##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors: Robert T. McGibbon
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
##############################################################################
# Imports
##############################################################################
import itertools
import os
import numpy as np
from mdtraj.formats.registry import FormatRegistry
from mdtraj.utils.unit import in_units_of
from mdtraj.utils.validation import cast_indices, ensure_type
__all__ = ["LAMMPSTrajectoryFile", "load_lammpstrj"]
class _EOF(IOError):
pass
[docs]
@FormatRegistry.register_loader(".lammpstrj")
def load_lammpstrj(
filename,
top=None,
stride=None,
atom_indices=None,
frame=None,
unit_set="real",
):
"""Load a LAMMPS trajectory file.
Parameters
----------
filename : path-like
Path of LAMMPS trajectory file.
top : {str, Trajectory, Topology}
The lammpstrj format does not contain topology information. Pass in
either the path to a pdb file, a trajectory, or a topology to supply
this information.
stride : int, default=None
Only read every stride-th frame
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file.
frame : int, optional
Use this option to load only a single frame from a trajectory on disk.
If frame is None, the default, the entire trajectory will be loaded.
If supplied, ``stride`` will be ignored.
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'.
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object.
See Also
--------
mdtraj.LAMMPSTrajectoryFile : Low level interface to lammpstrj files
"""
from mdtraj.core.trajectory import _parse_topology
# We make `top` required. Although this is a little weird, its good because
# this function is usually called by a dispatch from load(), where top comes
# from **kwargs. So if its not supplied, we want to give the user an
# informative error message.
if top is None:
raise ValueError('"top" argument is required for load_lammpstrj')
if not isinstance(filename, (str, os.PathLike)):
raise TypeError(
"filename must be of type path-like for load_lammpstrj. " "you supplied %s",
)
topology = _parse_topology(top)
atom_indices = cast_indices(atom_indices)
with LAMMPSTrajectoryFile(filename) as f:
# TODO: Support other unit sets.
if unit_set == "real":
f.distance_unit == "angstroms"
else:
raise ValueError(f"Unsupported unit set specified: {unit_set}.")
if frame is not None:
f.seek(frame)
n_frames = 1
else:
n_frames = None
return f.read_as_traj(
topology,
n_frames=n_frames,
stride=stride,
atom_indices=atom_indices,
)
[docs]
@FormatRegistry.register_fileobject(".lammpstrj")
class LAMMPSTrajectoryFile:
"""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 : path-like
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?
"""
distance_unit = "angstroms"
[docs]
def __init__(self, filename, mode="r", force_overwrite=True):
"""Open a LAMMPS lammpstrj file for reading/writing."""
self._is_open = False
self._filename = filename
self._mode = mode
self._frame_index = 0
# track which line we're on. this is not essential, but its useful
# when reporting errors to the user to say what line it occured on.
self._line_counter = 0
if mode == "r":
if not os.path.exists(filename):
raise OSError("The file '%s' doesn't exist" % filename)
self._fh = open(filename)
self._is_open = True
elif mode == "w":
if not force_overwrite and os.path.exists(filename):
raise OSError('"%s" already exists' % filename)
self._fh = open(filename, "w")
self._is_open = True
else:
raise ValueError(
'mode must be one of "r" or "w". ' f'you supplied "{mode}"',
)
def close(self):
"""Close the lammpstrj file."""
if self._is_open:
self._fh.close()
self._is_open = False
def __del__(self):
self.close()
def __enter__(self):
"""Support the context manager protocol."""
return self
def __exit__(self, *exc_info):
"""Support the context manager protocol."""
self.close()
def read_as_traj(self, 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:
1) x,y,z (unscaled coordinates)
2) xs,ys,zs (scaled atom coordinates)
3) xu,yu,zu (unwrapped atom coordinates)
4) 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.
"""
from mdtraj.core.trajectory import Trajectory
if atom_indices is not None:
topology = topology.subset(atom_indices)
initial = int(self._frame_index)
xyz, cell_lengths, cell_angles = self.read(
n_frames=n_frames,
stride=stride,
atom_indices=atom_indices,
)
if len(xyz) == 0:
return Trajectory(xyz=np.zeros((0, topology.n_atoms, 3)), topology=topology)
in_units_of(xyz, self.distance_unit, Trajectory._distance_unit, inplace=True)
in_units_of(
cell_lengths,
self.distance_unit,
Trajectory._distance_unit,
inplace=True,
)
if stride is None:
stride = 1
time = (stride * np.arange(len(xyz))) + initial
t = Trajectory(xyz=xyz, topology=topology, time=time)
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
def read(self, 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 (\alpha, \beta, \\gamma) defining the unit cell for
each frame, or None if the information is not present in the file.
"""
if not self._mode == "r":
raise ValueError(
"read() is only available when file is opened " 'in mode="r"',
)
if n_frames is None:
frame_counter = itertools.count()
else:
frame_counter = range(n_frames)
if stride is None:
stride = 1
all_coords, all_lengths, all_angles = [], [], []
for _ in frame_counter:
try:
frame_coords, frame_lengths, frame_angles = self._read()
if atom_indices is not None:
frame_coords = frame_coords[atom_indices, :]
except _EOF:
break
all_coords.append(frame_coords)
all_lengths.append(frame_lengths)
all_angles.append(frame_angles)
for j in range(stride - 1):
# throw away these frames
try:
self._read()
except _EOF:
break
all_coords = np.asarray(all_coords)
all_lengths = np.asarray(all_lengths)
all_angles = np.asarray(all_angles)
return all_coords, all_lengths, all_angles
def parse_box(self, 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
"""
box = np.empty(shape=(3, 2))
if style == "triclinic":
factors = np.empty(3)
for i in range(3):
line = self._fh.readline().split()
box[i] = line[:2]
factors[i] = line[2]
xy, xz, yz = factors
xlo = box[0, 0] - np.min([0.0, xy, xz, xy + xz])
xhi = box[0, 1] - np.max([0.0, xy, xz, xy + xz])
ylo = box[1, 0] - np.min([0.0, yz])
yhi = box[1, 1] - np.max([0.0, yz])
zlo = box[2, 0]
zhi = box[2, 1]
lx = xhi - xlo
ly = yhi - ylo
lz = zhi - zlo
a = lx
b = np.sqrt(ly**2 + xy**2)
c = np.sqrt(lz**2 + xz**2 + yz**2)
alpha = np.arccos((xy * xz + ly * yz) / (b * c))
beta = np.arccos(xz / c)
gamma = np.arccos(xy / b)
lengths = np.array([a, b, c])
angles = np.degrees(np.array([alpha, beta, gamma]))
elif style == "orthogonal":
box[0] = self._fh.readline().split() # x-dim of box
box[1] = self._fh.readline().split() # y-dim of box
box[2] = self._fh.readline().split() # z-dim of box
lengths = np.diff(box, axis=1).reshape(1, 3)[0] # box lengths
angles = np.empty(3)
angles.fill(90.0)
return lengths, angles
def _read(self):
"""Read a single frame."""
# --- begin header ---
first = self._fh.readline() # ITEM: TIMESTEP
if first == "":
raise _EOF()
self._fh.readline() # timestep
self._fh.readline() # ITEM: NUMBER OF ATOMS
self._n_atoms = int(self._fh.readline()) # num atoms
box_header = self._fh.readline().split() # ITEM: BOX BOUNDS
self._line_counter += 5
if len(box_header) == 9:
lengths, angles = self.parse_box("triclinic")
elif len(box_header) == 6:
lengths, angles = self.parse_box("orthogonal")
else:
raise OSError(
f'lammpstrj parse error on line {self._line_counter:d} of "{self._filename:s}". '
"This file does not appear to be a valid "
"lammpstrj file.",
)
column_headers = self._fh.readline().split()[2:] # ITEM: ATOMS ...
if self._frame_index == 0:
# Detect which columns the atom index, type and coordinates are.
columns = {header: idx for idx, header in enumerate(column_headers)}
# Make sure the file contains an x, y, and z-coordinate of the same
# style.
coord_keywords = [
("x", "y", "z"), # unscaled
("xs", "ys", "zs"), # scaled
("xu", "yu", "zu"), # unwrapped
("xsu", "ysu", "zsu"),
] # scaled and unwrapped
for keywords in coord_keywords:
if set(keywords).issubset(column_headers):
break
else:
raise OSError(
"Invalid .lammpstrj file. Must contain x, y, and "
"z coordinates that all adhere to the same style.",
)
try:
self._atom_index_column = columns["id"]
self._atom_type_column = columns["type"]
self._xyz_columns = [
columns[keywords[0]],
columns[keywords[1]],
columns[keywords[2]],
]
except KeyError:
raise OSError(
"Invalid .lammpstrj file. Must contain 'id', " "'type', 'x*', 'y*' and 'z*' entries.",
)
self._line_counter += 4
# --- end header ---
xyz = np.empty(shape=(self._n_atoms, 3))
types = np.empty(shape=self._n_atoms, dtype="int")
# --- begin body ---
for _ in range(self._n_atoms):
line = self._fh.readline()
if line == "":
raise _EOF()
split_line = line.split()
try:
atom_index = int(split_line[self._atom_index_column])
types[atom_index - 1] = int(split_line[self._atom_type_column])
xyz[atom_index - 1] = [float(split_line[column]) for column in self._xyz_columns]
except Exception:
raise OSError(
f'lammpstrj parse error on line {self._line_counter:d} of "{self._filename:s}". '
"This file does not appear to be a valid "
"lammpstrj file.",
)
self._line_counter += 1
# --- end body ---
self._frame_index += 1
return xyz, lengths, angles
def write_box(self, 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 (\alpha, \beta, \\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.
"""
if np.allclose(angles, np.array([90, 90, 90])):
self._fh.write("ITEM: BOX BOUNDS pp pp pp\n")
self._fh.write(f"{mins[0]} {mins[0] + lengths[0]}\n")
self._fh.write(f"{mins[1]} {mins[1] + lengths[1]}\n")
self._fh.write(f"{mins[2]} {mins[2] + lengths[2]}\n")
else:
a, b, c = lengths
alpha, beta, gamma = np.radians(angles)
lx = a
xy = b * np.cos(gamma)
xz = c * np.cos(beta)
ly = np.sqrt(b**2 - xy**2)
yz = (b * c * np.cos(alpha) - xy * xz) / ly
lz = np.sqrt(c**2 - xz**2 - yz**2)
xlo = mins[0]
xhi = xlo + lx
ylo = mins[1]
yhi = ylo + ly
zlo = mins[2]
zhi = zlo + lz
xlo_bound = xlo + np.min([0.0, xy, xz, xy + xz])
xhi_bound = xhi + np.max([0.0, xy, xz, xy + xz])
ylo_bound = ylo + np.min([0.0, yz])
yhi_bound = yhi + np.max([0.0, yz])
zlo_bound = zlo
zhi_bound = zhi
self._fh.write("ITEM: BOX BOUNDS xy xz yz pp pp pp\n")
self._fh.write(f"{xlo_bound} {xhi_bound} {xy}\n")
self._fh.write(f"{ylo_bound} {yhi_bound} {xz}\n")
self._fh.write(f"{zlo_bound} {zhi_bound} {yz}\n")
def write(self, 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 (\alpha, \beta, \\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'.
"""
if not self._mode == "w":
raise ValueError(
"write() is only available when file is opened " 'in mode="w"',
)
xyz = ensure_type(
xyz,
np.float64,
3,
"xyz",
can_be_none=False,
shape=(None, None, 3),
warn_on_cast=False,
add_newaxis_on_deficient_ndim=True,
)
cell_lengths = ensure_type(
cell_lengths,
np.float64,
2,
"cell_lengths",
can_be_none=False,
shape=(len(xyz), 3),
warn_on_cast=False,
add_newaxis_on_deficient_ndim=True,
)
if cell_angles is None:
cell_angles = np.empty_like(cell_lengths)
cell_angles.fill(90)
cell_angles = ensure_type(
cell_angles,
np.float64,
2,
"cell_angles",
can_be_none=False,
shape=(len(xyz), 3),
warn_on_cast=False,
add_newaxis_on_deficient_ndim=True,
)
if not types:
# Make all particles the same type.
types = np.ones(shape=(xyz.shape[1]))
types = ensure_type(
types,
int,
1,
"types",
can_be_none=True,
shape=(xyz.shape[1],),
warn_on_cast=False,
add_newaxis_on_deficient_ndim=False,
)
# TODO: Support other unit sets.
if unit_set == "real":
self.distance_unit == "angstroms"
else:
raise ValueError(f"Unsupported unit set specified: {unit_set}.")
for i in range(xyz.shape[0]):
# --- begin header ---
self._fh.write("ITEM: TIMESTEP\n")
self._fh.write(f"{i}\n") # TODO: Write actual time if known.
self._fh.write("ITEM: NUMBER OF ATOMS\n")
self._fh.write(f"{xyz.shape[1]}\n")
self.write_box(cell_lengths[i], cell_angles[i], xyz[i].min(axis=0))
# --- end header ---
# --- begin body ---
self._fh.write("ITEM: ATOMS id type xu yu zu\n")
for j, coord in enumerate(xyz[i]):
self._fh.write(
f"{j + 1:d} {types[j]:d} {coord[0]:8.3f} {coord[1]:8.3f} {coord[2]:8.3f}\n",
)
# --- end body ---
def seek(self, 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
"""
if self._mode == "r":
advance, absolute = None, None
if whence == 0 and offset >= 0:
if offset >= self._frame_index:
advance = offset - self._frame_index
else:
absolute = offset
elif whence == 1 and offset >= 0:
advance = offset
elif whence == 1 and offset < 0:
absolute = offset + self._frame_index
elif whence == 2 and offset <= 0:
raise NotImplementedError("offsets from the end are not supported yet")
else:
raise OSError("Invalid argument")
if advance is not None:
for i in range(advance):
self._read() # advance and throw away these frames
elif absolute is not None:
self._fh.close()
self._fh = open(self._filename)
self._frame_index = 0
self._line_counter = 0
for i in range(absolute):
self._read()
else:
raise RuntimeError()
else:
raise NotImplementedError("offsets in write mode are not supported yet")
def tell(self):
"""Current file position.
Returns
-------
offset : int
The current frame in the file.
"""
return int(self._frame_index)
def __len__(self):
"Number of frames in the file"
raise NotImplementedError()