def testEthaneInternalReducedMomentOfInertia(self):
"""
Uses an optimum geometry for ethane (CC) to test that the
proper moments of inertia for its internal hindered rotor is
calculated.
"""
# Masses should be in kg/mol
mass = numpy.array([12.0, 1.0, 1.0, 1.0, 12.0, 1.0, 1.0, 1.0],
numpy.float64) * 0.001
# Atomic numbers
number = numpy.array([6, 1, 1, 1, 6, 1, 1, 1], numpy.int)
# Coordinates should be in m
position = numpy.zeros((8, 3), numpy.float64)
position[0, :] = numpy.array([0.001294, 0.002015, 0.000152]) * 1e-10
position[1, :] = numpy.array([0.397758, 0.629904, -0.805418]) * 1e-10
position[2, :] = numpy.array([-0.646436, 0.631287, 0.620549]) * 1e-10
position[3, :] = numpy.array([0.847832, -0.312615, 0.620435]) * 1e-10
position[4, :] = numpy.array([-0.760734, -1.204707, -0.557036]) * 1e-10
position[5, :] = numpy.array([-1.15728, -1.832718, 0.248402]) * 1e-10
position[6, :] = numpy.array([-1.607276, -0.890277, -1.177452]) * 1e-10
position[7, :] = numpy.array([-0.11271, -1.833701, -1.177357]) * 1e-10
geometry = Geometry(position, number, mass)
pivots = [0, 4]
top = [0, 1, 2, 3]
# Returned moment of inertia is in kg*m^2; convert to amu*A^2
I = geometry.getInternalReducedMomentOfInertia(
pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 1.5595197928, 1.0, 2)
def testEthaneInternalReducedMomentOfInertia(self):
"""
Uses an optimum geometry for ethane (CC) to test that the
proper moments of inertia for its internal hindered rotor is
calculated.
"""
# Masses should be in kg/mol
mass = numpy.array([12.0, 1.0, 1.0, 1.0, 12.0, 1.0, 1.0, 1.0], numpy.float64) * 0.001
# Atomic numbers
number = numpy.array([6, 1, 1, 1, 6, 1, 1, 1], numpy.int)
# Coordinates should be in m
position = numpy.zeros((8,3), numpy.float64)
position[0,:] = numpy.array([ 0.001294, 0.002015, 0.000152]) * 1e-10
position[1,:] = numpy.array([ 0.397758, 0.629904, -0.805418]) * 1e-10
position[2,:] = numpy.array([-0.646436, 0.631287, 0.620549]) * 1e-10
position[3,:] = numpy.array([ 0.847832, -0.312615, 0.620435]) * 1e-10
position[4,:] = numpy.array([-0.760734, -1.204707, -0.557036]) * 1e-10
position[5,:] = numpy.array([-1.15728 , -1.832718, 0.248402]) * 1e-10
position[6,:] = numpy.array([-1.607276, -0.890277, -1.177452]) * 1e-10
position[7,:] = numpy.array([-0.11271 , -1.833701, -1.177357]) * 1e-10
geometry = Geometry(position, number, mass)
pivots = [0, 4]
top = [0, 1, 2, 3]
# Returned moment of inertia is in kg*m^2; convert to amu*A^2
I = geometry.getInternalReducedMomentOfInertia(pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 1.5595197928, 1.0, 2)
def testButanolInternalReducedMomentOfInertia(self):
"""
Uses an optimum geometry for s-butanol (CCC(O)C) to test that the
proper moments of inertia for its internal hindered rotors are
calculated.
"""
# Masses should be in kg/mol
mass = numpy.array([12.0107, 1.00794, 1.00794, 1.00794, 12.0107, 1.00794, 1.00794, 12.0107, 1.00794, 12.0107, 1.00794, 1.00794, 1.00794, 15.9994, 1.00794], numpy.float64) * 0.001
# Atomic numbers
number = numpy.array([6, 1, 1, 1, 6, 1, 1, 6, 1, 6, 1, 1, 1, 8, 1], numpy.int)
# Coordinates should be in m
position = numpy.zeros((15,3), numpy.float64)
position[0,:] = numpy.array([-2.066968, -0.048470, -0.104326]) * 1e-10
position[1,:] = numpy.array([-2.078133, 1.009166, 0.165745]) * 1e-10
position[2,:] = numpy.array([-2.241129, -0.116565, -1.182661]) * 1e-10
position[3,:] = numpy.array([-2.901122, -0.543098, 0.400010]) * 1e-10
position[4,:] = numpy.array([-0.729030, -0.686020, 0.276105]) * 1e-10
position[5,:] = numpy.array([-0.614195, -0.690327, 1.369198]) * 1e-10
position[6,:] = numpy.array([-0.710268, -1.736876, -0.035668]) * 1e-10
position[7,:] = numpy.array([ 0.482521, 0.031583, -0.332519]) * 1e-10
position[8,:] = numpy.array([ 0.358535, 0.069368, -1.420087]) * 1e-10
position[9,:] = numpy.array([ 1.803404, -0.663583, -0.006474]) * 1e-10
position[10,:] = numpy.array([ 1.825001, -1.684006, -0.400007]) * 1e-10
position[11,:] = numpy.array([ 2.638619, -0.106886, -0.436450]) * 1e-10
position[12,:] = numpy.array([ 1.953652, -0.720890, 1.077945]) * 1e-10
position[13,:] = numpy.array([ 0.521504, 1.410171, 0.056819]) * 1e-10
position[14,:] = numpy.array([ 0.657443, 1.437685, 1.010704]) * 1e-10
geometry = Geometry(position, number, mass)
pivots = [0, 4]
top = [0, 1, 2, 3]
I = geometry.getInternalReducedMomentOfInertia(pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 2.73090431938, 1.0, 3)
pivots = [4, 7]
top = [4, 5, 6, 0, 1, 2, 3]
I = geometry.getInternalReducedMomentOfInertia(pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 12.1318136515, 1.0, 3)
pivots = [13, 7]
top = [13, 14]
I = geometry.getInternalReducedMomentOfInertia(pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 0.853678578741, 1.0, 3)
pivots = [9, 7]
top = [9, 10, 11, 12]
I = geometry.getInternalReducedMomentOfInertia(pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 2.97944840397, 1.0, 3)
def testOutput(self):
"""
Test that a Geometry object can be successfully reconstructed
from its repr() output with no loss of information.
"""
# Masses should be in kg/mol
mass = numpy.array([12.0, 1.0, 1.0, 1.0, 12.0, 1.0, 1.0, 1.0],
numpy.float64) * 0.001
# Atomic numbers
number = numpy.array([6, 1, 1, 1, 6, 1, 1, 1], numpy.int)
# Coordinates should be in m
position = numpy.zeros((8, 3), numpy.float64)
position[0, :] = numpy.array([0.001294, 0.002015, 0.000152]) * 1e-10
position[1, :] = numpy.array([0.397758, 0.629904, -0.805418]) * 1e-10
position[2, :] = numpy.array([-0.646436, 0.631287, 0.620549]) * 1e-10
position[3, :] = numpy.array([0.847832, -0.312615, 0.620435]) * 1e-10
position[4, :] = numpy.array([-0.760734, -1.204707, -0.557036]) * 1e-10
position[5, :] = numpy.array([-1.15728, -1.832718, 0.248402]) * 1e-10
position[6, :] = numpy.array([-1.607276, -0.890277, -1.177452]) * 1e-10
position[7, :] = numpy.array([-0.11271, -1.833701, -1.177357]) * 1e-10
g0 = Geometry(position, number, mass)
exec('g = %r' % g0)
Natoms = len(g.number)
self.assertEqual(len(g0.number), len(g.number))
for i in range(Natoms):
for j in range(3):
self.assertAlmostEqual(g0.coordinates[i, j],
g.coordinates[i, j], 6)
self.assertEqual(g0.number[i], g.number[i])
self.assertAlmostEqual(g0.mass[i], g.mass[i], 6)
def testButanolInternalReducedMomentOfInertia(self):
"""
Uses an optimum geometry for s-butanol (CCC(O)C) to test that the
proper moments of inertia for its internal hindered rotors are
calculated.
"""
# Masses should be in kg/mol
mass = numpy.array([
12.0107, 1.00794, 1.00794, 1.00794, 12.0107, 1.00794, 1.00794,
12.0107, 1.00794, 12.0107, 1.00794, 1.00794, 1.00794, 15.9994,
1.00794
], numpy.float64) * 0.001
# Atomic numbers
number = numpy.array([6, 1, 1, 1, 6, 1, 1, 6, 1, 6, 1, 1, 1, 8, 1],
numpy.int)
# Coordinates should be in m
position = numpy.zeros((15, 3), numpy.float64)
position[0, :] = numpy.array([-2.066968, -0.048470, -0.104326]) * 1e-10
position[1, :] = numpy.array([-2.078133, 1.009166, 0.165745]) * 1e-10
position[2, :] = numpy.array([-2.241129, -0.116565, -1.182661]) * 1e-10
position[3, :] = numpy.array([-2.901122, -0.543098, 0.400010]) * 1e-10
position[4, :] = numpy.array([-0.729030, -0.686020, 0.276105]) * 1e-10
position[5, :] = numpy.array([-0.614195, -0.690327, 1.369198]) * 1e-10
position[6, :] = numpy.array([-0.710268, -1.736876, -0.035668]) * 1e-10
position[7, :] = numpy.array([0.482521, 0.031583, -0.332519]) * 1e-10
position[8, :] = numpy.array([0.358535, 0.069368, -1.420087]) * 1e-10
position[9, :] = numpy.array([1.803404, -0.663583, -0.006474]) * 1e-10
position[10, :] = numpy.array([1.825001, -1.684006, -0.400007]) * 1e-10
position[11, :] = numpy.array([2.638619, -0.106886, -0.436450]) * 1e-10
position[12, :] = numpy.array([1.953652, -0.720890, 1.077945]) * 1e-10
position[13, :] = numpy.array([0.521504, 1.410171, 0.056819]) * 1e-10
position[14, :] = numpy.array([0.657443, 1.437685, 1.010704]) * 1e-10
geometry = Geometry(position, number, mass)
pivots = [0, 4]
top = [0, 1, 2, 3]
I = geometry.getInternalReducedMomentOfInertia(
pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 2.73090431938, 1.0, 3)
pivots = [4, 7]
top = [4, 5, 6, 0, 1, 2, 3]
I = geometry.getInternalReducedMomentOfInertia(
pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 12.1318136515, 1.0, 3)
pivots = [13, 7]
top = [13, 14]
I = geometry.getInternalReducedMomentOfInertia(
pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 0.853678578741, 1.0, 3)
pivots = [9, 7]
top = [9, 10, 11, 12]
I = geometry.getInternalReducedMomentOfInertia(
pivots, top) * 1e23 * constants.Na
self.assertAlmostEqual(I / 2.97944840397, 1.0, 3)
