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import concurrent.futures
from ase.io.extxyz import ixyzchunks
from dynasor.trajectory.abstract_trajectory_reader import AbstractTrajectoryReader
from dynasor.trajectory.trajectory_frame import ReaderFrame
from itertools import count
import numpy as np
def chunk_to_atoms(chunk):
atoms = chunk.build()
return atoms
def iread(f, max_workers=None):
"""Reads extxyz in parallel using multiprocess."""
# chunks are simple objects
chunk_iterator = iter(ixyzchunks(f))
with concurrent.futures.ProcessPoolExecutor(max_workers=max_workers) as ex:
buff = []
for i in range(ex._max_workers):
try:
chunk = next(chunk_iterator)
buff.append(ex.submit(chunk_to_atoms, chunk))
except RuntimeError:
pass
except StopIteration:
pass
while True:
if len(buff) == 0:
break
res = buff.pop(0)
try:
chunk = next(chunk_iterator)
buff.append(ex.submit(chunk_to_atoms, chunk))
except RuntimeError:
pass
except StopIteration:
pass
atoms = res.result()
yield atoms
class ExtxyzTrajectoryReader(AbstractTrajectoryReader):
"""Read extend xyz trajectory file, typically produced by GPUMD
This is a naive (and comparatively slow) parallel implementation which
relies on the ASE xyz reader.
Parameters
----------
filename
Name of input file.
length_unit
Unit of length for the input trajectory (``'Angstrom'``, ``'nm'``, ``'pm'``, ``'fm'``).
time_unit
Unit of time for the input trajectory (``'fs'``, ``'ps'``, ``'ns'``).
max_workers
Number of working processes; defaults to ``None``, which means that the number of
processors on the machine is used.
"""
def __init__(self,
filename: str,
length_unit: str = 'Angstrom',
time_unit: str = 'fs',
max_workers: int = None):
# setup generator object
self._fobj = open(filename, 'r')
self._generator_xyz = iread(self._fobj, max_workers=max_workers)
self._open = True
self._frame_index = count(0)
# setup units
if length_unit not in self.lengthunits_to_nm_table:
raise ValueError(f'Specified length unit {length_unit} is not an available option.')
else:
self.x_factor = self.lengthunits_to_nm_table[length_unit]
if time_unit not in self.timeunits_to_fs_table:
raise ValueError(f'Specified time unit {time_unit} is not an available option.')
else:
self.t_factor = self.timeunits_to_fs_table[time_unit]
self.v_factor = self.x_factor / self.t_factor
def _get_next(self):
try:
atoms = next(self._generator_xyz)
except Exception:
self._fobj.close()
self._open = False
raise StopIteration
self._atom_types = np.array(list(atoms.symbols))
self._n_atoms = len(atoms)
self._cell = atoms.cell[:]
self._x = atoms.positions
if 'vel' in atoms.arrays:
self._v = atoms.arrays['vel']
else:
self._v = None
def __iter__(self):
return self
def close(self):
if not self._fobj.closed:
self._fobj.close()
self._open = False
def __next__(self):
if not self._open:
raise StopIteration
self._get_next()
if self._v is not None:
frame = ReaderFrame(frame_index=next(self._frame_index),
n_atoms=int(self._n_atoms),
cell=self.x_factor * self._cell.copy('F'),
positions=self.x_factor * self._x,
velocities=self.v_factor * self._v,
atom_types=self._atom_types
)
else:
frame = ReaderFrame(frame_index=next(self._frame_index),
n_atoms=int(self._n_atoms),
cell=self.x_factor * self._cell.copy('F'),
positions=self.x_factor * self._x,
atom_types=self._atom_types
)
return frame
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