pele.utils.rbtools#

Module source

class pele.utils.rbtools.CoordsAdapter[source]

Source

class CoordsAdapter:

Wrapper to access coordinate array for rigid body systems

The CoordsAdapter is a wrapper for a coords array. It creates views to directly access rigid body position & rotations, atom positions and lattice coordinates. This offers a convenient way to access coorinates without the hazzle of indexing

Example:

>>> import numpy as np
>>> from pele.utils.rbtools import CoordsAdapter
>>>
>>> nrigid = 10
>>> coords = np.zeros(6*nrigid)
>>> ca = CoordsAdapter(nrigid=nrigid, coords=coords)
>>>
>>> ca.posRigid[0] = np.random.random(3)
>>> ca.rotRigid[0] = np.random.random(3)
CoordsAdapter.__init__()[source]

Source

def __init__(self, nrigid=0, natoms=0, nlattice=0, coords=None):

initialise the coordinate wrapper

Initialises the coordinate wrapper. The coordinates array can be either specified directly in the constructor or later changed via updateCoords.

Parameters:

  • nrigid (int) – number of rigid bodies

  • natoms (int) – number of single atoms

  • nlattice (int) – number of lattice degrees of freedom

  • coords (numpy.ndarray) – the coordinate array

CoordsAdapter.updateCoords()[source]

Source

def updateCoords(self, coords):

update the coordinate array

This function can be called if the coordinate adapter should point to a different coordinate array.

Parameters:

coords (numpy.ndarray) – the coordinate array