Box¶

class pylimer_tools_cpp.Box(*args, **kwargs)¶

Bases: pybind11_object

The box that the simulation is run in.

Note

Currently, only rectangular boxes are supported.

Overloaded function.

__init__(self: pylimer_tools_cpp.Box, arg0: float, arg1: float, arg2: float) -> None
__init__(self: pylimer_tools_cpp.Box, arg0: float, arg1: float, arg2: float, arg3: float, arg4: float, arg5: float) -> None

Methods Summary

`apply_pbc`(self, distances)	Apply periodic boundary conditions (PBC): adjust the specified distances to fit into this box.
`apply_simple_shear`(self, shear_magnitude[, ...])	Apply a simple shear to the box.
`get_bounding_box`(self)	Get an orthogonal box that encloses this box.
`get_high_x`(self)	Get the upper bound of the box in x direction.
`get_high_y`(self)	Get the upper bound of the box in y direction.
`get_high_z`(self)	Get the upper bound of the box in z direction.
`get_l`(self)	Get the three lengths of the box in an array/list.
`get_low_x`(self)	Get the lower bound of the box in x direction.
`get_low_y`(self)	Get the lower bound of the box in y direction.
`get_low_z`(self)	Get the lower bound of the box in z direction.
`get_lx`(self)	Get the length of the box in x direction.
`get_ly`(self)	Get the length of the box in y direction.
`get_lz`(self)	Get the length of the box in z direction.
`get_offset`(self, distances)	Compute the offset required to compensate for periodic boundary conditions.
`get_volume`(self)	Compute the volume of the box.
`is_valid_offset`(self, potential_offset[, ...])	Check whether the passed offset is a valid one in this box.

Methods Documentation

apply_pbc(self: pylimer_tools_cpp.Box, distances: numpy.ndarray[numpy.float64[m, 1]]) → numpy.ndarray[numpy.float64[m, 1]]¶

Apply periodic boundary conditions (PBC): adjust the specified distances to fit into this box.

Parameters:: distances – The distances to adjust
Returns:: The adjusted distances

apply_simple_shear(self: pylimer_tools_cpp.Box, shear_magnitude: float, shear_direction: int = 0) → None¶

Apply a simple shear to the box.

Warning

Currently, this is not supported for all operations.

For shear magnitude, you specify the angle \(\gamma\).

Parameters:

shear_magnitude – The shear magnitude (angle \(\gamma\))
shear_direction – Direction of shear: 0 for x, 1 for y, 2 for z. Use any other integer to disable shear.

get_bounding_box(self: pylimer_tools_cpp.Box) → pylimer_tools_cpp.Box¶

Get an orthogonal box that encloses this box.

For non-sheared boxes, the resulting box is identical to the current box.

Returns:: A new Box object representing the bounding box

get_high_x(self: pylimer_tools_cpp.Box) → float¶

Get the upper bound of the box in x direction.

Returns:: The upper x-coordinate boundary

get_high_y(self: pylimer_tools_cpp.Box) → float¶

Get the upper bound of the box in y direction.

Returns:: The upper y-coordinate boundary

get_high_z(self: pylimer_tools_cpp.Box) → float¶

Get the upper bound of the box in z direction.

Returns:: The upper z-coordinate boundary

get_l(self: pylimer_tools_cpp.Box) → numpy.ndarray[numpy.float64[3, 1]]¶

Get the three lengths of the box in an array/list.

Returns:: Array containing [Lx, Ly, Lz] box dimensions

get_low_x(self: pylimer_tools_cpp.Box) → float¶

Get the lower bound of the box in x direction.

Returns:: The lower x-coordinate boundary

get_low_y(self: pylimer_tools_cpp.Box) → float¶

Get the lower bound of the box in y direction.

Returns:: The lower y-coordinate boundary

get_low_z(self: pylimer_tools_cpp.Box) → float¶

Get the lower bound of the box in z direction.

Returns:: The lower z-coordinate boundary

get_lx(self: pylimer_tools_cpp.Box) → float¶

Get the length of the box in x direction.

Returns:: The x-dimension length of the box

get_ly(self: pylimer_tools_cpp.Box) → float¶

Get the length of the box in y direction.

Returns:: The y-dimension length of the box

get_lz(self: pylimer_tools_cpp.Box) → float¶

Get the length of the box in z direction.

Returns:: The z-dimension length of the box

get_offset(self: pylimer_tools_cpp.Box, distances: numpy.ndarray[numpy.float64[m, 1]]) → numpy.ndarray[numpy.float64[m, 1]]¶

Compute the offset required to compensate for periodic boundary conditions.

Useful e.g. if you are using absolute coordinates for distances, but still need an infinite network, e.g., if the bonds need to be able to get longer than half the box.

Parameters:: distances – The distances to compute offset for
Returns:: The computed offset

get_volume(self: pylimer_tools_cpp.Box) → float¶

Compute the volume of the box.

\(V = L_x \cdot L_y \cdot L_z\)

Returns:: The volume of the box

is_valid_offset(self: pylimer_tools_cpp.Box, potential_offset: numpy.ndarray[numpy.float64[m, 1]], abs_precision: float = 1e-05) → bool¶

Check whether the passed offset is a valid one in this box.

Parameters:

potential_offset – The offset to validate
abs_precision – Absolute precision for the validation

Returns:

True if the offset is valid, False otherwise