ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
are convenience functions, giving the number of atoms in the two molecules constituting a dimer and the relative
intermolecular distance in a dimer (relative to the ‘1.0’ separation, and in Angstrom), respectively.
7.25 Trajectory files
The io.trajectory module defines Trajectory objects, that is objects storing the temporal evolution of a
simulation. A Trajectory file contains one or more Atoms objects, usually to be interpreted as a time series,
although that is not a requirement.
The io.trajectory module currently defines two kinds of Trajectory files, the PickleTrajectory and the
BundleTrajectory. PickleTrajectory is the recommended Trajectory format, BundleTrajectory is only intended
for large molecular dynamics simulations (large meaning millions of atoms).
In the future, other kinds of Trajectories may be defined, with similar Python interface but with different underlying
file formats.
7.25.1 PickleTrajectory
The PickleTrajectory has the interface
class ase.io.trajectory.PickleTrajectory(filename, mode=’r’, atoms=None, master=None,
backup=True)
Reads/writes Atoms objects into a .traj file.
A PickleTrajectory can be created in read, write or append mode.
Parameters:
filename: The name of the parameter file. Should end in .traj.
mode=’r’: The mode.
‘r’ is read mode, the file should already exist, and no atoms argument should be specified.
‘w’ is write mode. If the file already exists, is it renamed by appending .bak to the file name. The
atoms argument specifies the Atoms object to be written to the file, if not given it must instead be given
as an argument to the write() method.
‘a’ is append mode. It acts a write mode, except that data is appended to a preexisting file.
atoms=None: The Atoms object to be written in write or append mode.
master=None: Controls which process does the actual writing. The default is that process number 0 does
this. If this argument is given, processes where it is True will write.
backup=True: Use backup=False to disable renaming of an existing file.
close()
Close the trajectory file.
open(filename, mode)
Opens the file.
For internal use only.
post_write_attach(function, interval=1, *args, **kwargs)
Attach a function to be called after writing ends.
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.
7.25. Trajectory files 169