mdtraj.formats.LAMMPSTrajectoryFile¶

class mdtraj.formats.LAMMPSTrajectoryFile(filename, mode='r', force_overwrite=True)¶

Interface for reading and writing to a LAMMPS lammpstrj files. This is a file-like object, that both reading or writing depending on the mode flag. It implements the context manager protocol, so you can also use it with the python ‘with’ statement.

Parameters:

filename : str

The filename to open. A path to a file on disk.

mode : {‘r’, ‘w’}

The mode in which to open the file, either ‘r’ for read or ‘w’ for write.

force_overwrite : bool

If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?

__init__(filename, mode='r', force_overwrite=True)¶: Open a LAMMPS lammpstrj file for reading/writing.

Methods

`__init__`(filename[, mode, force_overwrite])	Open a LAMMPS lammpstrj file for reading/writing.
`close`()	Close the lammpstrj file.
`parse_box`(style)	Extract lengths and angles from a frame.
`read`([n_frames, stride, atom_indices])	Read data from a lammpstrj file.
`read_as_traj`(topology[, n_frames, stride, ...])	Read a trajectory from a lammpstrj file
`seek`(offset[, whence])	Move to a new file position.
`tell`()	Current file position.
`write`(xyz, cell_lengths[, cell_angles, ...])	Write one or more frames of data to a lammpstrj file.
`write_box`(lengths, angles, mins)	Write the box lines in the header of a frame.

Attributes

distance_unit

close()¶: Close the lammpstrj file.

read_as_traj(topology, n_frames=None, stride=None, atom_indices=None)¶

Read a trajectory from a lammpstrj file

Parameters:

topology : Topology

The system topology

n_frames : int, optional

If positive, then read only the next n_frames frames. Otherwise read all of the frames in the file.

stride : np.ndarray, optional

Read only every stride-th frame.

atom_indices : array_like, optional

If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it required an extra copy, but will save memory.

Returns:

trajectory : Trajectory

A trajectory object containing the loaded portion of the file.

See also

read: Returns the raw data from the file

Notes

If coordinates are specified in more than one style, the first complete trio of x/y/z coordinates will be read in according to the following order:

x,y,z (unscaled coordinates)

xs,ys,zs (scaled atom coordinates)

xu,yu,zu (unwrapped atom coordinates)

xsu,ysu,zsu (scaled unwrapped atom coordinates)

E.g., if the file contains x, y, z, xs, ys, zs then x, y, z will be used.: if the file contains x, y, xs, ys, zs then xs, ys, zs will be used.

read(n_frames=None, stride=None, atom_indices=None)¶

Read data from a lammpstrj file.

Parameters:

n_frames : int, None

The number of frames you would like to read from the file. If None, all of the remaining frames will be loaded.

stride : np.ndarray, optional

Read only every stride-th frame.

atom_indices : array_like, optional

If not none, then read only a subset of the atoms coordinates from the file.

Returns:

xyz : np.ndarray, shape=(n_frames, n_atoms, 3), dtype=np.float32

cell_lengths : np.ndarray, None

The lengths (a,b,c) of the unit cell for each frame, or None if the information is not present in the file.

cell_angles : np.ndarray, None

The angles (lpha, eta, gamma) defining the unit cell for each frame, or None if the information is not present in the file.

parse_box(style)¶

Extract lengths and angles from a frame.

Parameters:

style : str

Type of box, ‘triclinic’ or ‘orthogonal’.

Returns:

lengths : ndarray

angles : ndarray

Notes

For more info on how LAMMPS defines boxes: http://lammps.sandia.gov/doc/Section_howto.html#howto_12

write_box(lengths, angles, mins)¶

Write the box lines in the header of a frame.

Parameters:

lengths : np.ndarray, dtype=np.double, shape=(3, )

The lengths (a,b,c) of the unit cell for each frame.

angles : np.ndarray, dtype=np.double, shape=(3, )

The angles (lpha, eta, gamma) defining the unit cell for each frame.

mins : np.ndarray, dtype=np.double, shape=(3, )

The minimum coordinates in the x-, y- and z-directions.

write(xyz, cell_lengths, cell_angles=None, types=None, unit_set='real')¶

Write one or more frames of data to a lammpstrj file.

Parameters:

xyz : np.ndarray, shape=(n_frames, n_atoms, 3)

The cartesian coordinates of the atoms to write. By convention, the lengths should be in units of angstroms.

cell_lengths : np.ndarray, dtype=np.double, shape=(n_frames, 3)

The lengths (a,b,c) of the unit cell for each frame. By convention, the lengths should be in units of angstroms.

cell_angles : np.ndarray, dtype=np.double, shape=(n_frames, 3)

The angles (lpha, eta, gamma) defining the unit cell for each frame. (Units of degrees).

types : np.ndarray, shape(3, ), dtype=int

The numeric type of each particle.

unit_set : str, optional

The LAMMPS unit set that the simulation was performed in. See http://lammps.sandia.gov/doc/units.html for options. Currently supported unit sets: ‘real’.

seek(offset, whence=0)¶

Move to a new file position.

Parameters:

offset : int

A number of frames.

whence : {0, 1, 2}

0: offset from start of file, offset should be >=0. 1: move relative to the current position, positive or negative 2: move relative to the end of file, offset should be <= 0. Seeking beyond the end of a file is not supported

tell()¶

Current file position.

Returns:

offset : int

The current frame in the file.