Source code for MDAnalysis.coordinates.GSD

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"""GSD trajectory reader  --- :mod:`MDAnalysis.coordinates.GSD`
============================================================

Class to read the GSD trajectory, output of `HOOMD-blue`_. The GSD format
specifies both the topology and the trajectory of the particles in the
simulation. The topology is read by the
:class:`~MDAnalysis.topology.GSDParser.GSDParser` class.

The GSD format was developed having in mind the possibility of changing number
of particles, particle types, particle identities and changing topology.
Currently this class has limited functionality, due to the fact that the number
of particles and the topology are kept fixed in most MD simulations. The user
will get an error only if at any time step the number of particles is detected
to be different to the one that was set at the first time step. No check on
changes in particle identity or topology is currently implemented.

.. _`HOOMD-blue`: http://codeblue.umich.edu/hoomd-blue/index.html

Classes
-------

.. autoclass:: GSDReader
   :inherited-members:

"""
from __future__ import absolute_import, division
from six import raise_from

import numpy as np
import os
import gsd.hoomd

from . import base

class GSDReader(base.ReaderBase):
    """Reader for the GSD format.

    """
    format = 'GSD'
    units = {'time': None, 'length': None}

    def __init__(self, filename, **kwargs):
        """
        Parameters
        ----------
        filename : str
            trajectory filename
        **kwargs : dict
            General reader arguments.


        .. versionadded:: 0.17.0
        """
        super(GSDReader, self).__init__(filename, **kwargs)
        self.filename = filename
        self.open_trajectory()
        self.n_atoms = self._file[0].particles.N
        self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
        self._read_next_timestep()

    def open_trajectory(self) :
        """opens the trajectory file using gsd.hoomd module"""
        self._frame = -1
        self._file = gsd.hoomd.open(self.filename,mode='rb')

    def close(self):
        """close reader"""
        self._file.file.close()

    @property
    def n_frames(self):
        """number of frames in trajectory"""
        return len(self._file)

    def _reopen(self):
        """reopen trajectory"""
        self.close()
        self.open_trajectory()

    def _read_frame(self, frame):
        try :
            myframe = self._file[frame]
        except IndexError:
            raise_from(IOError, None)

        # set frame number
        self._frame = frame

        # sets the Timestep object
        self.ts.frame = frame
        self.ts.data['step'] = myframe.configuration.step

        # set frame box dimensions
        self.ts.dimensions = myframe.configuration.box
        for i in range(3,6) :
            self.ts.dimensions[i] = np.arccos(self.ts.dimensions[i]) * 180.0 / np.pi

        # set particle positions
        frame_positions = myframe.particles.position
        n_atoms_now = frame_positions.shape[0]
        if n_atoms_now != self.n_atoms :
            raise ValueError("Frame %d has %d atoms but the initial frame has %d"
                " atoms. MDAnalysis in unable to deal with variable"
                " topology!"%(frame, n_atoms_now, self.n_atoms))
        else :
            self.ts.positions = frame_positions
        return self.ts

    def _read_next_timestep(self) :
        """read next frame in trajectory"""
        return self._read_frame(self._frame + 1)