def __init__(self, name):
self.name = name
self.input_name = self.get_input_name()
self.linear = 0
self.n_atoms = ri.read_molecule(self.get_molecule_input_name())[4]
self.coordinates = ri.read_molecule(self.get_molecule_input_name())[0]
self.atom_list = ri.read_molecule(self.get_molecule_input_name())[5]
self.n_coordinates = self.get_coordinates()
self.number_of_normal_modes = self.get_number_of_normal_modes()
self.hessian = self.get_hessian()
self.eigenvalues,\
self.eigenvectors,\
self.frequencies, \
self.eigenvalues_full, \
self.eigenvectors_full = self.diagonalize(self.hessian)
self.cff_norm = self.to_normal_coordinates_3D\
(ri.read_cubic_force_field_anal(self.get_cubic_force_field_name(), self.n_coordinates))
#self.qff_norm = self.to_normal_coordinates_4D(ri.read_quartic_force_field1(self.input_name + 'quartic', self.n_coordinates))
self.effective_geometry = self.get_effective_geometry()
open(self.get_output_name(), 'w').close() # As we are appending to the output, the old results must be deleted before each run
def diagonalize(self, hessian):
"""Computes the normal coordinates, eigenvalues and fundamental
frequencies of the molecule.
hessian: The hessian of the molecule as an np.array
num_atoms_list: A list of the how many of each atoms type there are
charge list: A list over the charges of the atoms in the molecle
coordinates: The cartessian coordinates of the molecule as an np.array
n_atoms: The number of atoms composing the molecule as an int
masses: The masses of the atoms in a molecule along the diagonal of
an np.array
returns: The non-zero eigenvalues of the molecule as an np.array
The normal coordinates of the molecule, ie. the eigenvectors
corresponding the non-zero eigevalues as an np.array
The fundalmental frequencies of the molecule as an np.array
All the eigenvectos of the molecules, both the ones
corresponding the zero and non-zero eigenvalues as an np.array
"""
coordinates, masses, num_atoms_list, charge_list,\
n_atoms, atom_list = ri.read_molecule(self.get_molecule_input_name())
M_I = self.mass_hessian(masses)
if (self.linear):
n_nm += 1
hess_proj = self.hessian_trans_rot(hessian, coordinates, self.number_of_normal_modes, n_atoms)
hessian_proj = dot(M_I.transpose(), hess_proj)
hessian_proj = dot(hessian_proj, M_I)
v, La = linalg.eig(hessian_proj)
v_reduced = v[:self.number_of_normal_modes]
v_args = v_reduced.argsort()[::-1]
v_reduced = array(v_reduced, double)
v_reduced = v_reduced[v_args]
La= dot(M_I, array(La, double))
La_reduced = La[:,v_args]
freq = sqrt(absolute(v_reduced))
closefunc = lambda x: abs(x) < 0.0001
closevect = vectorize(closefunc)
reldiff = lambda x, y: x/y
reldiff = vectorize(reldiff)
eqsign = lambda x, y: x*y > 0
eqsign = vectorize(eqsign)
return v_reduced, La_reduced, freq, v, La