region

Functions and attributes

class atomman.region.Cylinder(center1: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], center2: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], radius: float, endcaps: bool = True)

Bases: Shape

Class representing a cylinder in space.

property axis: ndarray

3D unit vector parallel to cylinder axis.

Type:

numpy.NDArray

property center1: ndarray

3D vector position of one cylinder end

Type:

numpy.NDArray

property center2: ndarray

3D vector position of one cylinder end

Type:

numpy.NDArray

property endcaps: float

indicates if the endcaps are included in inside/outside determination

Type:

bool

inside(pos: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], inclusive: bool = True) → ndarray

Indicates if position(s) are inside the shape.

Parameters:

  • pos (array-like object) – Nx3 array of coordinates.

  • inclusive (bool, optional) – Indicates if points on the shape’s boundaries are to be included. Default value is True.

Returns:

N array of bool values: True if inside shape

Return type:

numpy.NDArray

property radius: float

the cylinder’s radius

Type:

float

class atomman.region.Plane(normal: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], point: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]])

Bases: object

Class representing a plane in space. Useful for making slices.

above(pos: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], inclusive: bool = False) → ndarray

Indicates if position(s) are above the plane. Note that identifying points as above or below is dependent on the sign of the plane normal.

Parameters:

  • pos (array-like object) – Nx3 array of coordinates.

  • inclusive (bool, optional) – Indicates if points in the plane are to be included. Default value is False.

Returns:

N array of bool values: True if above the plane

Return type:

numpy.NDArray

below(pos: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], inclusive: bool = True) → ndarray

Indicates if position(s) are below the plane. Note that identifying points as above or below is dependent on the sign of the plane normal.

Parameters:

  • pos (array-like object) – Nx3 array of coordinates.

  • inclusive (bool, optional) – Indicates if points in the plane are to be included. Default value is True.

Returns:

N array of bool values: True if below the plane

Return type:

numpy.NDArray

isclose(other: Plane, atol: float = 1e-08) → bool

Check the plane and a given one represent the same. Note that if the normal vectors of the two planes are antiparallel, they are considered to be different.

Parameters:

  • other (Plane) – a plane to be compared with

  • rtol (float) – the relative tolerance parameter used in numpy.isclose

  • atol (float) – the absolute tolerance parameter used in numpy.isclose

Returns:

Return true if the plane and a given one represent the same within tolerance.

Return type:

bool

property normal: ndarray

3D normal unit vector of the plane.

Type:

numpy.NDArray

operate(rotation: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], translation: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]]) → Plane

Return a new plane transformed by given symmetry operation

Parameters:

  • rotation (array-like, (3, 3)) – rotation matrix in cartedian coordinates

  • translation (array-like, (3, )) – translation matrix in cartedian coordinates

Returns:

A new plane transformed by the specified operations.

Return type:

Plane

property point: ndarray

a 3D vector position on the plane.

Type:

numpy.NDArray

class atomman.region.PlaneSet(planes: Union[Plane, List[Plane]])

Bases: Shape

Class consisting of a shape defined by a set of planes

inside(pos: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], inclusive: bool = True) → ndarray

Indicates if position(s) are inside the shape.

Parameters:

  • pos (array-like object) – Nx3 array of coordinates.

  • inclusive (bool, optional) – Indicates if points on the shape’s boundaries are to be included. Default value is True.

Returns:

N array of bool values: True if inside shape

Return type:

numpy.NDArray

property planes: List[Plane]

The planes that make up the shape

Type:

list of atomman.region.Plane

class atomman.region.Shape

Bases: object

Template class for defining geometric regions in space.

inside(pos: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], inclusive: bool = True) → ndarray

Indicates if position(s) are inside the shape.

Parameters:

  • pos (array-like object) – Nx3 array of coordinates.

  • inclusive (bool, optional) – Indicates if points on the shape’s boundaries are to be included. Default value is True.

Returns:

N array of bool values: True if inside shape

Return type:

numpy.NDArray

outside(pos: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], inclusive: bool = False) → ndarray

Indicates if position(s) are inside the shape.

Parameters:

  • pos (array-like object) – Nx3 array of coordinates.

  • inclusive (bool, optional) – Indicates if points on the shape’s boundaries are to be included. Default value is False.

Returns:

N array of bool values: True if outside shape

Return type:

numpy.NDArray

class atomman.region.Sphere(center: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], radius: float)

Bases: Shape

Class representing a sphere in space.

property center: ndarray

3D vector position of sphere’s center

Type:

numpy.NDArray

inside(pos: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype], Sequence[_SupportsArray[dtype]], Sequence[Sequence[_SupportsArray[dtype]]], Sequence[Sequence[Sequence[_SupportsArray[dtype]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]], inclusive: bool = True) → ndarray

Indicates if position(s) are inside the shape.

Parameters:

  • pos (array-like object) – Nx3 array of coordinates.

  • inclusive (bool, optional) – Indicates if points on the shape’s boundaries are to be included. Default value is True.

Returns:

N array of bool values: True if inside shape

Return type:

numpy.NDArray

property radius: float

the sphere’s radius

Type:

float