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 |