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 test_q_points_data(self):
import yaml
trajectory = io.initialize_from_hdf5_file('test_gan.h5',
self.structure,
read_trajectory=True,
initial_cut=1,
final_cut=3000,
memmap=True)
self.calculation = dynaphopy.Quasiparticle(trajectory)
self.calculation.select_power_spectra_algorithm(2)
self.calculation.write_atomic_displacements([0, 0, 1],
'atomic_displacements.dat')
self.calculation.write_quasiparticles_data(
filename='quasiparticles_data.yaml')
self.calculation.write_renormalized_phonon_dispersion_bands(
filename='bands_data.yaml')
reference = np.loadtxt('GaN_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.load(stream)
with open('GaN_data/' + file) as stream:
reference = yaml.load(stream)
for dict_data, dict_reference in zip(data, reference):
assertDictAlmostEqual(dict_data, dict_reference, decimal=1)
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 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 test_force_constants_self_consistency(self):
trajectory = io.initialize_from_hdf5_file('test_gan.h5',
self.structure,
read_trajectory=False,
initial_cut=1,
final_cut=3000,
memmap=True)
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=1.e-2), True)
def test_thermal_properties(self):
trajectory = io.initialize_from_hdf5_file('test_gan.h5',
self.structure,
read_trajectory=False,
initial_cut=1000,
final_cut=4000,
memmap=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
self.calculation.select_power_spectra_algorithm(2)
harmonic = np.array(self.calculation.get_thermal_properties())
anharmonic = np.array(
self.calculation.get_thermal_properties(
force_constants=self.calculation.
get_renormalized_force_constants()))
print(harmonic)
print(anharmonic)
maximum = np.max((harmonic - anharmonic)**2 / harmonic)
print('maximum: {}'.format(maximum))
self.assertLess(maximum, 0.4)
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_adp(self):
trajectory = io.initialize_from_hdf5_file('test_gan.h5',
self.structure,
read_trajectory=True,
initial_cut=1,
final_cut=4000,
memmap=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
self.calculation.get_anisotropic_displacement_parameters()
positions_average = self.calculation.dynamic.average_positions(
to_unit_cell=True).real
positions = self.structure.get_positions()
difference = positions - positions_average
norm = np.linalg.norm(self.structure.get_cell(), axis=1)
difference = np.mod(difference, norm)
multiples = np.divide(difference, norm)
self.assertLess(np.max(np.abs(multiples - np.round(multiples))), 1e-4)
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)
############################### READING TRAJECTORY FILES #####################################
# 4. Set the location of OUTCAR/LAMMPS file containing the Molecular Dynamics trajectory
# trajectory = parsers.read_vasp_trajectory('/home/abel/VASP/Si/Si-FINAL3/Si_0.5_600/No1/OUTCAR', structure, initial_cut=10000, end_cut=60000)
# or
trajectory = parsers.read_VASP_XDATCAR(
'/home/abel/VASP/Si/Si-FINAL3/Si_0.5_800/No1/XDATCAR',
structure,
initial_cut=10000,
end_cut=40000,
time_step=0.0005)
# or
#trajectory = parsers.read_lammps_trajectory('/home/abel/LAMMPS/Si/Si_400.lammpstrj', structure, initial_cut=10000, end_cut=12000, time_step=0.001)
quasiparticle = dynaphopy.Quasiparticle(trajectory)
############################# DEFINE CALCULATION PARAMETERS ##################################
# 5. All this options are totally optional and independent, just comment or uncomment the desired ones
# Other option not yet shown in this example script may be available (take a look at dynaphopt/__init__.py)
# 5a. Set the power spectrum algorithm
# 0: Direct Fourier transform (Not recommended)
# 1: Maximum entropy method (MEM)
# 2; numpy FFT
# 3: FFTW (Needs FFTW installed in the system)
# 4: CUDA (Needs cuda_functions installed in the system)
quasiparticle.select_power_spectra_algorithm(1) # MEM
quasiparticle.set_number_of_mem_coefficients(
1000) # Only is used if MEM is selected
curses.endwin()
# SUB OPT 8 : # Frequency range
if x2 == ord('8'):
frequency_limits = np.array([float(Fraction(s)) for s in
get_param(screen, "Insert frequency range (min, max)").split(',')])
print(frequency_limits)
calculation.set_frequency_limits(frequency_limits)
curses.endwin()
curses.endwin()
# Testing
if __name__ == 'test_gui.py':
import dynaphopy as controller
import dynaphopy.functions.iofunctions as reading
# Get data from input file
input_parameters = reading.read_parameters_from_input_file(sys.argv[1])
structure = reading.read_from_file_structure_outcar(input_parameters['structure_file_name'])
structure.set_force_set( file_IO.parse_FORCE_SETS(filename=input_parameters['force_constants_file_name']))
structure.set_primitive_matrix(input_parameters['primitive_matrix'])
structure.set_supercell_phonon(input_parameters['supercell_matrix'])
trajectory_file_name = sys.argv[2]
trajectory = reading.read_from_file_trajectory(trajectory_file_name,structure,last_steps=5000)
calculation = controller.Quasiparticle(trajectory)
calculation.set_band_ranges(input_parameters['bands'])
