class pele.angleaxis.RigidFragment[source]

Defines a single rigid fragment

See also



This defines a collection of atoms that compose a single rigid bodies. This class collects all the information necessary to perform operations on the rigid body such as converting from center of mass + angle axis rotataion to atomistic coordinates. In the most simple case, this is just a whole molecule

We have tried to logically separate the concept of a rigid body (a rigid collection atoms) from an angle axis site, which might describe a single atom with a dipolar interaction.


S (3x3 array) weighted tensor of gyration S_ij = sum w_i x_i x_j. This is used for computing distances between angle axis sites. We find that weighting all atoms the same (w_i = 1) gives the best distance metric.
Sm (3x3 array) mass-weighted tensor of gyration S_ij = sum m_i x_i x_j. This is used to compute physical properties like normal mode vibrational frequncies.
M (float) The total mass of the angle axis site
W (float) The sum of all the weights. For this is just the number of atoms.
cog (np.array) center of geometry. If the atom masses are not all the same this can be different from the center of mass. Normally the center of mass is located at the origin.
symmetries (list of 3x3 np.arrays) list of all symmetry operations (expressed as matrices) which can be performed on the angle axis site. Excluding inversion. These are computed automatically.
atom_positions (list of arrays of length 3) the position of the atoms in the lab frame
atom_types (list of strings) list of atom types
atom_masses (list of floats)


add_atom(atomtype, pos[, mass]) Add a new atom to the rigid fragment
distance_squared(com1, p1, com2, p2) distance measure between 2 angle axis bodies of same type
distance_squared_grad(com1, p1, com2, p2) calculate spring force between 2 sites
finalize_setup([shift_com]) finalize setup after all sites have been added
get_smallest_rij(com1, com2) return the shortest vector from com1 to com2
metric_tensor(p) calculate the mass weighted metric tensor
metric_tensor_cog(p) calculate the metric tensor when for w_i != m_i
redistribute_forces(p, grad_com, grad_p)
to_atomistic(com, p) convert the center of mass position + angle axis vector to atomistic coords
transform_grad(p, g)

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