def test_vibrations_on_surface(self, testdir):
atoms = self.n2_on_ag.copy()
atoms.calc = EMT()
vibs = Vibrations(atoms, indices=[-2, -1])
vibs.run()
freqs = vibs.get_frequencies()
vib_data = vibs.get_vibrations()
assert_array_almost_equal(freqs, vib_data.get_frequencies())
def test_consistency_with_vibrationsdata(self, testdir, n2_emt):
atoms = n2_emt
vib = Vibrations(atoms)
vib.run()
vib_data = vib.get_vibrations()
assert_array_almost_equal(vib.get_energies(), vib_data.get_energies())
# Compare the last mode as the others may be re-ordered by negligible
# energy changes
assert_array_almost_equal(vib.get_mode(5), vib_data.get_modes()[5])
def test_consistency_with_vibrationsdata(self, testdir, random_dimer):
vib = Vibrations(random_dimer, delta=1e-6, nfree=4)
vib.run()
vib_data = vib.get_vibrations()
assert_array_almost_equal(vib.get_energies(), vib_data.get_energies())
for mode_index in range(3 * len(vib.atoms)):
assert_array_almost_equal(vib.get_mode(mode_index),
vib_data.get_modes()[mode_index])
# Hessian should be close to the ForceConstantCalculator input
assert_array_almost_equal(random_dimer.calc.D,
vib_data.get_hessian_2d(),
decimal=6)
def test_vibration_on_surface(self, testdir):
from ase.build import fcc111, add_adsorbate
ag_slab = fcc111('Ag', (4, 4, 2), a=2)
n2 = Atoms('N2',
positions=[[0., 0., 0.], [0., np.sqrt(2),
np.sqrt(2)]])
add_adsorbate(ag_slab, n2, height=1, position='fcc')
# Add an interaction between the N atoms
hessian_bottom_corner = np.zeros((2, 3, 2, 3))
hessian_bottom_corner[-1, :, -2] = [1, 1, 1]
hessian_bottom_corner[-2, :, -1] = [1, 1, 1]
hessian = np.zeros((34, 3, 34, 3))
hessian[32:, :, 32:, :] = hessian_bottom_corner
ag_slab.calc = ForceConstantCalculator(hessian.reshape(
(34 * 3, 34 * 3)),
ref=ag_slab.copy(),
f0=np.zeros((34, 3)))
# Check that Vibrations with restricted indices returns correct Hessian
vibs = Vibrations(ag_slab, indices=[-2, -1])
vibs.run()
vibs.read()
assert_array_almost_equal(vibs.get_vibrations().get_hessian(),
hessian_bottom_corner)
# These should blow up if the vectors don't match number of atoms
vibs.summary()
vibs.write_jmol()
for i in range(6):
# Frozen atoms should have zero displacement
assert_array_almost_equal(vibs.get_mode(i)[0], [0., 0., 0.])
# The N atoms should have finite displacement
assert np.all(vibs.get_mode(i)[-2:, :])
def test_vibrations_on_surface(self, testdir):
atoms = self.n2_on_ag.copy()
atoms.calc = EMT()
vibs = Vibrations(atoms, indices=[-2, -1])
vibs.run()
freqs = vibs.get_frequencies()
assert len(freqs) == 6
vib_data = vibs.get_vibrations()
assert_array_almost_equal(freqs, vib_data.get_frequencies())
# These should blow up if the vectors don't match number of atoms
vibs.summary()
vibs.write_jmol()
for i in range(6):
# Frozen atoms should have zero displacement
assert_array_almost_equal(vibs.get_mode(i)[0], [0., 0., 0.])
# At least one of the N atoms should have finite displacement
# (It's a strange test system, the N aren't interacting.)
assert np.any(vibs.get_mode(i)[-2:, :])