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 endcaps: float
indicates if the endcaps are included in inside/outside determination
- Type:
- 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
- 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:
- Returns:
Return true if the plane and a given one represent the same within tolerance.
- Return type:
- 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:
- 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
- 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.
- 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