def test_force_constants_self_consistency(self):
trajectory = io.generate_test_trajectory(self.structure, supercell=[2, 2, 2], total_time=10, silent=False)
calculation = dynaphopy.Quasiparticle(trajectory)
calculation.select_power_spectra_algorithm(2)
renormalized_force_constants = calculation.get_renormalized_force_constants().get_array()
harmonic_force_constants = calculation.dynamic.structure.get_force_constants().get_array()
self.assertEqual(np.allclose(renormalized_force_constants, harmonic_force_constants, rtol=1, atol=1.e-2), True)
def setUp(self):
structure = io.read_from_file_structure_poscar('MgO_data/POSCAR')
structure.set_primitive_matrix([[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]])
structure.set_force_constants(get_force_constants_from_file(file_name='MgO_data/FORCE_CONSTANTS',
fc_supercell=[[2, 0, 0],
[0, 2, 0],
[0, 0, 2]]))
trajectory = io.generate_test_trajectory(structure, supercell=[2, 2, 2], total_time=5, silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
def test_q_points_data(self):
import yaml
trajectory = io.generate_test_trajectory(self.structure,
supercell=[2, 2, 2],
total_time=5,
silent=False)
calculation = dynaphopy.Quasiparticle(trajectory)
calculation.select_power_spectra_algorithm(2)
calculation.write_atomic_displacements([0, 0, 1],
'atomic_displacements.dat')
calculation.write_quasiparticles_data(
filename='quasiparticles_data.yaml')
calculation.write_renormalized_phonon_dispersion_bands(
filename='bands_data.yaml')
reference = np.loadtxt('Si_data/atomic_displacements.dat')
data = np.loadtxt('atomic_displacements.dat')
test_range = np.arange(-5, 5, 0.1)
for i in range(1, data.shape[1]):
diff_square = np.square(
np.interp(test_range, data[:, 0], data[:,
i], right=0, left=0) -
np.interp(test_range,
reference[:, 0],
reference[:, i],
right=0,
left=0))
rms = np.sqrt(np.average(diff_square))
self.assertLess(rms, 0.05)
def assertDictAlmostEqual(dict, reference, decimal=6):
for key, value in dict.items():
np.testing.assert_array_almost_equal(np.array(value),
np.array(reference[key]),
decimal=decimal)
files = ['quasiparticles_data.yaml']
for file in files:
print('file: {}'.format(file))
with open(file) as stream:
data = yaml.safe_load(stream)
with open('Si_data/' + file) as stream:
reference = yaml.safe_load(stream)
for dict_data, dict_reference in zip(data, reference):
assertDictAlmostEqual(dict_data, dict_reference, decimal=1)
def test_force_constants_self_consistency(self):
trajectory = io.generate_test_trajectory(self.structure,
supercell=[2, 2, 2],
total_time=3,
time_step=0.001,
temperature=300,
silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
self.calculation.select_power_spectra_algorithm(2)
renormalized_force_constants = self.calculation.get_renormalized_force_constants().get_array()
harmonic_force_constants = self.calculation.dynamic.structure.get_force_constants().get_array()
self.assertEqual(np.allclose(renormalized_force_constants, harmonic_force_constants, rtol=1, atol=5.e-2), True)
def setUp(self):
self.structure = io.read_from_file_structure_poscar('GaN_data/POSCAR')
self.structure.set_primitive_matrix([[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
self.structure.set_force_constants(get_force_constants_from_file(file_name='GaN_data/FORCE_CONSTANTS',
fc_supercell=[[3, 0, 0],
[0, 3, 0],
[0, 0, 3]]))
if not os.path.exists('test_gan.h5'):
trajectory = io.generate_test_trajectory(self.structure, supercell=[3, 3, 3], total_time=8, silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
self.calculation.save_velocity_hdf5('test_gan.h5', save_trajectory=True)
def setUp(self):
import phonopy
print ('Using phonopy {}'.format(phonopy.__version__))
# structure = io.read_from_file_structure_poscar('Si_data/POSCAR')
structure = io.read_from_file_structure_outcar('Si_data/OUTCAR')
structure.set_primitive_matrix([[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]])
structure.set_force_constants(get_force_constants_from_file(file_name='Si_data/FORCE_CONSTANTS',
fc_supercell=[[2, 0, 0],
[0, 2, 0],
[0, 0, 2]]))
trajectory = io.generate_test_trajectory(structure, supercell=[2, 2, 2], total_time=5, silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
def setUp(self):
self.structure = io.read_from_file_structure_poscar('GaN_data/POSCAR')
self.structure.set_force_constants(
parse_FORCE_CONSTANTS(filename='GaN_data/FORCE_CONSTANTS'))
self.structure.set_primitive_matrix([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
self.structure.set_supercell_phonon([[3, 0, 0], [0, 3, 0], [0, 0, 3]])
if not os.path.exists('test_gan.h5'):
trajectory = io.generate_test_trajectory(self.structure,
supercell=[3, 3, 3],
total_time=8,
silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
self.calculation.save_velocity_hdf5('test_gan.h5',
save_trajectory=True)
def setUp(self):
import phonopy
print('Using phonopy {}'.format(phonopy.__version__))
# structure = io.read_from_file_structure_poscar('Si_data/POSCAR')
structure = io.read_from_file_structure_outcar('Si_data/OUTCAR')
structure.set_primitive_matrix([[0.0, 0.5, 0.5], [0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]])
structure.set_force_constants(
get_force_constants_from_file(file_name='Si_data/FORCE_CONSTANTS',
fc_supercell=[[2, 0, 0], [0, 2, 0],
[0, 0, 2]]))
trajectory = io.generate_test_trajectory(structure,
supercell=[2, 2, 2],
total_time=5,
silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
def _test_average(self):
trajectory = io.generate_test_trajectory(self.structure,
supercell=[1, 2, 3],
total_time=5,
silent=False,
temperature=10)
self.calculation = dynaphopy.Quasiparticle(trajectory)
positions_average = self.calculation.dynamic.average_positions(to_unit_cell=True).real
print(positions_average)
reference = [[-1.94173041e+00, 2.81396066e+00, 5.39755913e+00],
[ 1.08905801e+00, 1.40691916e+00, 5.39306914e+00],
[ 5.09064600e+00, 1.40718064e+00, 2.68983555e+00],
[ 2.05985758e+00, 1.39139630e-04, 2.69432553e+00],
[ 1.56812170e+00, 1.40719153e+00, 1.56230533e+00],
[ 2.55169805e+00, 1.40716376e+00, 3.82629282e+00],
[ 4.59891013e+00, 1.50025412e-04, 1.55781535e+00],
[-4.79090372e-01, 1.22256709e-04, 3.83078280e+00]]
np.testing.assert_array_almost_equal(positions_average, reference, decimal=1)
