# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://mdanalysis.googlecode.com
# Copyright (c) 2006-2011 Naveen Michaud-Agrawal,
# Elizabeth J. Denning, Oliver Beckstein,
# and contributors (see website for details)
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# 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`_ binary trajectories.
Reads coordinates, velocities and more (see attributes of the
:class:`Timestep`).
.. _IBIsCO: http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html
.. _YASP: http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html
"""
import os, errno
import base
from base import Timestep
import MDAnalysis.core
import numpy
from MDAnalysis.coordinates.core import triclinic_box
[docs]class Timestep(base.Timestep):
""" TRZ custom Timestep
:Attributes:
.. attribute:: frame
Index of the frame, (1 based)
.. attribute:: numatoms
Number of atoms in the frame (will be constant through trajectory)
.. attribute:: time
Current time of the system in ps (will not always start at 0)
.. attribute:: pressure
Pressure of the system box in kPa
.. 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
Private Attributes
.. attribute:: _unitcell
Unitcell for system. ``[Lx, 0.0, 0.0, 0.0, Ly, 0.0, 0.0, 0.0, Lz]``.
Use the attribute :attr:`dimensions` to access this information.
.. attribute:: _pos
Position of particles in box (native nm)
.. attribute:: _velocities
Velocities of particles in box (native nm/ps)
"""
def __init__(self, arg, **kwargs):
if numpy.dtype(type(arg)) == numpy.dtype(int):
self.frame = 0
self.step = 0
self.numatoms = arg
self.time = 0.0 #System time in ps
self.pressure = 0.0 #pressure in kPa
self.pressure_tensor = numpy.zeros((6), dtype=numpy.float64) #ptxx, ptxy, ptyy, ptxz, ptyz, ptzz
self.total_energy = 0.0 # Energies all kJ mol-1
self.potential_energy = 0.0
self.kinetic_energy = 0.0
self.temperature = 0.0 #Temperature in Kelvin
self._pos = numpy.zeros((self.numatoms, 3), dtype=numpy.float32, order ='F')
self._velocities = numpy.zeros((self.numatoms, 3), dtype=numpy.float32, order ='F')
self._unitcell = numpy.zeros((9), dtype=numpy.float64, order ='F')
elif isinstance(arg, Timestep): # Copy constructor
# This makes a deepcopy of the timestep
self.frame = arg.frame
self.step = arg.step
self.numatoms = arg.numatoms
self.time = arg.time
self.pressure = arg.pressure
self.pressure_tensor = numpy.array(arg.pressure_tensor)
self.total_energy = arg.total_energy
self.potential_energy = arg.potential_energy
self.kinetic_energy = arg.kinetic_energy
self.temperature = arg.temperature
self._unitcell = numpy.array(arg._unitcell)
self._pos = numpy.array(arg._pos, order='F')
self._velocities = numpy.array(arg._velocities, order='F')
elif isinstance(arg, numpy.ndarray):
if len(arg.shape) != 2:
raise ValueError("numpy array can only have 2 dimensions")
self._unitcell = numpy.zeros((9), dtype=numpy.float64)
self.frame = 0
self.step = 0
self.numatoms = arg.shape[0]
self.time = 0.0
self.pressure = 0.0
self.pressure_tensor = numpy.zeros((6), dtype=numpy.float64)
self.total_energy = 0.0
self.potential_energy = 0.0
self.kinetic_energy = 0.0
self.temperature = 0.0 #Temperature in Kelvin
self._velocities = numpy.zeros((self.numatoms, 3), dtype=numpy.float32, order ='F')
self._pos = arg.astype(numpy.float32).copy('Fortran',)
else:
raise ValueError("Cannot create an empty Timestep")
self._x = self._pos[:,0]
self._y = self._pos[:,1]
self._z = self._pos[:,2]
@property
[docs] 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)
[docs]class TRZReader(base.Reader):
""" Reads an IBIsCO or YASP trajectory file
:Data:
ts
:class:`~MDAnalysis.coordinates.TRZ.Timestep` object
containing coordinates of current frame
:Methods:
``len(trz)``
returns the number of frames
``for ts in trz``
iterates through the trajectory
:Format:
TRZ format detailed below, each line is a single fortran write statement, so is surrounded by 4 bytes of metadata
In brackets after each entry is the size of the content of each line:
``Header``::
title(80c)
nrec (int4)
``Frame``::
nframe, ntrj*nframe, natoms, treal (3*int4, real8)
boxx, 0.0, 0.0, 0.0, boxy, 0.0, 0.0, 0.0, boxz (real8 * 9)
pressure, pt11, pt12, pt22, pt13, pt23, pt33 (real8 *7)
6, etot, ptot, ek, t, 0.0, 0.0 (int4, real8 * 6)
rx (real4 * natoms)
ry
rz
vx
vy
vz
"""
format = "TRZ"
units = {'time':'ps', 'length':'nm', 'velocity':'nm/ps'}
def __init__(self, trzfilename, numatoms=None, convert_units=None, **kwargs):
"""Creates a TRZ Reader
:Arguments:
*trzfilename*
name of input file
*numatoms*
number of atoms in trajectory, must taken from topology file!
*convert_units*
converts units to MDAnalysis defaults
"""
if numatoms is None:
raise ValueError('TRZReader requires the numatoms keyword')
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units
self.filename = trzfilename
self.trzfile = open(self.filename, 'rb')
self.__numatoms = numatoms
self.__numframes = None
self.__delta = None
self.__dt = None
self.__skip_timestep = None
self.fixed = 0 #Are any atoms fixed in place? Not used in trz files
self.skip = 1 #Step size for iterating through trajectory
self.periodic = False # Box info for PBC
# structured dtype of a single trajectory frame
readarg = str(numatoms) + 'f4'
self._dtype = numpy.dtype([('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),
('pad7','i4')])
self._read_trz_header()
self.ts = Timestep(self.numatoms)
self._read_next_timestep()
def _read_trz_header(self):
"""Reads the header of the trz trajectory"""
#Read the header of the file
headerdtype = numpy.dtype([('p1','i4'),
('title','80c'),
('p2','4i4')])
data = numpy.fromfile(self.trzfile, dtype=headerdtype, count=1)
self.title = ''.join(data['title'][0])
def _read_next_timestep(self, ts=None): # self.next() is from base Reader class and calls this
#Read a timestep from binary file
if ts is None:
ts = self.ts
try:
data = numpy.fromfile(self.trzfile, dtype=self._dtype, count=1)
ts.frame = data['nframe'][0]
ts.step = data['ntrj'][0]
ts.time = data['treal'][0]
ts._unitcell[:] = data['box']
ts.pressure = data['pressure']
ts.pressure_tensor[:] = data['ptensor']
ts.total_energy = data['etot']
ts.potential_energy = data['ptot']
ts.kinetic_energy = data['ek']
ts.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.convert_units: #Convert things read into MDAnalysis' native formats (nm -> angstroms in this case)
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
except IndexError: #Raises indexerror if data has no data (EOF)
raise IOError
@property
[docs] def numatoms(self):
"""Number of atoms in a frame"""
if not self.__numatoms is None:
return self.__numatoms
try:
self._reopen()
self.__numatoms = self._read_trz_natoms(self.trzfile)
except IOError:
return 0
else:
return self.__numatoms
def _read_trz_natoms(self, trzfile):
#Read start of next frame and reopen file
try:
data = numpy.fromfile(trzfile, dtype=self._dtype, count=1)
natoms = data['natoms']
except IndexError:
raise IOError
else:
self._reopen()
return natoms
@property
[docs] def numframes(self):
"""Total number of frames in a trajectory"""
if not self.__numframes is None:
return self.__numframes
try:
self.__numframes = self._read_trz_numframes(self.trzfile)
except IOError:
return 0
else:
return self.__numframes
def _read_trz_numframes(self, trzfile):
framecounter = 0
self._reopen()
while True:
try:
self._read_next_timestep()
framecounter += 1
except IOError:
self.rewind()
return framecounter
@property
[docs] def dt(self):
"""Time step 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
"""
if not self.__dt is None:
return self.__dt
try:
t0 = self.ts.time
self.next()
t1 = self.ts.time
self.__dt = t1 - t0
except IOError:
return 0
finally:
self.rewind()
return self.__dt
@property
[docs] def delta(self):
"""MD integration timestep"""
if not self.__delta is None:
return self.__delta
self.__delta = self.dt / self.skip_timestep
return self.__delta
@property
[docs] def skip_timestep(self):
"""Timesteps between trajectory frames"""
if not self.__skip_timestep is None:
return self.__skip_timestep
try:
t0 = self.ts.step
self.next()
t1 = self.ts.step
self.__skip_timestep = t1 - t0
except IOERROR:
return 0
finally:
self.rewind()
return self.__skip_timestep
def __iter__(self):
self._reopen()
while True:
try:
yield self._read_next_timestep()
except IOError:
self.rewind()
raise StopIteration
# can use base.Reader __getitem__ implementation
def _read_frame(self, frame):
"""Move to *frame* and fill timestep with data."""
move = frame - (self.ts.frame - 1) # difference from current frame to desired frame
if move < 0: # if a backward frame is wanted
self.rewind() #reopen and start from beginning
for i in range(frame):
self.next()
else:
for i in range(move): # else skip ahead the required number
self.next()
return self.ts
[docs] def rewind(self):
"""Reposition reader onto first frame"""
self._reopen()
self.next()
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 not self.trzfile is 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 = file(self.filename, 'rb')
#Reset ts
ts = self.ts
ts.status = 1
ts.frame =0
ts.step = 0
ts.time = 0
return self.trzfile
def Writer(self, filename, numatoms=None):
if numatoms == None:
# guess that they want to write the whole timestep unless told otherwise?
numatoms = self.ts.numatoms
return TRZWriter(filename, numatoms)
[docs] def close(self):
"""Close trz file if it was open"""
if self.trzfile is None:
return
self.trzfile.close()
self.trzfile = None
def __del__(self):
if not self.trzfile is None:
self.close()
[docs]class TRZWriter(base.Writer):
"""
Writes TRZ format.
"""
format='TRZ'
units = {'time':'ps', 'length':'nm', 'velocity':'nm/ps'}
def __init__(self, filename, numatoms, title='TRZ', convert_units=None):
"""Create a TRZWriter
:Arguments:
*filename*
name of output file
*numatoms*
number of atoms in trajectory
:Keywords:
*title*
title of the trajectory
"""
self.filename = filename
if numatoms is None:
raise ValueError("TRZWriter requires the numatoms keyword")
if numatoms == 0:
raise ValueError("TRZWriter: no atoms in output trajectory")
self.numatoms = numatoms
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units
self.trzfile = open(self.filename, 'wb')
self._writeheader(title)
floatsize = str(numatoms) + 'f4'
self.frameDtype = numpy.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 = numpy.dtype([('pad1','i4'),('title','80c'),('pad2','i4'),
('pad3','i4'),('nrec','i4'),('pad4','i4')])
out = numpy.zeros((), dtype = hdt)
out['pad1'], out['pad2'] = 80, 80
out['title'] = title
out['pad3'], out['pad4'] = 4, 4
out['nrec'] = 10
out.tofile(self.trzfile)
def write_next_timestep(self, ts):
# Check size of ts is same as initial
if not ts.numatoms == self.numatoms:
raise ValueError("Number of atoms in ts different to initialisation")
out = numpy.zeros((), dtype=self.frameDtype)
out['p1a'], out['p1b'] = 20, 20
out['nframe'] = ts.frame
out['ntrj'] = ts.step
out['treal'] = ts.time
out['p2a'], out['p2b'] = 72, 72
out['box'] = self.convert_pos_to_native(ts._unitcell, inplace=False)
out['p3a'], out['p3b'] = 56, 56
out['pressure'] = ts.pressure
out['ptensor'] = ts.pressure_tensor
out['p4a'], out['p4b'] = 60, 60
out['six'] = 6
out['etot'] = ts.total_energy
out['ptot'] = ts.potential_energy
out['ek'] = ts.kinetic_energy
out['T'] = ts.temperature
out['blanks'] = 0.0, 0.0
size = ts.numatoms * 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(ts._velocities[:,0], inplace=False)
out['p9a'], out['p9b'] = size, size
out['vy'] = self.convert_velocities_to_native(ts._velocities[:,1], inplace=False)
out['p10a'], out['p10b'] = size, size
out['vz'] = self.convert_velocities_to_native(ts._velocities[:,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