pele.angleaxis.RBTopology

class pele.angleaxis.RBTopology[source]

This defines the topology of a collection of rigid bodies.

Attributes

cpp_topology  

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()
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

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