Atom

class pylimer_tools_cpp.Atom(*args, **kwargs)

Bases: pybind11_object

A single bead or atom.

Overloaded function.

1. __init__(self: pylimer_tools_cpp.Atom, id: typing.SupportsInt, type: typing.SupportsInt, x: typing.SupportsFloat, y: typing.SupportsFloat, z: typing.SupportsFloat, nx: typing.SupportsInt, ny: typing.SupportsInt, nz: typing.SupportsInt) -> None

   Construct this atom.

   param id:

   Unique identifier for the atom

   param type:

   Type classification of the atom

   param x:

   X coordinate position

   param y:

   Y coordinate position

   param z:

   Z coordinate position

   param nx:

   Periodic image flag in x direction

   param ny:

   Periodic image flag in y direction

   param nz:

   Periodic image flag in z direction

2. __init__(self: pylimer_tools_cpp.Atom, properties: collections.abc.Mapping[str, typing.SupportsFloat]) -> None

   Construct this atom from a properties dictionary.

   The dictionary should contain at least the following keys: - “id”: Unique identifier for the atom - “type”: Type classification of the atom - “x”, “y”, “z”: Coordinate positions - “nx”, “ny”, “nz”: Periodic image flags

   Any additional properties will be stored as extra data.

   param properties:

   Dictionary containing atom properties

Methods Summary

compute_vector_to(self, to_atom, pbc_box)	Compute the vector to another atom.
distance_to(self, to_atom, pbc_box)	Compute the distance to another atom.
distance_to_unwrapped(self, arg0, arg1)	Compute the distance to another atom respecting the periodic image flags.
get_coordinates(self)	Get the coordinates of this atom as a vector.
get_extra_data(self)	Get all extra data properties stored with this atom (e.g., charge, dipole, etc.).
get_id(self)	Get the ID of the atom.
get_nx(self)	Get the box image that the atom is in in x direction (also known as ix or nx).
get_ny(self)	Get the box image that the atom is in in y direction (also known as iy or ny).
get_nz(self)	Get the box image that the atom is in in z direction (also known as iz or nz).
get_property(self, property)	Get a specific property value from the extra data.
get_type(self)	Get the type of the atom.
get_unwrapped_coordinates(self, arg0)	Get the unwrapped coordinates of this atom.
get_unwrapped_x(self, box)	Get the unwrapped x coordinate of the atom.
get_unwrapped_y(self, box)	Get the unwrapped y coordinate of the atom.
get_unwrapped_z(self, box)	Get the unwrapped z coordinate of the atom.
get_x(self)	Get the x coordinate of the atom.
get_y(self)	Get the y coordinate of the atom.
get_z(self)	Get the z coordinate of the atom.
mean_position_with(self, other_atom, pbc_box)	Compute the mean position between this atom and another atom, considering periodic boundaries.
mean_position_with_unwrapped(self, ...)	Compute the mean position between this atom and another atom using unwrapped coordinates.
vector_to_unwrapped(self, arg0, arg1)	Compute the vector to another atom respecting the periodic image flags.

Methods Documentation

compute_vector_to(self: pylimer_tools_cpp.Atom, to_atom: pylimer_tools_cpp.Atom, pbc_box: pylimer_tools_cpp.Box) → Annotated[numpy.typing.NDArray[numpy.float64], '[3, 1]']

Compute the vector to another atom.

Parameters:

• to_atom – The target atom

• pbc_box – The periodic boundary conditions box

Returns:

Vector pointing from this atom to the target atom

distance_to(self: pylimer_tools_cpp.Atom, to_atom: pylimer_tools_cpp.Atom, pbc_box: pylimer_tools_cpp.Box) → float

Compute the distance to another atom.

Parameters:

• to_atom – The target atom

• pbc_box – The periodic boundary conditions box

Returns:

Euclidean distance between the atoms

distance_to_unwrapped(self: pylimer_tools_cpp.Atom, arg0: pylimer_tools_cpp.Atom, arg1: pylimer_tools_cpp.Box) → float

Compute the distance to another atom respecting the periodic image flags.

Parameters:

to_atom – The target atom

Returns:

Unwrapped distance to the target atom

get_coordinates(self: pylimer_tools_cpp.Atom) → Annotated[numpy.typing.NDArray[numpy.float64], '[3, 1]']

Get the coordinates of this atom as a vector.

Returns:

A vector containing the x, y, z coordinates

get_extra_data(self: pylimer_tools_cpp.Atom) → dict[str, float]

Get all extra data properties stored with this atom (e.g., charge, dipole, etc.).

Returns:

Dictionary containing all extra properties

get_id(self: pylimer_tools_cpp.Atom) → int

Get the ID of the atom.

Returns:

The atom’s unique identifier

get_nx(self: pylimer_tools_cpp.Atom) → int

Get the box image that the atom is in in x direction (also known as ix or nx).

Returns:

The periodic image flag in x direction

get_ny(self: pylimer_tools_cpp.Atom) → int

Get the box image that the atom is in in y direction (also known as iy or ny).

Returns:

The periodic image flag in y direction

get_nz(self: pylimer_tools_cpp.Atom) → int

Get the box image that the atom is in in z direction (also known as iz or nz).

Returns:

The periodic image flag in z direction

get_property(self: pylimer_tools_cpp.Atom, property: str) → float

Get a specific property value from the extra data.

Parameters:

property – The name of the property to retrieve

Returns:

The value of the specified property

Raises:

std::out_of_range if the property doesn’t exist

get_type(self: pylimer_tools_cpp.Atom) → int

Get the type of the atom.

Returns:

The atom’s type classification

get_unwrapped_coordinates(self: pylimer_tools_cpp.Atom, arg0: pylimer_tools_cpp.Box) → Annotated[numpy.typing.NDArray[numpy.float64], '[3, 1]']

Get the unwrapped coordinates of this atom.

Parameters:

box – The simulation box to use for unwrapping

Returns:

A vector containing the unwrapped x, y, z coordinates

get_unwrapped_x(self: pylimer_tools_cpp.Atom, box: pylimer_tools_cpp.Box) → float

Get the unwrapped x coordinate of the atom.

Parameters:

box – The simulation box to use for unwrapping

Returns:

The unwrapped x coordinate

get_unwrapped_y(self: pylimer_tools_cpp.Atom, box: pylimer_tools_cpp.Box) → float

Get the unwrapped y coordinate of the atom.

Parameters:

box – The simulation box to use for unwrapping

Returns:

The unwrapped y coordinate

get_unwrapped_z(self: pylimer_tools_cpp.Atom, box: pylimer_tools_cpp.Box) → float

Get the unwrapped z coordinate of the atom.

Parameters:

box – The simulation box to use for unwrapping

Returns:

The unwrapped z coordinate

get_x(self: pylimer_tools_cpp.Atom) → float

Get the x coordinate of the atom.

Returns:

The x coordinate

get_y(self: pylimer_tools_cpp.Atom) → float

Get the y coordinate of the atom.

Returns:

The y coordinate

get_z(self: pylimer_tools_cpp.Atom) → float

Get the z coordinate of the atom.

Returns:

The z coordinate

mean_position_with(self: pylimer_tools_cpp.Atom, other_atom: pylimer_tools_cpp.Atom, pbc_box: pylimer_tools_cpp.Box) → Annotated[numpy.typing.NDArray[numpy.float64], '[3, 1]']

Compute the mean position between this atom and another atom, considering periodic boundaries.

Parameters:

• other_atom – The other atom

• pbc_box – The periodic boundary conditions box

Returns:

Vector representing the mean position

mean_position_with_unwrapped(self: pylimer_tools_cpp.Atom, other_atom: pylimer_tools_cpp.Atom, pbc_box: pylimer_tools_cpp.Box) → Annotated[numpy.typing.NDArray[numpy.float64], '[3, 1]']

Compute the mean position between this atom and another atom using unwrapped coordinates.

Parameters:

• other_atom – The other atom

• pbc_box – The periodic boundary conditions box

Returns:

Vector representing the mean position (unwrapped)

vector_to_unwrapped(self: pylimer_tools_cpp.Atom, arg0: pylimer_tools_cpp.Atom, arg1: pylimer_tools_cpp.Box) → Annotated[numpy.typing.NDArray[numpy.float64], '[3, 1]']

Compute the vector to another atom respecting the periodic image flags.

Parameters:

to_atom – The target atom

Returns:

Unwrapped vector to the target atom