Source code for MDAnalysis.coordinates.TRZ

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# 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