atoms#
Module for modifying ASE Atoms objects for use in abTEM.
Functions
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Crop atoms outside the cell. |
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Find the closest orthogonal cell for a given cell given a maximum number of repetitions in all directions. |
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Fit the given atoms into a given cell by cropping atoms that are outside the cell, ignoring periodicity. |
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Decompose an affine transform into rotation, scale and shear. |
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Convert sequence of Euler angles to Cartesian rotation matrix. |
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Inverts the positions of atoms along a given axis. |
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Check whether the cell of given atoms is hexagonal. |
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Check whether atoms have an orthogonal cell. |
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Check whether the cell of given atoms can be converted to a structure usable by abTEM. |
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Merge atoms that are closer in distance to each other than the given tolerance. |
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Make the cell of the given atoms orthogonal. |
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Repeat the atoms in the x and y directions, retaining only the repeated atoms within the margin distance from the cell boundary. |
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Convert string representation of Cartesian axes to numerical. |
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Print a decomposed transformation in an easy-to-read manner. |
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Rotate the positions and cell vectors of atoms using Euler angles. |
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Rotate atoms so that their xy plane is rotated into a given plane. |
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Give the rotation matrix corresponding to a rotation from a given plane to the xy plane. |
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Convert a Cartesian rotation matrix to Euler angles. |
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Find and return the smallest non-repeating cell for the given atoms. |
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Standardize the cell of given atoms. |
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Wrap atoms that are closer to cell boundaries than the given tolerance. |