This is a collection of samples, parsers and writers for formats used in the Glotzer Group at the University of Michigan, Ann Arbor.
- Luis Y. Rivera-Rivera, lyrivera@umich.edu
- Kelly Wang, kelwang@umich.edu
- Carl Simon Adorf, csadorf@umich.edu
- Bradley Dice, bdice@umich.edu
To install this package with pip, execute:
pip install garnett --userThe package's documentation is available at: https://garnett.readthedocs.io/
To build the documentation yourself using sphinx, execute within the repository:
cd doc
make html
open _build/html/index.htmlimport garnett
# Autodetects file format for a uniform trajectory API
with garnett.read('gsdfile.gsd') as traj:
for frame in traj:
pos = frame.position
# Simple conversion of trajectory formats
with garnett.read('posfile.pos') as traj:
garnett.write(traj, 'gsdfile.gsd')Access individual frames by indexing or create subsets of trajectories with slicing:
first_frame = traj[0]
last_frame = traj[-1]
nth_frame = traj[n]
# and so on
sub_trajectory = traj[i:j]Access properties of trajectories:
traj.load_arrays()
traj.box # M
traj.N # M
traj.types # MxT
traj.type_shapes # MxT
traj.typeid # MxN
traj.position # MxNx3
traj.orientation # MxNx4
traj.velocity # MxNx3
traj.mass # MxN
traj.charge # MxN
traj.diameter # MxN
traj.moment_inertia # MxNx3
traj.angmom # MxNx4
traj.image # MxNx3
# M is the number of frames
# T is the number of particle types in a frame
# N is the number of particles in a frameAccess properties of individual frames:
frame = traj[i]
frame.box # garnett.trajectory.Box object
frame.N # scalar, number of particles
frame.types # T, string names for each type
frame.type_shapes # T, list of shapes for each type
frame.typeid # N, type indices of each particle
frame.position # Nx3
frame.orientation # Nx4
frame.velocity # Nx3
frame.mass # N
frame.charge # N
frame.diameter # N
frame.moment_inertia # Nx3
frame.angmom # Nx4
frame.image # Nx3
frame.data # Dictionary of lists for each attribute
frame.data_key # List of stringsAll matrices are NumPy arrays.
See the examples directory for additional examples.
pos_reader = PosFileReader()
with open('cube.pos') as posfile:
traj = pos_reader.read(posfile)
# Initialize from last frame
snapshot = traj[-1].to_hoomd_snapshot()
system = init.read_snapshot(snapshot)
# Restore last frame
snapshot = system.take_snapshot()
traj[-1].to_hoomd_snapshot(snapshot)To run all garnett tests, ddt, HOOMD-blue (hoomd), and pycifrw must be installed in the testing environments.
Execute the tests with:
python -m unittest discover tests