Source code for MDAnalysis.transformations.boxdimensions

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# 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.
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"""\
Set box dimensions --- :mod:`MDAnalysis.transformations.boxdimensions`
=======================================================================

Set dimensions of the simulation box to a constant vector across all timesteps.


.. autoclass:: set_dimensions
"""
import numpy as np

from .base import TransformationBase


class set_dimensions(TransformationBase):
    """
    Set simulation box dimensions.

    Timestep dimensions are modified in place.

    Example
    -------

    e.g. set simulation box dimensions to a vector containing unit cell
    dimensions [*a*, *b*, *c*, *alpha*, *beta*, *gamma*], lengths *a*,
    *b*, *c* are in the MDAnalysis length unit (Å), and angles are in degrees.

    .. code-block:: python

        dim = [2, 2, 2, 90, 90, 90]
        transform = mda.transformations.boxdimensions.set_dimensions(dim)
        u.trajectory.add_transformations(transform)

    Parameters
    ----------
    dimensions: iterable of floats
        vector that contains unit cell lengths and angles.
        Expected shapes are (6, 0) or (1, 6)

    Returns
    -------
    :class:`~MDAnalysis.coordinates.base.Timestep` object
    """

    def __init__(self,
                 dimensions,
                 max_threads=None,
                 parallelizable=True):
        super().__init__(max_threads=max_threads,
                         parallelizable=parallelizable)
        self.dimensions = dimensions

        try:
            self.dimensions = np.asarray(self.dimensions, np.float32)
        except ValueError:
            errmsg = (f'{self.dimensions} cannot be converted into '
                       'np.float32 numpy.ndarray')
            raise ValueError(errmsg)
        try:
            self.dimensions = self.dimensions.reshape(6, )
        except ValueError:
            errmsg = (f'{self.dimensions} array does not have valid box '
                       'dimension shape.\nSimulation box dimensions are '
                       'given by an float array of shape (6, ), '
                       ' containing 3 lengths and 3 angles: '
                       '[a, b, c, alpha, beta, gamma]')
            raise ValueError(errmsg)

    def _transform(self, ts):
        ts.dimensions = self.dimensions
        return ts