Source code for MDAnalysis.coordinates.DLPoly
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# Please cite your use of MDAnalysis in published work:
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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
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# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""DL_Poly format reader :mod:`MDAnalysis.coordinates.DLPoly`
=============================================================
Read DL Poly_ format coordinate files
.. _Poly: http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx
"""
import numpy as np
from . import base
from . import core
from ..lib import util
from ..lib.util import cached, store_init_arguments
_DLPOLY_UNITS = {'length': 'Angstrom', 'velocity': 'Angstrom/ps', 'time': 'ps'}
[docs]
class ConfigReader(base.SingleFrameReaderBase):
"""DLPoly Config file Reader
.. versionadded:: 0.11.0
.. versionchanged:: 2.0.0
coordinates, velocities, and forces are no longer stored in 'F' memory
layout, instead now using the numpy default of 'C'.
"""
format = 'CONFIG'
units = _DLPOLY_UNITS
def _read_first_frame(self):
unitcell = np.zeros((3, 3), dtype=np.float32)
with open(self.filename, 'r') as inf:
self.title = inf.readline().strip()
levcfg, imcon, megatm = np.int64(inf.readline().split()[:3])
if not imcon == 0:
unitcell[0][:] = inf.readline().split()
unitcell[1][:] = inf.readline().split()
unitcell[2][:] = inf.readline().split()
ids = []
coords = []
if levcfg > 0:
has_vels = True
velocities = []
else:
has_vels = False
if levcfg == 2:
has_forces = True
forces = []
else:
has_forces = False
line = inf.readline().strip()
# Read records infinitely
while line:
try:
idx = int(line[8:])
except ValueError: # dl_poly classic doesn't have this
pass
else:
ids.append(idx)
xyz = np.float32(inf.readline().split())
coords.append(xyz)
if has_vels:
vxyz = np.float32(inf.readline().split())
velocities.append(vxyz)
if has_forces:
fxyz = np.float32(inf.readline().split())
forces.append(fxyz)
line = inf.readline().strip()
coords = np.array(coords, dtype=np.float32)
if has_vels:
velocities = np.array(velocities, dtype=np.float32)
if has_forces:
forces = np.array(forces, dtype=np.float32)
self.n_atoms = len(coords)
if ids:
# If we have indices then sort based on them
ids = np.array(ids)
order = np.argsort(ids)
coords = coords[order]
if has_vels:
velocities = velocities[order]
if has_forces:
forces = forces[order]
ts = self.ts = self._Timestep(self.n_atoms,
velocities=has_vels,
forces=has_forces,
**self._ts_kwargs)
ts._pos = coords
if has_vels:
ts._velocities = velocities
if has_forces:
ts._forces = forces
if not imcon == 0:
ts.dimensions = core.triclinic_box(*unitcell)
ts.frame = 0
[docs]
class HistoryReader(base.ReaderBase):
"""Reads DLPoly format HISTORY files
.. versionadded:: 0.11.0
"""
format = 'HISTORY'
units = _DLPOLY_UNITS
@store_init_arguments
def __init__(self, filename, **kwargs):
super(HistoryReader, self).__init__(filename, **kwargs)
self._cache = {}
# "private" file handle
self._file = util.anyopen(self.filename, 'r')
self.title = self._file.readline().strip()
header = np.int64(self._file.readline().split()[:3])
self._levcfg, self._imcon, self.n_atoms = header
self._has_vels = True if self._levcfg > 0 else False
self._has_forces = True if self._levcfg == 2 else False
rwnd = self._file.tell()
self._file.readline()
if (len(self._file.readline().split())) == 3:
self._has_cell = True
else:
self._has_cell = False
self._file.seek(rwnd)
self.ts = self._Timestep(self.n_atoms,
velocities=self._has_vels,
forces=self._has_forces,
**self._ts_kwargs)
self._read_next_timestep()
def _read_next_timestep(self, ts=None):
if ts is None:
ts = self.ts
line = self._file.readline() # timestep line
if not line.startswith('timestep'):
raise IOError
if self._has_cell:
unitcell = np.zeros((3, 3))
unitcell[0] = self._file.readline().split()
unitcell[1] = self._file.readline().split()
unitcell[2] = self._file.readline().split()
ts.dimensions = core.triclinic_box(*unitcell)
# If ids are given, put them in here
# and later sort by them
ids = []
for i in range(self.n_atoms):
line = self._file.readline().strip() # atom info line
try:
idx = int(line.split()[1])
except IndexError:
pass
else:
ids.append(idx)
# Read in this order for now, then later reorder in place
ts._pos[i] = self._file.readline().split()
if self._has_vels:
ts._velocities[i] = self._file.readline().split()
if self._has_forces:
ts._forces[i] = self._file.readline().split()
i += 1
if ids:
ids = np.array(ids)
# if ids aren't strictly sequential
if not np.all(ids == (np.arange(self.n_atoms) + 1)):
order = np.argsort(ids)
ts._pos[:] = ts._pos[order]
if self._has_vels:
ts._velocities[:] = ts._velocities[order]
if self._has_forces:
ts._forces[:] = ts._forces[order]
ts.frame += 1
return ts
def _read_frame(self, frame):
"""frame is 0 based, error checking is done in base.getitem"""
self._file.seek(self._offsets[frame])
self.ts.frame = frame - 1 # gets +1'd in read_next_frame
return self._read_next_timestep()
@property
@cached('n_frames')
def n_frames(self):
# Second line is traj_key, imcom, n_atoms, n_frames, n_records
offsets = []
with open(self.filename, 'r') as f:
f.readline()
f.readline()
position = f.tell()
line = f.readline()
while line.startswith('timestep'):
offsets.append(position)
if self._has_cell:
f.readline()
f.readline()
f.readline()
for _ in range(self.n_atoms):
f.readline()
f.readline()
if self._has_vels:
f.readline()
if self._has_forces:
f.readline()
position = f.tell()
line = f.readline()
self._offsets = offsets
return len(self._offsets)
def _reopen(self):
self.close()
self._file = open(self.filename, 'r')
self._file.readline() # header is 2 lines
self._file.readline()
self.ts.frame = -1