pele.angleaxis.RBTopology

class pele.angleaxis.RBTopology

This defines the topology of a collection of rigid bodies.

Methods

add_sites(sites)	add sites to the Rigid Body topology
align_path(path)	ensure a series of images are aligned with each other
coords_adapter([coords])	Create a coords adapter to easy access coordinate array
distance_squared(coords1, coords2)	Calculate the squared distance between 2 configurations
distance_squared_grad(coords1, coords2)	Calculate gradient with respect to coords 1 for the squared distance
finalize_setup([use_cpp])
get_atom_labels()
get_atommasses()
get_atomtypes()
get_nrigid()
interpolate(initial, final, t)	interpolate between 2 sets of angle axis configurations
metric_tensor(coords)	get the metric tensor for a current configuration
neb_distance(coords1, coords2[, distance, grad])	wrapper function called by neb to get distance between 2 images
orthogopt(v, coords)	make v orthogonal to the zero eigenvectors at position coords
redistribute_gradient(rbcoords, rbgrad)
set_cpp_topology(cpp_topology)	provide class to access the fast c++ topology routines
to_atomistic(rbcoords)	convert rigid body coords to atomistic coords
transform_gradient(rbcoords, grad)	convert atomistic gradient into a gradient in rigid body coords
zeroEV(x)	return a list of zero eigenvectors

Attributes

cpp_topology