vasppy.cell module

class Cell(matrix)

Bases: object

Initialise a Cell object.

Parameters:

matrix (np.array) – 3x3 numpy array containing the cell matrix.

Returns:

None

angles()

The cell angles (in degrees).

Parameters:

None –

Returns:

The cell angles.

Return type:

(list(alpha,beta,gamma))

cartesian_to_fractional_coordinates(coordinates)

Convert a set of Cartesian coordinates to fractional coordinates in the cell.

Parameters:

coordinates (np.array(dim(N,3))) – The set of Cartesian coordinates.

Returns:

The corresponding set of fractional coordinates.

Return type:

(np.array(dim(N,3)))

dr(r1, r2, cutoff=None)

Calculate the distance between two fractional coordinates in the cell.

Parameters:

• r1 (np.array) – fractional coordinates for position 1.

• r2 (np.array) – fractional coordinates for position 2.

• (optional (cutoff) – Bool): If set, returns None for distances greater than the cutoff. Default None (unset).

Returns:

the distance between r1 and r2.

Return type:

(float)

fractional_to_cartesian_coordinates(coordinates)

Convert a set of fractional coordinates in the cell to Cartesian coordinates.

Parameters:

coordinates (np.array(dim(N,3))) – The set of fractional coordinates.

Returns:

The corresponding set of Cartesian coordinates.

Return type:

(np.array(dim(N,3)))

inside_cell(r)

Given a fractional-coordinate, if this lies outside the cell return the equivalent point inside the cell.

Parameters:

r (np.array) – Fractional coordinates of a point (this may be outside the cell boundaries).

Returns:

Fractional coordinates of an equivalent point, inside the cell boundaries.

Return type:

(np.array)

lengths()

The cell lengths.

Parameters:

None –

Returns:

The cell lengths.

Return type:

(np.array(a,b,c))

minimum_image(r1, r2)

Find the minimum image vector from point r1 to point r2.

Parameters:

• r1 (np.array) – fractional coordinates of point r1.

• r2 (np.array) – fractional coordinates of point r2.

Returns:

the fractional coordinate vector from r1 to the nearest image of r2.

Return type:

(np.array)

minimum_image_dr(r1, r2, cutoff=None)

Calculate the shortest distance between two points in the cell, accounting for periodic boundary conditions.

Parameters:

• r1 (np.array) – fractional coordinates of point r1.

• r2 (np.array) – fractional coordinates of point r2.

• ( (cutoff) – obj: float, optional): if set, return zero if the minimum distance is greater than cutoff. Defaults to None.

Returns:

The distance between r1 and r2.

Return type:

(float)

nearest_image(origin, point)

Find the fractional_coordinates of the nearest periodic image to a point of origin.

Parameters:

• origin (np.array) – fractional coordinates of the point of origin.

• point (np.array) – fractional coordinates of the other point.

Returns:

the fractional coordinates of the nearest image of point to origin.

Return type:

(np.array)

rotate(axis, theta)

unit_vectors()

The unit vectors for the cell vectors.

Parameters:

None –

Returns:

The unit vectors for the cell vectors.

Return type:

(np.array)

volume()

The cell volume.

Parameters:

None –

Returns:

The cell volume.

Return type:

(float)

angle(x, y)

Calculate the angle between two vectors, in degrees.

Parameters:

• x (np.array) – one vector.

• y (np.array) – the other vector.

Returns:

the angle between x and y in degrees.

Return type:

(float)

rotation_matrix(axis, theta)

Return the 3D rotation matrix associated with counterclockwise rotation about the given axis by theta radians.

Parameters:

• axis (np.array) – length 3 numpy array defining the axis of rotation.

• theta (float) – rotation angle in radians.

Returns:

the corredponding rotation matrix.

Return type:

(np.array)