Source code for MDAnalysis.coordinates.DLPoly

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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
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"""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
[docs] def close(self): self._file.close()