pantea.descriptors.acsf package#

Submodules#

pantea.descriptors.acsf.acsf module#

pantea.descriptors.acsf.acsf.ACSF#

alias of AtomCenteredSymmetryFunction

class pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction(central_element, radial_symmetry_functions, angular_symmetry_functions)[source]#

Bases: BaseJaxPytreeDataClass

Atom-centered Symmetry Function (ACSF) descriptor captures information about the distribution of neighboring atoms around a central atom by considering both radial (two-body) and angular (three-body) symmetry functions within a cutoff distance. Radial symmetry functions describe the distances, while angular symmetry functions hold information about the angles formed by the central atom with pairs of neighboring atoms.

The ACSF represents a fingerprint of the local atomic environment and can be used in various machine learning potentials.

angular_symmetry_functions: Tuple[Tuple[AngularSymmetryFunction, NeighborElements], ...]#
central_element: str#
grad(structure, atom_index=None)[source]#

Compute gradient of the ACSF descriptor respect to the atom position.

Parameters

  • structure (Structure) – input Structure instance

  • atom_index (Optional[ArrayImpl]) – atom index in Structure [0, natoms)

Return type

ArrayImpl

Returns

gradient of the descriptor value respect to the atom position

Please note that grad_per_element method is way much faster than the current implementation of this method method.

property num_angular_symmetry_functions: int#

Return number of three-body (angular) symmetry functions.

Return type

int

property num_radial_symmetry_functions: int#

Return number of two-body (radial) symmetry functions.

Return type

int

property num_symmetry_functions: int#

Return the total (two-body and tree-body) number of symmetry functions.

Return type

int

property r_cutoff: float#

Return the maximum cutoff radius for list of the symmetry functions.

Return type

float

radial_symmetry_functions: Tuple[Tuple[RadialSymmetryFunction, NeighborElements], ...]#

pantea.descriptors.acsf.angular module#

class pantea.descriptors.acsf.angular.AngularSymmetryFunction(cfn)[source]#

Bases: BaseSymmetryFunction

A base class for three body (angular) symmetry functions.

class pantea.descriptors.acsf.angular.G3(cfn, eta, zeta, lambda0, r_shift)[source]#

Bases: AngularSymmetryFunction

Angular symmetry function.

cfn: CutoffFunction#
eta: float#
lambda0: float#
r_shift: float#
zeta: float#
class pantea.descriptors.acsf.angular.G9(cfn, eta, zeta, lambda0, r_shift)[source]#

Bases: AngularSymmetryFunction

Modified angular symmetry function.

  1. Behler, J. Chem. Phys. 134, 074106 (2011).

cfn: CutoffFunction#
eta: float#
lambda0: float#
r_shift: float#
zeta: float#

pantea.descriptors.acsf.cutoff module#

class pantea.descriptors.acsf.cutoff.CutoffFunction(r_cutoff, cutoff_function)[source]#

Bases: BaseJaxPytreeDataClass

Cutoff function for ACSF descriptor.

Cutoff functions are utilized in the calculation of Atom-centered Symmetry Function (ACSF) descriptors. These functions serve to limit the influence of atoms located beyond a specified distance from the central atom.

The ACSF descriptors employ cutoff functions to determine the range within which neighboring atoms contribute to the descriptor calculation. In fact, cutoff function assigns a weight to each neighbor atom based on its distance from the central atom. Typically, a smooth cutoff function is employed to smoothly taper off the contribution of atoms as they move away from the central atom.

The choice of cutoff function can vary depending on the specific application. Examples of commonly used cutoff functions include the hyperbolic tangent (tanh) cutoff, exponential, or exponential.

See cutoff function and cutoff type for more details.

cutoff_function: Callable#
classmethod from_type(cutoff_type, r_cutoff)[source]#

Create a cutoff function from the input cutoff type.

Return type

CutoffFunction

r_cutoff: float#

pantea.descriptors.acsf.radial module#

class pantea.descriptors.acsf.radial.G1(cfn)[source]#

Bases: RadialSymmetryFunction

Plain cutoff function as symmetry function.

cfn: CutoffFunction#
class pantea.descriptors.acsf.radial.G2(cfn, r_shift, eta)[source]#

Bases: RadialSymmetryFunction

Radial exponential symmetry function.

cfn: CutoffFunction#
eta: float#
r_shift: float#
class pantea.descriptors.acsf.radial.RadialSymmetryFunction(cfn)[source]#

Bases: BaseSymmetryFunction

A base class for two body (radial) symmetry functions.

pantea.descriptors.acsf.symmetry module#

class pantea.descriptors.acsf.symmetry.BaseSymmetryFunction(cfn)[source]#

Bases: BaseJaxPytreeDataClass

A base class for symmetry functions. All symmetry functions (i.e. radial and angular) must derive from this base class.

property r_cutoff: float#
Return type

float

class pantea.descriptors.acsf.symmetry.NeighborElements(neighbor_j: str, neighbor_k: Optional[str] = None)[source]#

Bases: tuple

Represent the chemical environment including neighbor elements.

Create new instance of NeighborElements(neighbor_j, neighbor_k)

neighbor_j: str#

Alias for field number 0

neighbor_k: Optional[str]#

Alias for field number 1

Module contents#

pantea.descriptors.acsf.ACSF#

alias of AtomCenteredSymmetryFunction

class pantea.descriptors.acsf.AngularSymmetryFunction(cfn)[source]#

Bases: BaseSymmetryFunction

A base class for three body (angular) symmetry functions.

class pantea.descriptors.acsf.AtomCenteredSymmetryFunction(central_element, radial_symmetry_functions, angular_symmetry_functions)[source]#

Bases: BaseJaxPytreeDataClass

Atom-centered Symmetry Function (ACSF) descriptor captures information about the distribution of neighboring atoms around a central atom by considering both radial (two-body) and angular (three-body) symmetry functions within a cutoff distance. Radial symmetry functions describe the distances, while angular symmetry functions hold information about the angles formed by the central atom with pairs of neighboring atoms.

The ACSF represents a fingerprint of the local atomic environment and can be used in various machine learning potentials.

angular_symmetry_functions: Tuple[Tuple[AngularSymmetryFunction, NeighborElements], ...]#
central_element: str#
grad(structure, atom_index=None)[source]#

Compute gradient of the ACSF descriptor respect to the atom position.

Parameters

  • structure (Structure) – input Structure instance

  • atom_index (Optional[ArrayImpl]) – atom index in Structure [0, natoms)

Return type

ArrayImpl

Returns

gradient of the descriptor value respect to the atom position

Please note that grad_per_element method is way much faster than the current implementation of this method method.

property num_angular_symmetry_functions: int#

Return number of three-body (angular) symmetry functions.

Return type

int

property num_radial_symmetry_functions: int#

Return number of two-body (radial) symmetry functions.

Return type

int

property num_symmetry_functions: int#

Return the total (two-body and tree-body) number of symmetry functions.

Return type

int

property r_cutoff: float#

Return the maximum cutoff radius for list of the symmetry functions.

Return type

float

radial_symmetry_functions: Tuple[Tuple[RadialSymmetryFunction, NeighborElements], ...]#
class pantea.descriptors.acsf.CutoffFunction(r_cutoff, cutoff_function)[source]#

Bases: BaseJaxPytreeDataClass

Cutoff function for ACSF descriptor.

Cutoff functions are utilized in the calculation of Atom-centered Symmetry Function (ACSF) descriptors. These functions serve to limit the influence of atoms located beyond a specified distance from the central atom.

The ACSF descriptors employ cutoff functions to determine the range within which neighboring atoms contribute to the descriptor calculation. In fact, cutoff function assigns a weight to each neighbor atom based on its distance from the central atom. Typically, a smooth cutoff function is employed to smoothly taper off the contribution of atoms as they move away from the central atom.

The choice of cutoff function can vary depending on the specific application. Examples of commonly used cutoff functions include the hyperbolic tangent (tanh) cutoff, exponential, or exponential.

See cutoff function and cutoff type for more details.

cutoff_function: Callable#
classmethod from_type(cutoff_type, r_cutoff)[source]#

Create a cutoff function from the input cutoff type.

Return type

CutoffFunction

r_cutoff: float#
class pantea.descriptors.acsf.G1(cfn)[source]#

Bases: RadialSymmetryFunction

Plain cutoff function as symmetry function.

cfn: CutoffFunction#
class pantea.descriptors.acsf.G2(cfn, r_shift, eta)[source]#

Bases: RadialSymmetryFunction

Radial exponential symmetry function.

cfn: CutoffFunction#
eta: float#
r_shift: float#
class pantea.descriptors.acsf.G3(cfn, eta, zeta, lambda0, r_shift)[source]#

Bases: AngularSymmetryFunction

Angular symmetry function.

cfn: CutoffFunction#
eta: float#
lambda0: float#
r_shift: float#
zeta: float#
class pantea.descriptors.acsf.G9(cfn, eta, zeta, lambda0, r_shift)[source]#

Bases: AngularSymmetryFunction

Modified angular symmetry function.

  1. Behler, J. Chem. Phys. 134, 074106 (2011).

cfn: CutoffFunction#
eta: float#
lambda0: float#
r_shift: float#
zeta: float#
class pantea.descriptors.acsf.NeighborElements(neighbor_j: str, neighbor_k: Optional[str] = None)[source]#

Bases: tuple

Represent the chemical environment including neighbor elements.

Create new instance of NeighborElements(neighbor_j, neighbor_k)

neighbor_j: str#

Alias for field number 0

neighbor_k: Optional[str]#

Alias for field number 1

class pantea.descriptors.acsf.RadialSymmetryFunction(cfn)[source]#

Bases: BaseSymmetryFunction

A base class for two body (radial) symmetry functions.