soprano.properties.symmetry.symmetry

soprano.properties.symmetry.symmetry#

Implementation of AtomProperties that relate to symmetry

Classes

`SymmetryDataset`([name])	Extracts SPGLIB's standard symmetry dataset from a given system, including spacegroup symbol, symmetry operations etc.
`WyckoffPoint`(fpos, pos, operations, hessian)	Create new instance of WyckoffPoint(fpos, pos, operations, hessian)
`WyckoffPoints`([name])	Returns a list of the found high symmetry points for a given system, including information about their point group operations, and the properties of Hessian-like quantities at that point, namely, if they are constrained to be isotropic, definite (positive/negative), or can be anything.

class soprano.properties.symmetry.symmetry.SymmetryDataset(name=None, **params)[source]#

Bases: AtomsProperty

Extracts SPGLIB’s standard symmetry dataset from a given system, including spacegroup symbol, symmetry operations etc.

Parameters:

symprec (float): distance tolerance, in Angstroms, applied when

searching symmetry.

Returns:

symm_dataset (dict): dictionary of symmetry information

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False, selection=None)#: Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

selection (str): a selection string to filter the atoms or AtomSelection

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, symprec)[source]#: Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, selection=None, **kwargs)#: Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

selection (str): a selection string to filter the atoms or AtomSelection

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

mean(s, axis=None, weights=None, **kwargs)#

Compute the mean of the property over a list of structures.

The default behaviours are: - For a list of scalars, compute the mean along the specified axis. - For a list of dictionaries, compute the mean for each key across all dictionaries. - For a list of NMRTensor objects, compute the mean using the NMRTensor.mean method. - For a list of arrays, convert to numpy array and then compute the mean along the specified axis.

Parameters:

s (list[ase.Atoms] | AtomsCollection) – The structure or collection from which to extract the property.
axis (int | None) – Axis along which the means are computed. If None, compute the mean of scalars.
weights (np.ndarray | None) – An array of weights associated with the values. If specified, the weighted average will be computed. Must have the same shape as the property values.
**kwargs – Additional arguments passed to the property’s get method.

Returns:

The mean value of the property for the given structures.

Return type:

dict | float | np.ndarray | NMRTensor

Raises:

ValueError – If s is not a collection/list, if property values are None, or if there’s an incompatible shape for computing the mean.
TypeError – If the property values are of a type that cannot be averaged.

class soprano.properties.symmetry.symmetry.WyckoffPoint(fpos, pos, operations, hessian)#

Bases: tuple

Create new instance of WyckoffPoint(fpos, pos, operations, hessian)

_asdict()#: Return a new dict which maps field names to their values.

classmethod _make(iterable)#: Make a new WyckoffPoint object from a sequence or iterable

_replace(**kwds)#: Return a new WyckoffPoint object replacing specified fields with new values

count(value, /)#: Return number of occurrences of value.

fpos#: Alias for field number 0

hessian#: Alias for field number 3

index(value, start=0, stop=9223372036854775807, /)#

Return first index of value.

Raises ValueError if the value is not present.

operations#: Alias for field number 2

pos#: Alias for field number 1

class soprano.properties.symmetry.symmetry.WyckoffPoints(name=None, **params)[source]#