def test_vibrationalModes(self):
vmodes = NormalModes.VibrationalModes(self.universe)
freq = vmodes.frequencies[6:]
self.assertAlmostEqual(freq[0], 87.220841117866954)
self.assertAlmostEqual(freq[1], 112.01238171677888)
self.assertAlmostEqual(freq[2], 181.05242207954848)
for i in range(len(vmodes)):
mi = vmodes.rawMode(i)
norm_sq = mi.dotProduct(mi)
self.assertAlmostEqual(norm_sq, 1.)
for j in range(i + 1, len(vmodes)):
overlap = mi.dotProduct(vmodes.rawMode(j))
self.assert_(overlap < 1.e-15)
self.assertAlmostEqual(vmodes[6].norm(), 0.0038454773367577063)
self.assertAlmostEqual(vmodes[7].norm(), 0.0030509249071616175)
self.assertAlmostEqual(vmodes[8].norm(), 0.001953454891033823)
f = vmodes.fluctuations()
self.assertAlmostEqual(f[self.universe.water.O],
8.0141737611250569e-08)
self.assertAlmostEqual(f[self.universe.water.H1],
6.9381391949153065e-06)
self.assertAlmostEqual(f[self.universe.water.H2],
6.9381391949153023e-06)
af = vmodes.anisotropicFluctuations()
self.assertAlmostEqual(f[self.universe.water.O],
af[self.universe.water.O].trace())
self.assertAlmostEqual(f[self.universe.water.H1],
af[self.universe.water.H1].trace())
self.assertAlmostEqual(f[self.universe.water.H2],
af[self.universe.water.H2].trace())
def test_subspaceModes(self):
vmodes = NormalModes.VibrationalModes(self.universe,
subspace=self.subspace)
freq = vmodes.frequencies[6:]
self.assertAlmostEqual(freq[0], 3.29430105)
self.assertAlmostEqual(freq[1], 3.5216842)
self.assertAlmostEqual(freq[2], 6.36658335)
self.assertAlmostEqual(freq[3], 6.81335036)
self.assertAlmostEqual(freq[4], 8.96368475)
self.assertAlmostEqual(freq[5], 9.80151378)
self.assertAlmostEqual(freq[6], 12.26528168)
self.assertAlmostEqual(freq[7], 12.64098176)
self.assertAlmostEqual(freq[8], 16.13558466)
self.assertAlmostEqual(freq[9], 17.15343073)
self.assertAlmostEqual(freq[10], 24.86662786)
self.assertAlmostEqual(freq[11], 29.0265789)
for i in range(len(vmodes)):
mi = vmodes.rawMode(i)
norm_sq = mi.dotProduct(mi)
self.assertAlmostEqual(norm_sq, 1.)
for j in range(i + 1, len(vmodes)):
overlap = mi.dotProduct(vmodes.rawMode(j))
self.assert_(overlap < 1.e-13)
self.assertAlmostEqual(vmodes[6].norm(), 0.0577716669202)
self.assertAlmostEqual(vmodes[7].norm(), 0.0571769348227)
self.assertAlmostEqual(vmodes[8].norm(), 0.0276758947516)
self.assertAlmostEqual(vmodes[9].norm(), 0.0254182530029)
self.assertAlmostEqual(vmodes[10].norm(), 0.0213488665278)
self.assertAlmostEqual(vmodes[11].norm(), 0.0195579088896)
self.assertAlmostEqual(vmodes[12].norm(), 0.0194026958464)
self.assertAlmostEqual(vmodes[13].norm(), 0.0251256023118)
self.assertAlmostEqual(vmodes[14].norm(), 0.0100970642246)
self.assertAlmostEqual(vmodes[15].norm(), 0.00935723869926)
self.assertAlmostEqual(vmodes[16].norm(), 0.00561663849164)
self.assertAlmostEqual(vmodes[17].norm(), 0.00541615037839)
def test_energeticModes(self):
emodes = NormalModes.EnergeticModes(self.universe)
fc = emodes.force_constants[6:]
self.assertAlmostEqual(fc[0], 757849.3957485439, 5)
self.assertAlmostEqual(fc[1], 1041551.2240706938, 5)
self.assertAlmostEqual(fc[2], 1388251.2, 5)
for i in range(len(emodes)):
mi = emodes.rawMode(i)
norm_sq = mi.dotProduct(mi)
self.assertAlmostEqual(norm_sq, 1.)
for j in range(i + 1, len(emodes)):
overlap = mi.dotProduct(emodes.rawMode(j))
self.assert_(overlap < 1.e-15)
self.assertAlmostEqual(emodes[6].norm(), 0.0025656740328985168)
self.assertAlmostEqual(emodes[7].norm(), 0.0021885627126988836)
self.assertAlmostEqual(emodes[8].norm(), 0.0018956532696964624)
f = emodes.fluctuations()
self.assertAlmostEqual(f[self.universe.water.O], 3.359215370401356e-06)
self.assertAlmostEqual(f[self.universe.water.H1],
2.061890142153454e-06)
self.assertAlmostEqual(f[self.universe.water.H2],
2.061890142153454e-06)
af = emodes.anisotropicFluctuations()
self.assertAlmostEqual(f[self.universe.water.O],
af[self.universe.water.O].trace())
self.assertAlmostEqual(f[self.universe.water.H1],
af[self.universe.water.H1].trace())
self.assertAlmostEqual(f[self.universe.water.H2],
af[self.universe.water.H2].trace())
def setUp(self):
self.universe = MMTK.InfiniteUniverse(HarmonicForceField())
self.universe.peptide = Protein('bala1')
self.emodes = NormalModes.EnergeticModes(self.universe)
self.rm = RigidMotionSubspace(self.universe,
self.universe.peptide.residues())
self.pd = PairDistanceSubspace(self.universe, [
(self.universe.peptide[0][0].O, self.universe.peptide[0][-1].CH3)
])
def test_normal_modes(self):
emodes = NormalModes.EnergeticModes(self.universe)
MMTK.save(emodes, 'test.pickle')
restored_modes = MMTK.load('test.pickle')
for i in range(len(emodes)):
self.assertEqual(emodes[i].force_constant,
restored_modes[i].force_constant)
err = N.minimum.reduce(
N.fabs(N.ravel(emodes[i].array - restored_modes[i].array)))
self.assert_(err < 1.e-15)
def test_subspaceModesWithExclusion(self):
excluded = PairDistanceSubspace(self.universe, [
(self.universe.peptide[0][0].O, self.universe.peptide[0][-1].CH3)
])
vmodes = NormalModes.VibrationalModes(self.universe,
subspace=(excluded,
self.subspace))
freq = vmodes.frequencies[6:]
self.assertAlmostEqual(freq[0], 3.48436894)
self.assertAlmostEqual(freq[1], 5.36671021)
self.assertAlmostEqual(freq[2], 6.57184292)
self.assertAlmostEqual(freq[3], 8.37798098)
self.assertAlmostEqual(freq[4], 8.95620773)
self.assertAlmostEqual(freq[5], 12.06606868)
self.assertAlmostEqual(freq[6], 12.62157723)
self.assertAlmostEqual(freq[7], 16.02985338)
self.assertAlmostEqual(freq[8], 16.90566338)
self.assertAlmostEqual(freq[9], 23.55890937)
self.assertAlmostEqual(freq[10], 28.92170134)
self.assertAlmostEqual(freq[11], 41.55110572)
for i in range(len(vmodes)):
mi = vmodes.rawMode(i)
norm_sq = mi.dotProduct(mi)
self.assertAlmostEqual(norm_sq, 1.)
for j in range(i + 1, len(vmodes)):
overlap = mi.dotProduct(vmodes.rawMode(j))
self.assert_(overlap < 2.e-14)
self.assertAlmostEqual(vmodes[6].norm(), 0.0578155246705)
self.assertAlmostEqual(vmodes[7].norm(), 0.030148251724)
self.assertAlmostEqual(vmodes[8].norm(), 0.0275287609872)
self.assertAlmostEqual(vmodes[9].norm(), 0.0225332103616)
self.assertAlmostEqual(vmodes[10].norm(), 0.0216566218055)
self.assertAlmostEqual(vmodes[11].norm(), 0.0215173538578)
self.assertAlmostEqual(vmodes[12].norm(), 0.0249366816925)
self.assertAlmostEqual(vmodes[13].norm(), 0.0102016850103)
self.assertAlmostEqual(vmodes[14].norm(), 0.00939822099626)
self.assertAlmostEqual(vmodes[15].norm(), 0.00611049609175)
self.assertAlmostEqual(vmodes[16].norm(), 0.0053756335944)
self.assertAlmostEqual(vmodes[17].norm(), 0.00475443155674)
def test_subspaceModesWithNumericalDifferentiation(self):
vmodes = NormalModes.VibrationalModes(self.universe,
subspace=self.subspace,
delta=0.01)
freq = vmodes.frequencies[6:]
self.assertAlmostEqual(freq[0], 3.31849983, 5)
self.assertAlmostEqual(freq[1], 3.54902184, 5)
self.assertAlmostEqual(freq[2], 6.39993263, 5)
self.assertAlmostEqual(freq[3], 6.82609026, 5)
self.assertAlmostEqual(freq[4], 8.97880448, 5)
self.assertAlmostEqual(freq[5], 9.85460764, 5)
self.assertAlmostEqual(freq[6], 12.34554287, 5)
self.assertAlmostEqual(freq[7], 12.89029636, 5)
self.assertAlmostEqual(freq[8], 16.13726961, 5)
self.assertAlmostEqual(freq[9], 17.15617066, 5)
self.assertAlmostEqual(freq[10], 24.86718661, 5)
self.assertAlmostEqual(freq[11], 29.02770494, 5)
for i in range(len(vmodes)):
mi = vmodes.rawMode(i)
norm_sq = mi.dotProduct(mi)
self.assertAlmostEqual(norm_sq, 1.)
for j in range(i + 1, len(vmodes)):
overlap = mi.dotProduct(vmodes.rawMode(j))
self.assert_(overlap < 1.e-14)
self.assertAlmostEqual(vmodes[6].norm(), 0.057265850728, 5)
self.assertAlmostEqual(vmodes[7].norm(), 0.0568157841206, 5)
self.assertAlmostEqual(vmodes[8].norm(), 0.0272242339256, 5)
self.assertAlmostEqual(vmodes[9].norm(), 0.0253529888364, 5)
self.assertAlmostEqual(vmodes[10].norm(), 0.0212445420919, 5)
self.assertAlmostEqual(vmodes[11].norm(), 0.0188740025114, 5)
self.assertAlmostEqual(vmodes[12].norm(), 0.0190325360167, 5)
self.assertAlmostEqual(vmodes[13].norm(), 0.0252070482368, 5)
self.assertAlmostEqual(vmodes[14].norm(), 0.010099061532, 5)
self.assertAlmostEqual(vmodes[15].norm(), 0.00935799475998, 5)
self.assertAlmostEqual(vmodes[16].norm(), 0.00561654885265, 5)
self.assertAlmostEqual(vmodes[17].norm(), 0.00541642076462, 5)