def __init__(self, numbers, coordinates, masses, energy, gradient, hessian, multiplicity=None, symmetry_number=None, periodic=False, title=None, graph=None, symbols=None, unit_cell=None):
"""
Arguments:
| ``numbers`` -- The atom numbers (integer numpy array with shape N)
| ``coordinates`` -- the atom coordinates in Bohr (float numpy array
with shape Nx3)
| ``masses`` -- The atomic masses in atomic units (float numpy array
with shape N)
| ``energy`` -- The molecular energy in Hartree
| ``gradient`` -- The gradient of the energy, i.e. the derivatives
towards Cartesian coordinates, in atomic units
(float numpy array with shape Nx3)
| ``hessian`` -- The hessian of the energy, i.e. the matrix with
second order derivatives towards Cartesian
coordinates, in atomic units (float numpy array
with shape 3Nx3N)
| ``multiplicity`` -- The spin multiplicity of the electronic system
Optional arguments:
| ``symmetry_number`` -- The rotational symmetry number, None when
not known or computed [default=None]
| ``periodic`` -- True when the system is periodic in three
dimensions [default=False]
| ``title`` -- The title of the system
| ``graph`` -- The molecular graph of the system
| ``symbols`` -- A list with atom symbols
| ``unit_cell`` -- The unit cell vectors for periodic structures
"""
BaseMolecule.__init__(self, numbers, coordinates, title, masses, graph, symbols, unit_cell)
self.energy = energy
self.gradient = gradient
self.hessian = hessian
self.multiplicity = multiplicity
self.symmetry_number = symmetry_number
self.periodic = periodic
def __init__(self,
numbers,
coordinates,
masses,
energy,
gradient,
hessian,
multiplicity=None,
symmetry_number=None,
periodic=False,
title=None,
graph=None,
symbols=None,
unit_cell=None,
fixed=None):
"""
Arguments:
| ``numbers`` -- The atom numbers (integer numpy array with shape N)
| ``coordinates`` -- the atom coordinates in Bohr (float numpy array
with shape Nx3)
| ``masses`` -- The atomic masses in atomic units (float numpy array
with shape N)
| ``energy`` -- The molecular energy in Hartree
| ``gradient`` -- The gradient of the energy, i.e. the derivatives
towards Cartesian coordinates, in atomic units
(float numpy array with shape Nx3)
| ``hessian`` -- The hessian of the energy, i.e. the matrix with
second order derivatives towards Cartesian
coordinates, in atomic units (float numpy array
with shape 3Nx3N)
| ``multiplicity`` -- The spin multiplicity of the electronic system
Optional arguments:
| ``symmetry_number`` -- The rotational symmetry number, None when
not known or computed [default=None]
| ``periodic`` -- True when the system is periodic in three
dimensions [default=False]
| ``title`` -- The title of the system
| ``graph`` -- The molecular graph of the system
| ``symbols`` -- A list with atom symbols
| ``unit_cell`` -- The unit cell vectors for periodic structures
| ``fixed`` -- An array with indices of fixed atoms
"""
BaseMolecule.__init__(self, numbers, coordinates, title, masses, graph,
symbols, unit_cell)
self.energy = energy
self.gradient = gradient
self.hessian = hessian
self.multiplicity = multiplicity
self.symmetry_number = symmetry_number
self.periodic = periodic
self.fixed = fixed
