def _getAlignmentOperations(molecule): # fold>>
xyz_mol = molecule.createXYZMolecule()
center_of_mass = XYZMolecule.centerOfMass(xyz_mol)
xyz_mol.translate(-center_of_mass)
moments_of_inertia = XYZMolecule.momentsOfInertia(xyz_mol)
# we multiply the eigenvectors by -1 if needed.
# we want to keep the molecule oriented so that it does not change dramatically
# (ex. we don't want it to flip just because the diagonalization returned the
# inertial axis in the other direction)
v0 = numpy.array(moments_of_inertia[0][1].value())
if v0[0] < 0.0:
v0 = -v0
v1 = numpy.array(moments_of_inertia[1][1].value())
if v1[1] < 0.0:
v1 = -v1
v2 = numpy.array(moments_of_inertia[2][1].value())
if v2[2] < 0.0:
v2 = -v2
rotation = numpy.zeros((3, 3))
rotation[0, 0] = v0[0]
rotation[0, 1] = v0[1]
rotation[0, 2] = v0[2]
rotation[1, 0] = v1[0]
rotation[1, 1] = v1[1]
rotation[1, 2] = v1[2]
rotation[2, 0] = v2[0]
rotation[2, 1] = v2[1]
rotation[2, 2] = v2[2]
return (-center_of_mass, rotation)
def testMomentsOfInertia(self): # fold>>
mol = XYZMolecule.XYZMolecule( [
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,0.0000000000,0.0000000000 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,1.7920231678,-3.1038751750 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,4.0095495535,2.3149145141 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,6.3710924130,-3.1870231249 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,8.5886187987,2.2317665642 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,10.3806419665,-0.8721086108), Units.bohr) ),
(PeriodicTable.C, Measure.Measure( ( 0.0000000000,1.7920231678,-1.0346250583 ), Units.bohr) ),
(PeriodicTable.C, Measure.Measure( ( 0.0000000000,4.0095495535,0.2456643974 ), Units.bohr) ),
(PeriodicTable.C, Measure.Measure( ( 0.0000000000,6.3710924130,-1.1177730082 ), Units.bohr) ),
(PeriodicTable.C, Measure.Measure( ( 0.0000000000,8.5886187987,0.1625164475 ), Units.bohr) ),
]
)
inertia = XYZMolecule.momentsOfInertia(mol)
self.assertEqual(len(inertia), 3)
self.assertAlmostEqual(inertia[0][0].asUnit(Units.dalton * Units.angstrom * Units.angstrom).value(), 12.836878, 5)
self.assertAlmostEqual(inertia[1][0].asUnit(Units.dalton * Units.angstrom * Units.angstrom).value(), 110.58507, 5)
self.assertAlmostEqual(inertia[2][0].asUnit(Units.dalton * Units.angstrom * Units.angstrom).value(), 123.421950, 5)
self.assertAlmostEqual(inertia[0][1].value()[0], 0.0)
self.assertAlmostEqual(inertia[0][1].value()[1], 0.994406, 5)
self.assertAlmostEqual(inertia[0][1].value()[2], 0.105628, 5)
self.assertAlmostEqual(inertia[1][1].value()[0], 0.0)
self.assertAlmostEqual(inertia[1][1].value()[1], -0.105628, 5)
self.assertAlmostEqual(inertia[1][1].value()[2], 0.994406, 5)
self.assertAlmostEqual(inertia[2][1].value()[0], 1.0)
self.assertAlmostEqual(inertia[2][1].value()[1], 0.0, 5)
self.assertAlmostEqual(inertia[2][1].value()[2], 0.0, 5)