pyvibdmc.simulation_utilities.tensorflow_descriptors.distance_descriptors

Classes

DistIt

Calculates the Distance matrix, coulomb matrix, or SPF matrix (delta_r / r) for a given molecule. Returns a cupy or

Module Contents

class pyvibdmc.simulation_utilities.tensorflow_descriptors.distance_descriptors.DistIt(zs, method, eq_xyz=None, sorted_groups=None, sorted_atoms=None, full_mat=False, force_numpy=False)[source]

Calculates the Distance matrix, coulomb matrix, or SPF matrix (delta_r / r) for a given molecule. Returns a cupy or numpy multidimensional array. If cupy is installed, this will default to using it. This means in the run(cds) function, you must pass cds as a cupy array

zs

method

eq_xyz = None

sorted_groups = None

sorted_atoms = None

full_mat = False

force_numpy = False

check_cupy()[source]

dist_matrix(atm_vec)[source]: If full matrix required, calculate it here.

atm_atm_dists(cds)[source]: Takes in coordinates, will return a vector of the atm-atm dists.

sort_atoms(d_mat)[source]

sort_groups(d_mat)[source]: Swap 2 or more groups of atoms according to the sum of the norm of the group’s columns. Only one type of group can swapped.

get_prepped_vec(atm_atm_vec)[source]

run(cds)[source]: Takes in cartesian coordinates, outputs the descriptor matrix in either vector form (upper triangle) or matrix form.