pyvibdmc.simulation_utilities.xyz_npy

Classes

XYZNPY

Handler of xyz <-> npy conversion, like a personal version of openBabel.

Module Contents

class pyvibdmc.simulation_utilities.xyz_npy.XYZNPY

Handler of xyz <-> npy conversion, like a personal version of openBabel.

static extract_xyz(file_name, num_atoms)

Extracts the coordinates from an xyz file and returns it as an np array of dimension nxmx3, where n = number of geometries, m = number of atoms, and 3 = cartesian coordinates

Parameters:

• file_name (str) – Name of the .xyz file, including extension

• num_atoms (int) – Number of atoms in molecule.

Returns:

nxmx3 numpy array of coordinates

static write_xyz(coords, fname, atm_strings, cmt=None)

Writes a numpy array of x,y,z coordinates to a .xyz file

Parameters:

• fname – name of xyz file

• coords – numpy array, either mx3 or nxmx3, where n = number of geometries and m = number of atoms

• atm_strings – list of strings that correspond to the atom type e.g. [“H”,”H”,”O”]

Returns:

np.ndarray