wrap

mdhelper.algorithm.topology.wrap(positions: ndarray[float], dimensions: ndarray[float], *, in_place: bool = True) → ndarray[float]

Wraps particle positions back into the primary simulation cell.

Parameters:

positionsnumpy.ndarray

Particle positions.

Shape: \((N,\,3)\).

Reference unit: \(\mathrm{nm}\).

dimensionsnumpy.ndarray

System dimensions.

Shape: \((3,)\).

Reference unit: \(\mathrm{nm}\).

in_placebool, keyword-only, default: False

Determines whether the input array is modified in-place.

Returns:

positionsnumpy.ndarray

Wrapped particle positions. Only returned if in_place=False.

Shape: \((N,\,3)\).

Reference unit: \(\mathrm{nm}\).