Source code for

import logging
import numpy as np

log = logging.getLogger(__name__)

[docs]class SymmetryGroup: """Detect symmetry group automatically (use spglib?).""" def __init__(self, mol, xtol=1e-8, check_basis=True, check_label=False): self.mol = mol self.xtol = xtol self.check_basis = check_basis self.check_label = check_label self.translation = None @property def natom(self): return self.mol.natm @property def nao(self): return self.mol.nao @property def dimension(self): return getattr(self.mol, "dimension", 0)
[docs] def compare_atoms(self, atom1, atom2, check_basis=None, check_label=None): """Compare atom symbol and (optionally) basis between atom1 and atom2.""" if check_basis is None: check_basis = self.check_basis if check_label is None: check_label = self.check_label if check_label: type1 = self.mol.atom_symbol(atom1) type2 = self.mol.atom_symbol(atom2) else: type1 = self.mol.atom_pure_symbol(atom1) type2 = self.mol.atom_pure_symbol(atom2) if type1 != type2: return False if not check_basis: return True bas1 = self.mol._basis[self.mol.atom_symbol(atom1)] bas2 = self.mol._basis[self.mol.atom_symbol(atom2)] return bas1 == bas2
[docs] def get_closest_atom(self, coords): """pos in internal coordinates.""" dists = np.linalg.norm(self.mol.atom_coords() - coords, axis=1) idx = np.argmin(dists) return idx, dists[idx]
[docs] def add_rotation(self, order, axis, center, unit="ang"): log.critical( ( "The specification of rotational symmetry between fragments has changed." " Check examples/ewf/ for the new syntax." ) ) raise NotImplementedError
[docs] def set_translations(self, nimages): """Set translational symmetry. Parameters ---------- nimages : array(3) Number of translationally symmetric images in the direction of the first, second, and third lattice vector. """ self.translation = np.asarray(nimages)
[docs] def clear_translations(self): self.translations = None