symmetrize(max_n=10, tolerance=0.3, epsilon=0.001)¶
Returns a symmetrized molecule
The equivalent atoms obtained via
get_equivalent_atoms()are rotated, mirrored... unto one position. Then the average position is calculated. The average position is rotated, mirrored... back with the inverse of the previous symmetry operations, which gives the symmetrized molecule. This operation is repeated iteratively
max_ntimes at maximum until the difference between subsequently symmetrized structures is smaller than
- max_n (int) – Maximum number of iterations.
- tolerance (float) – Tolerance for detecting symmetry.
Gets passed as Argument into
- epsilon (float) – If the elementwise absolute difference of two
subsequently symmetrized structures is smaller epsilon,
the iteration stops before
The returned dictionary has three possible keys:
sym_mol: A symmetrized molecule
eq_sets: A dictionary of indices mapping to sets of indices, each key maps to indices of all equivalent atoms. The keys are guaranteed to be not symmetry-equivalent.
sym_ops: Twofold nested dictionary.
operations[i][j]gives the symmetry operation that maps atom