleTrajectory
trajectory = BundleTrajectory(trajectory)
else:
raise ValueError("Cannot open '%': unsupported file format" %
trajectory)
# trajectory is now a BundleTrajectory object (or compatible)
if atoms is None:
atoms = trajectory[frame]
init_data = trajectory.read_extra_data('npt_init', 0)
frame_data = trajectory.read_extra_data('npt_dynamics', frame)
dyn = cls(atoms,
timestep=init_data['dt'],
temperature=init_data['temperature'],
externalstress=init_data['externalstress'],
ttime=init_data['ttime'],
pfactor=init_data['pfactor_given'],
mask=init_data['mask'])
dyn.desiredEkin = init_data['desiredEkin']
dyn.tfact = init_data['tfact']
dyn.pfact = init_data['pfact']
dyn.frac_traceless = init_data['frac_traceless']
for k, v in frame_data.items():
setattr(dyn, k, v)
return (dyn, atoms)
