soprano.properties.map.map

soprano.properties.map.map#

Classes

`Remap`([name])	Returns a structure remapped to the one given as reference.
`RemapIndices`([name])	Returns a list of the indices which will remap a given structure to the one given as reference.

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

Bases: AtomsProperty

Returns a structure remapped to the one given as reference. Remapping means creating a one-to-one correspondence between atoms based on their distances (which may include the periodic boundaries).

Parameters:

reference (ase.Atoms): Reference structure to map to. Required

mic (bool): If True, take into account periodic boundaries

via the minimum image convention. We use the general method
from ASE. It’s slow but robust.
Default is True.

check_species (bool): If True, only compare atoms of the same species.

Default is True.

tolerance (float): Tolerance for the distance comparison.

Default is 0.1 Angstrom.

Returns:

remap_indices ([int]): List of indices for the structure in the order

in which they will make it map to the reference

best

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, reference, mic, check_species, tolerance)[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.map.map.RemapIndices(name=None, **params)[source]#