pyxtal_ff.descriptors.SO3

pyxtal_ff.descriptors.SO3.Cosine(Rij, Rc, derivative=False)

pyxtal_ff.descriptors.SO3.Exponent(Rij, Rc, derivative=False)

pyxtal_ff.descriptors.SO3.GaussChebyshevQuadrature(nmax, lmax)

pyxtal_ff.descriptors.SO3.Poly1(Rij, Rc, derivative=False)

pyxtal_ff.descriptors.SO3.Poly2(Rij, Rc, derivative=False)

pyxtal_ff.descriptors.SO3.Poly3(Rij, Rc, derivative=False)

pyxtal_ff.descriptors.SO3.Poly4(Rij, Rc, derivative=False)

class pyxtal_ff.descriptors.SO3.SO3(nmax=3, lmax=3, rcut=3.5, alpha=2.0, derivative=True, stress=False, cutoff_function='cosine', weight_on=False, primitive=False)

Bases: object

A class to generate the SO3 power spectrum components based off of the Gaussian atomic neighbor density function defined in “On Representing Atomic Environments”.

Parameters:

• nmax – int, degree of radial expansion
• lmax – int, degree of spherical harmonic expansion
• rcut – float, cutoff radius for neighbor calculation
• alpha – float, gaussian width parameter
• derivative – bool, whether to calculate the gradient of not
• weight_on – bool, if True, the neighbors with different type will be counted as negative
• primitive – bool, use the asePrimitiveNeighborList

alpha

build_neighbor_list(atom_ids=None)

Builds a neighborlist for the calculation of bispectrum components for a given ASE atoms object given in the calculate method.

calculate(atoms, atom_ids=None)

Calculates the SO(3) power spectrum components of the smoothened atomic neighbor density function for given nmax, lmax, rcut, and alpha.

Parameters:

• atoms – an ASE atoms object corresponding to the desired atomic arrangement
• backend – string, specifies the method to compute the neighborlist elements, either ASE or pymatgen

clear_memory()

Clears all memory that isn’t an essential attribute for the calculator

cutoff_function

derivative

initialize_arrays()

lmax

load_from_dict(dict0)

nmax

rcut

save_dict()

save the model as a dictionary in json

stress

pyxtal_ff.descriptors.SO3.Tanh(Rij, Rc, derivative=False)

pyxtal_ff.descriptors.SO3.Unity(Rij, Rc, derivative=False)

pyxtal_ff.descriptors.SO3.W(nmax)

pyxtal_ff.descriptors.SO3.compute_cs(pos, nmax, lmax, rcut, alpha, cutoff)

pyxtal_ff.descriptors.SO3.compute_dcs(pos, nmax, lmax, rcut, alpha, cutoff)

pyxtal_ff.descriptors.SO3.g(r, n, nmax, rcut, w)

pyxtal_ff.descriptors.SO3.phi(r, alpha, rcut)

See g below