- class matlantis_features.features.phonon.symmetry.SymmetryOperations(atoms: Atoms, symprec: float = 1e-05)#
-
Bases:
object
All the symmetry operations in the input structure.
Methods
__init__
(atoms[, symprec])Initialize an instance.
get_permutations
(index)If the initial structure R is transformed with rotation[index] and translation[index] and get the rotated structure R’.
get_permutations_on_atom
(index)If the initial strucutre R = {R_i} was rotated with matrix {r} on the atoms[index] and get the rotated structure R’ = {R_i}’, we can get a serial of index from this function that makes R'[ind] = R.
get_rotation_on_atom
(index[, return_indices])Find the rotation matrix center on the given atom.
get_rotations_coord
(index)The rotation matrix for the cartesian coordinations instead of fractional coordinations.
get_translations_on_atom
(index)To find a set of symmetry operation (both rotation and translation) that does not change the position of atoms[index].
- __init__(atoms: Atoms, symprec: float = 1e-05) None #
-
Initialize an instance.
- Parameters
-
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atoms (Atoms) – The input structure.
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symprec (float, optional) – Distance tolerance to find crystal symmetry. Defaults to 1e-05.
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- get_permutations(index: int) ndarray #
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If the initial structure R is transformed with rotation[index] and translation[index] and get the rotated structure R’. we can get a serial of index from this function which enable R’ = R[ind].
- Parameters
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index (int) – the index of symmetry operation.
- Returns
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the permutations index.
- Return type
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np.ndarray
- get_permutations_on_atom(index: int) ndarray #
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If the initial strucutre R = {R_i} was rotated with matrix {r} on the atoms[index] and get the rotated structure R’ = {R_i}’, we can get a serial of index from this function that makes R’[ind] = R.
- Parameters
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index (int) – the index of the center atom.
- Returns
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the permutations index.
- Return type
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np.ndarray
- get_rotation_on_atom(index: int, return_indices: bool = False) Union[ndarray, Tuple[ndarray, ndarray]] #
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Find the rotation matrix center on the given atom.
- Parameters
-
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index (int) – The index of the center atom.
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return_indices (bool, optional) – If True, also return the indices of rotation matrix.
Defaults to False.
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- Returns
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The rotation matrix center on the given atom.
- Return type
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np.ndarray or tuple[np.ndarray, np.ndarray]
- get_rotations_coord(index: int) ndarray #
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The rotation matrix for the cartesian coordinations instead of fractional coordinations.
- Parameters
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index (int) – The index of rotation operation.
- Returns
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The rotation matrix for the cartesian coordinations.
- Return type
-
np.ndarray
- get_translations_on_atom(index: int) int #
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To find a set of symmetry operation (both rotation and translation) that does not change the position of atoms[index].
- Parameters
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index (int) – the index of the unmoved atom
- Returns
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the index of rotation and translation operations.
- Return type
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int
Resource Library
matlantis_features.features.phonon.symmetry.SymmetryOperations