Structure¶

class aimstools.structuretools.structure.Structure(geometry=None, **kwargs)[source]¶

Bases: ase.atoms.Atoms

Extends the ase.atoms.Atoms class with some specific functions.

Parameters:	geometry (str) – Path to structure file (.cif, .xyz ..) or atoms object.
Variables:	atoms (Atoms) – ASE atoms object. sg (spacegroup) – Spglib spacegroup object. lattice (str) – Description of Bravais lattice.

is_1d() → bool[source]¶

Evaluates if structure is qualitatively one-dimensional.

Note

A structure is considered 1D if two axes are non-periodic.

Returns:	bool – 1-dimensional or not.

is_2d() → bool[source]¶

Evaluates if structure is qualitatively two-dimensional.

Note

A structure is considered 2D if only one axis is non-periodic.

Returns:	bool – 2D or not to 2D, that is the question.

is_3d() → bool[source]¶

Evaluates if structure is qualitatively three-dimensional.

Note

A structure is considered 3D if all axes are periodic.

Returns:	bool – 3-dimensional or not.

periodic_axes¶: Corresponds to ASE periodic boundary conditions pbc. Kept separate for transferability reasons within FHI-aims.

recenter() → None[source]¶

Recenters atoms to be in the unit cell, with vacuum on both sides.

The unit cell length c is always chosen such that it is larger than a and b.

Returns:	atoms – modified atoms object.

Note

The ase.atoms.center() method is supposed to do that, but sometimes separates the layers. I didn’t find a good way to circumvene that.

standardize(to_primitive=True, symprec=0.0001, angle_tolerance=5) → None[source]¶

Wrapper of the spglib standardize() function with extra features.

For 2D systems, the non-periodic axis is enforced as the z-axis.

Parameters:	to_primitive (bool) – If True, primitive cell is obtained. If False, conventional cell is obtained. symprec (float) – Precision to determine new cell.

Note

The combination of to_primitive=True and a larger value of symprec (1e-2) can be used to refine a structure.