soprano.properties.order.order

Implementation of AtomsProperties that relate to bond order parameters

Classes

BondOrder([name])

Computes the order parameters defined by Steinhardt et al. [PRB 28, 784 (1983)] for an atom or group of atoms in the system.

class soprano.properties.order.order.BondOrder(name=None, **params)

Bases: AtomsProperty

Computes the order parameters defined by Steinhardt et al. [PRB 28, 784 (1983)] for an atom or group of atoms in the system. Here for each atom all closest periodic copies of the others are used; a sigmoidal cutoff is used to reduce the impact of those beyond a certain distance while keeping the behaviour smooth upon small fluctuations.

Parameters:

l_channels (list[int]): list of angular momentum channels to be used

for the calculation. Must be integers >= 1.

Default is all channels 1 to 10.

center_atoms (AtomSelection): AtomSelection, integer index or list of

indices of all atoms around which the

bond order parameters are to be computed

and summed over. Default is None, which

means all atoms of the system.

environment_atoms (AtomSelection): AtomSelection, integer index or

list of indices of all atoms that

used as environment to compute the

bond order parameters. For each

‘center’ atom, all its links to

‘environment’ atoms other than

itself will be considered. Default

is None, which means all atoms of

the system.

cutoff_radius (float): radius at which to cut the smoothing sigmoid

function, in Angstroms. Default is 2.0.

cutoff_width (float): width parameter of the sigmoid, controlling the

steepness with which it falls to zero, in

Angstroms. Default is 0.05.

compute_W (bool): whether to also compute the W parameter (third

order) besides the Q (second order).

Returns:

bond_order_pars (dict): dictionary containing arrays with Q and, if

required, W for each l in l_channels.

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)

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

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, l_channels, center_atoms, environment_atoms, cutoff_radius, cutoff_width, compute_W)

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, **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

Returns:

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

a list of values if a collection has been passed

soprano.properties.order.order._steinhardt_pars(vecs, l_channels, compute_W=False, weights=None)

Compute the Steinhardt bond order parameters (Q and optionally W)

soprano.properties.order.order._valid_triples(l)

Valid triples for angular momentum l for which m1 + m2 + m3 = 0