unwrap_edge

mdhelper.algorithm.topology.unwrap_edge(*, group: AtomGroup = None, positions: ndarray[float] = None, bonds: ndarray[int] = None, dimensions: ndarray[float] = None, thresholds: ndarray[float] = None, masses: ndarray[float] = None) → ndarray[float]

Locally unwraps the positions of molecules at the edge of the simulation box.

Parameters:

groupMDAnalysis.AtomGroup, optional

Atom group. If not provided, the atom positions, bonds, and dimensions must be provided in positions, bonds, and dimensions, respectively.

positionsnumpy.ndarray, optional

Atom positions.

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

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

bondsnumpy.ndarray, optional

Pairs of all bonded atom indices with respect to positions.

Shape: \((N_\mathrm{bonds},\,2)\).

dimensionsnumpy.ndarray, optional

System dimensions and, optionally, angles.

Shape: \((3,)\) or \((6,)\).

Reference unit: \(\mathrm{nm}\) (lengths) and \(^\circ\) (angles).

thresholdsnumpy.ndarray, optional

Maximum distances in each direction an atom can move before it is considered to have crossed a boundary.

Shape: \((3,)\).

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

massesnumpy.ndarray, optional

Atom masses. If not specified, all atoms are assumed to have the same mass.

Shape: \((N,)\).

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

Returns:

positionsnumpy.ndarray

Unwrapped atom positions.

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

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