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#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# 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
#
# 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
#
# TRZ Reader written by Richard J. Gowers (2013)
"""TRZ trajectory I/O --- :mod:`MDAnalysis.coordinates.TRZ`
============================================================
Classes to read `IBIsCO`_ / `YASP`_ TRZ binary trajectories, including
coordinates, velocities and more (see attributes of the :class:`Timestep`).
Data are read and written in binary representation but because this depends on
the machine hardware architecture, MDAnalysis *always* reads and writes TRZ
trajectories in *little-endian* byte order.
.. _IBIsCO: http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html
.. _YASP: http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html
Classes
-------
.. autoclass:: MDAnalysis.coordinates.TRZ.Timestep
:members:
.. attribute:: frame
Index of current frame number (0 based)
.. attribute:: time
Current system time in ps
.. attribute:: n_atoms
Number of atoms in the frame (will be constant throughout trajectory)
.. attribute:: pressure
System pressure in pascals
.. attribute:: pressure_tensor
Array containing pressure tensors in order: xx, xy, yy, xz, yz, zz
.. attribute:: total_energy
Hamiltonian for the system in kJ/mol
.. attribute:: potential_energy
Potential energy of the system in kJ/mol
.. attribute:: kinetic_energy
Kinetic energy of the system in kJ/mol
.. attribute:: temperature
Temperature of the system in Kelvin
.. autoclass:: TRZReader
:members:
.. autoclass:: TRZWriter
:members:
"""
from __future__ import division, absolute_import
import six
from six.moves import range
import sys
import warnings
import numpy as np
import os
import errno
from . import base
from ..lib import util
from ..lib.util import cached
from .core import triclinic_box, triclinic_vectors
[docs]class Timestep(base.Timestep):
""" TRZ custom Timestep"""
def _init_unitcell(self):
return np.zeros(9)
@property
def dimensions(self):
"""
Unit cell dimensions ``[A,B,C,alpha,beta,gamma]``.
"""
x = self._unitcell[0:3]
y = self._unitcell[3:6]
z = self._unitcell[6:9]
return triclinic_box(x, y, z)
@dimensions.setter
def dimensions(self, box):
"""Set the Timestep dimensions with MDAnalysis format cell
(*A*, *B*, *C*, *alpha*, *beta*, *gamma*)
.. versionadded:: 0.9.0
"""
self._unitcell[:] = triclinic_vectors(box).reshape(9)
[docs]class TRZReader(base.ReaderBase):
"""Reads an IBIsCO or YASP trajectory file
Attributes
----------
ts : TRZ.Timestep
:class:`~MDAnalysis.coordinates.TRZ.Timestep` object containing
coordinates of current frame
Note
----
Binary TRZ trajectories are *always* assumed to be written in
*little-endian* byte order and are read as such.
.. versionchanged:: 0.11.0
Frames now 0-based instead of 1-based.
Extra data (Temperature, Energies, Pressures, etc) now read
into ts.data dictionary.
Now passes a weakref of self to ts (ts._reader).
.. versionchanged:: 1.0.1
Now checks for the correct `n_atoms` on reading
and can raise :exc:`ValueError`.
"""
format = "TRZ"
units = {'time': 'ps', 'length': 'nm', 'velocity': 'nm/ps'}
def __init__(self, trzfilename, n_atoms=None, **kwargs):
"""Creates a TRZ Reader
Parameters
----------
trzfilename : str
name of input file
n_atoms : int
number of atoms in trajectory, must be taken from topology file!
convert_units : bool (optional)
converts units to MDAnalysis defaults
Raises
------
ValueError
If `n_atoms` or the number of atoms in the topology file do not
match the number of atoms in the trajectory.
"""
super(TRZReader, self).__init__(trzfilename, **kwargs)
if n_atoms is None:
raise ValueError('TRZReader requires the n_atoms keyword')
self.trzfile = util.anyopen(self.filename, 'rb')
self._cache = dict()
self._n_atoms = n_atoms
self._read_trz_header()
self.ts = Timestep(self.n_atoms,
velocities=True,
forces=self.has_force,
reader=self,
**self._ts_kwargs)
# structured dtype of a single trajectory frame
readarg = str(n_atoms) + '<f4'
frame_contents = [
('p1', '<i4'),
('nframe', '<i4'),
('ntrj', '<i4'),
('natoms', '<i4'),
('treal', '<f8'),
('p2', '<2i4'),
('box', '<9f8'),
('p3', '<2i4'),
('pressure', '<f8'),
('ptensor', '<6f8'),
('p4', '<3i4'),
('etot', '<f8'),
('ptot', '<f8'),
('ek', '<f8'),
('T', '<f8'),
('p5', '<6i4'),
('rx', readarg),
('pad2', '<2i4'),
('ry', readarg),
('pad3', '<2i4'),
('rz', readarg),
('pad4', '<2i4'),
('vx', readarg),
('pad5', '<2i4'),
('vy', readarg),
('pad6', '<2i4'),
('vz', readarg)]
if not self.has_force:
frame_contents += [('pad7', '<i4')]
else:
frame_contents += [
('pad7', '<2i4'),
('fx', readarg),
('pad8', '<2i4'),
('fy', readarg),
('pad9', '<2i4'),
('fz', readarg),
('pad10', '<i4')]
self._dtype = np.dtype(frame_contents)
self._read_next_timestep()
def _read_trz_header(self):
"""Reads the header of the trz trajectory"""
self._headerdtype = np.dtype([
('p1', '<i4'),
('title', '80c'),
('p2', '<2i4'),
('force', '<i4'),
('p3', '<i4')])
data = np.fromfile(self.trzfile, dtype=self._headerdtype, count=1)
self.title = ''.join(c.decode('utf-8') for c in data['title'][0]).strip()
if data['force'] == 10:
self.has_force = False
elif data['force'] == 20:
self.has_force = True
else:
raise IOError
def _read_next_timestep(self, ts=None):
if ts is None:
ts = self.ts
try:
data = np.fromfile(self.trzfile, dtype=self._dtype, count=1)
if data['natoms'][0] != self.n_atoms:
raise ValueError("Supplied n_atoms {} is incompatible "
"with provided trajectory file. "
"Maybe `topology` is wrong?".format(
self.n_atoms))
ts.frame = data['nframe'][0] - 1 # 0 based for MDA
ts._frame = data['ntrj'][0]
ts.time = data['treal'][0]
ts._unitcell[:] = data['box']
ts.data['pressure'] = data['pressure']
ts.data['pressure_tensor'] = data['ptensor']
ts.data['total_energy'] = data['etot']
ts.data['potential_energy'] = data['ptot']
ts.data['kinetic_energy'] = data['ek']
ts.data['temperature'] = data['T']
ts._x[:] = data['rx']
ts._y[:] = data['ry']
ts._z[:] = data['rz']
ts._velocities[:, 0] = data['vx']
ts._velocities[:, 1] = data['vy']
ts._velocities[:, 2] = data['vz']
if self.has_force:
ts._forces[:, 0] = data['fx']
ts._forces[:, 1] = data['fy']
ts._forces[:, 2] = data['fz']
except IndexError: # Raises indexerror if data has no data (EOF)
six.raise_from(IOError, None)
else:
# Convert things read into MDAnalysis' native formats (nm -> angstroms)
if self.convert_units:
self.convert_pos_from_native(self.ts._pos)
self.convert_pos_from_native(self.ts._unitcell)
self.convert_velocities_from_native(self.ts._velocities)
return ts
@property
def n_atoms(self):
"""Number of atoms in a frame"""
return self._n_atoms
@property
@cached('n_frames')
def n_frames(self):
"""Total number of frames in a trajectory"""
try:
return self._read_trz_n_frames(self.trzfile)
except IOError:
return 0
def _read_trz_n_frames(self, trzfile):
"""Uses size of file and dtype information to determine how many frames exist
.. versionchanged:: 0.9.0
Now is based on filesize rather than reading entire file
"""
fsize = os.fstat(trzfile.fileno()).st_size # size of file in bytes
if not (fsize - self._headerdtype.itemsize) % self._dtype.itemsize == 0:
raise IOError("Trajectory has incomplete frames") # check that division is sane
nframes = int((fsize - self._headerdtype.itemsize) / self._dtype.itemsize) # returns long int otherwise
return nframes
def _get_dt(self):
"""The amount of time between frames in ps
Assumes that this step is constant (ie. 2 trajectories with different steps haven't been
stitched together)
Returns 0 in case of IOError
"""
curr_frame = self.ts.frame
try:
t0 = self.ts.time
self.next()
t1 = self.ts.time
dt = t1 - t0
except StopIteration:
return 0
else:
return dt
finally:
self._read_frame(curr_frame)
@property
@cached('delta')
def delta(self):
"""MD integration timestep"""
return self.dt / self.skip_timestep
@property
@cached('skip_timestep')
def skip_timestep(self):
"""Timesteps between trajectory frames"""
curr_frame = self.ts.frame
try:
t0 = self.ts._frame
self.next()
t1 = self.ts._frame
skip_timestep = t1 - t0
except StopIteration:
return 0
else:
return skip_timestep
finally:
self._read_frame(curr_frame)
def _read_frame(self, frame):
"""Move to *frame* and fill timestep with data.
.. versionchanged:: 0.11.0
Frames now 0-based instead of 1-based
"""
move = frame - self.ts.frame
self._seek(move - 1)
self._read_next_timestep()
return self.ts
def _seek(self, nframes):
"""Move *nframes* in the trajectory
Note that this doens't read the trajectory (ts remains unchanged)
.. versionadded:: 0.9.0
"""
# On python 2, seek has issues with long int. This is solve in python 3
# where there is no longer a distinction between int and long int.
if six.PY2:
framesize = long(self._dtype.itemsize)
seeksize = framesize * nframes
maxi_l = long(sys.maxint)
else:
framesize = self._dtype.itemsize
seeksize = framesize * nframes
maxi_l = seeksize + 1
if seeksize > maxi_l:
# Workaround for seek not liking long ints
# On python 3 this branch will never be used as we defined maxi_l
# greater than seeksize.
framesize = long(framesize)
seeksize = framesize * nframes
nreps = int(seeksize / maxi_l) # number of max seeks we'll have to do
rem = int(seeksize % maxi_l) # amount leftover to do once max seeks done
for _ in range(nreps):
self.trzfile.seek(maxint, 1)
self.trzfile.seek(rem, 1)
else:
seeksize = int(seeksize)
self.trzfile.seek(seeksize, 1)
def _reopen(self):
self.close()
self.open_trajectory()
self._read_trz_header() # Moves to start of first frame
[docs] def open_trajectory(self):
"""Open the trajectory file"""
if self.trzfile is not None:
raise IOError(errno.EALREADY, 'TRZ file already opened', self.filename)
if not os.path.exists(self.filename):
raise IOError(errno.ENOENT, 'TRZ file not found', self.filename)
self.trzfile = util.anyopen(self.filename, 'rb')
#Reset ts
ts = self.ts
ts.frame = -1
return self.trzfile
[docs] def Writer(self, filename, n_atoms=None):
if n_atoms is None:
# guess that they want to write the whole timestep unless told otherwise?
n_atoms = self.ts.n_atoms
return TRZWriter(filename, n_atoms)
[docs] def close(self):
"""Close trz file if it was open"""
if self.trzfile is not None:
self.trzfile.close()
self.trzfile = None
[docs]class TRZWriter(base.WriterBase):
"""Writes a TRZ format trajectory.
Note
----
Binary TRZ trajectories are *always* written in *little-endian* byte order.
"""
format = 'TRZ'
multiframe = True
units = {'time': 'ps', 'length': 'nm', 'velocity': 'nm/ps'}
def __init__(self, filename, n_atoms, title='TRZ', convert_units=True):
"""Create a TRZWriter
Parameters
----------
filename : str
name of output file
n_atoms : int
number of atoms in trajectory
title : str (optional)
title of the trajectory; the title must be 80 characters or
shorter, a longer title raises a ValueError exception.
convert_units : bool (optional)
units are converted to the MDAnalysis base format; [``True``]
"""
self.filename = filename
if n_atoms is None:
raise ValueError("TRZWriter requires the n_atoms keyword")
if n_atoms == 0:
raise ValueError("TRZWriter: no atoms in output trajectory")
self.n_atoms = n_atoms
if len(title) > 80:
raise ValueError("TRZWriter: 'title' must be 80 characters of shorter")
self.convert_units = convert_units
self.trzfile = util.anyopen(self.filename, 'wb')
self._writeheader(title)
floatsize = str(n_atoms) + '<f4'
self.frameDtype = np.dtype([
('p1a', '<i4'),
('nframe', '<i4'),
('ntrj', '<i4'),
('natoms', '<i4'),
('treal', '<f8'),
('p1b', '<i4'),
('p2a', '<i4'),
('box', '<9f8'),
('p2b', '<i4'),
('p3a', '<i4'),
('pressure', '<f8'),
('ptensor', '<6f8'),
('p3b', '<i4'),
('p4a', '<i4'),
('six', '<i4'),
('etot', '<f8'),
('ptot', '<f8'),
('ek', '<f8'),
('T', '<f8'),
('blanks', '<2f8'),
('p4b', '<i4'),
('p5a', '<i4'),
('rx', floatsize),
('p5b', '<i4'),
('p6a', '<i4'),
('ry', floatsize),
('p6b', '<i4'),
('p7a', '<i4'),
('rz', floatsize),
('p7b', '<i4'),
('p8a', '<i4'),
('vx', floatsize),
('p8b', '<i4'),
('p9a', '<i4'),
('vy', floatsize),
('p9b', '<i4'),
('p10a', '<i4'),
('vz', floatsize),
('p10b', '<i4')])
def _writeheader(self, title):
hdt = np.dtype([
('pad1', '<i4'), ('title', '80c'), ('pad2', '<i4'),
('pad3', '<i4'), ('nrec', '<i4'), ('pad4', '<i4')])
out = np.zeros((), dtype=hdt)
out['pad1'], out['pad2'] = 80, 80
out['title'] = title + ' ' * (80 - len(title))
out['pad3'], out['pad4'] = 4, 4
out['nrec'] = 10
out.tofile(self.trzfile)
def _write_next_frame(self, obj):
"""Write information associated with ``obj`` at current frame into trajectory
Parameters
----------
ag : AtomGroup or Universe
.. versionchanged:: 1.0.0
Renamed from `write_next_timestep` to `_write_next_frame`.
"""
# Check size of ts is same as initial
# TODO: Remove Timestep logic in 2.0
if isinstance(obj, base.Timestep):
ts = obj
if not ts.n_atoms == self.n_atoms:
raise ValueError("Number of atoms in ts different to initialisation")
else:
try: # atomgroup?
ts = obj.ts
except AttributeError: # universe?
ts = obj.trajectory.ts
if not obj.atoms.n_atoms == self.n_atoms:
raise ValueError("Number of atoms in ts different to initialisation")
# Gather data, faking it when unavailable
data = {}
faked_attrs = []
for att in ['pressure', 'pressure_tensor', 'total_energy',
'potential_energy', 'kinetic_energy', 'temperature']:
try:
data[att] = ts.data[att]
except KeyError:
if att == 'pressure_tensor':
data[att] = np.zeros(6, dtype=np.float64)
else:
data[att] = 0.0
faked_attrs.append(att)
try:
data['step'] = ts._frame
except AttributeError:
data['step'] = ts.frame
faked_attrs.append('step')
try:
data['time'] = ts.time
except AttributeError:
data['time'] = float(ts.frame)
faked_attrs.append('time')
if faked_attrs:
warnings.warn("Timestep didn't have the following attributes: '{0}', "
"these will be set to 0 in the output trajectory"
"".format(", ".join(faked_attrs)))
# Convert other stuff into our format
unitcell = triclinic_vectors(ts.dimensions).reshape(9)
try:
vels = ts._velocities
except AttributeError:
vels = np.zeros((self.n_atoms, 3), dtype=np.float32, order='F')
warnings.warn("Timestep didn't have velocity information, "
"this will be set to zero in output trajectory. ")
out = np.zeros((), dtype=self.frameDtype)
out['p1a'], out['p1b'] = 20, 20
out['nframe'] = ts.frame + 1 # TRZ wants 1 based
out['ntrj'] = data['step']
out['natoms'] = self.n_atoms
out['treal'] = data['time']
out['p2a'], out['p2b'] = 72, 72
out['box'] = self.convert_pos_to_native(unitcell, inplace=False)
out['p3a'], out['p3b'] = 56, 56
out['pressure'] = data['pressure']
out['ptensor'] = data['pressure_tensor']
out['p4a'], out['p4b'] = 60, 60
out['six'] = 6
out['etot'] = data['total_energy']
out['ptot'] = data['potential_energy']
out['ek'] = data['kinetic_energy']
out['T'] = data['temperature']
out['blanks'] = 0.0, 0.0
size = ts.n_atoms * 4 # size of float for vels & coords
out['p5a'], out['p5b'] = size, size
out['rx'] = self.convert_pos_to_native(ts._x, inplace=False)
out['p6a'], out['p6b'] = size, size
out['ry'] = self.convert_pos_to_native(ts._y, inplace=False)
out['p7a'], out['p7b'] = size, size
out['rz'] = self.convert_pos_to_native(ts._z, inplace=False)
out['p8a'], out['p8b'] = size, size
out['vx'] = self.convert_velocities_to_native(vels[:, 0], inplace=False)
out['p9a'], out['p9b'] = size, size
out['vy'] = self.convert_velocities_to_native(vels[:, 1], inplace=False)
out['p10a'], out['p10b'] = size, size
out['vz'] = self.convert_velocities_to_native(vels[:, 2], inplace=False)
out.tofile(self.trzfile)
[docs] def close(self):
"""Close if it was open"""
if self.trzfile is None:
return
self.trzfile.close()
self.trzfile = None