def test_repeated_calculate_qpoint_phonon_modes_doesnt_change_result(self):
fc = get_fc('quartz')
qpt_ph_modes1 = fc.calculate_qpoint_phonon_modes(get_test_qpts(),
asr='realspace')
qpt_ph_modes2 = fc.calculate_qpoint_phonon_modes(get_test_qpts(),
asr='realspace')
check_qpt_ph_modes(qpt_ph_modes1, qpt_ph_modes2)
def test_cext_called_with_n_threads_default_and_no_env_var(
self, mocked_cext):
n_threads = cpu_count()
try:
os.environ.pop('EUPHONIC_NUM_THREADS')
except KeyError:
pass
fc = get_fc('quartz')
fc.calculate_qpoint_phonon_modes(get_test_qpts())
assert mocked_cext.call_args[0][-2] == n_threads
def get_cahgo2_qpt_ph_modes(self, request):
fc = ForceConstants.from_phonopy(
path=get_phonopy_path('CaHgO2', ''),
summary_name='mp-7041-20180417.yaml')
kwargs = self.get_multithreaded_kwargs(request.param)
return fc.calculate_qpoint_phonon_modes(get_test_qpts(), **kwargs)
def get_si2_qpt_ph_modes(self, request):
fc = ForceConstants.from_castep(
get_castep_path('Si2-sc-skew', 'Si2-sc-skew.castep_bin'))
kwargs = self.get_multithreaded_kwargs(request.param)
return fc.calculate_qpoint_phonon_modes(get_test_qpts(), **kwargs)
def get_quartz_qpt_ph_modes(self, request):
fc = ForceConstants.from_castep(
get_castep_path('quartz', 'quartz.castep_bin'))
kwargs = self.get_multithreaded_kwargs(request.param)
return fc.calculate_qpoint_phonon_modes(
get_test_qpts('split'), **kwargs)
def test_cext_called_with_n_threads_default_and_env_var(self, mocked_cext):
n_threads = 4
os.environ['EUPHONIC_NUM_THREADS'] = str(n_threads)
fc = get_fc('quartz')
fc.calculate_qpoint_phonon_modes(get_test_qpts())
assert mocked_cext.call_args[0][-2] == n_threads
def test_cext_called_with_n_threads_arg(self, mocked_cext):
n_threads = 3
fc = get_fc('quartz')
fc.calculate_qpoint_phonon_modes(get_test_qpts(), n_threads=n_threads)
assert mocked_cext.call_args[0][-2] == n_threads
def test_cext_not_called_with_use_c_false(self, mocked_cext):
fc = get_fc('quartz')
fc.calculate_qpoint_phonon_modes(get_test_qpts(), use_c=False)
mocked_cext.assert_not_called()
def test_cext_called_with_use_c_default(self, mocked_cext):
fc = get_fc('quartz')
fc.calculate_qpoint_phonon_modes(get_test_qpts())
mocked_cext.assert_called()
def test_with_use_c_false_doesnt_raise_error_or_warn(
self, mocked_cext_with_importerror):
fc = get_fc('quartz')
with pytest.warns(None) as warn_record:
fc.calculate_qpoint_phonon_modes(get_test_qpts(), use_c=False)
assert len(warn_record) == 0
def test_with_use_c_default_warns(self, mocked_cext_with_importerror):
fc = get_fc('quartz')
with pytest.warns(None) as warn_record:
fc.calculate_qpoint_phonon_modes(get_test_qpts())
assert len(warn_record) == 1
def test_with_use_c_true_raises_importcerror(self,
mocked_cext_with_importerror):
fc = get_fc('quartz')
with pytest.raises(ImportCError):
fc.calculate_qpoint_phonon_modes(get_test_qpts(), use_c=True)
def test_calc_qpt_ph_mds_asr_with_nonsense_fc_raises_warning(self, asr):
fc = ForceConstants.from_json_file(
os.path.join(get_fc_dir(), 'quartz_random_force_constants.json'))
with pytest.warns(UserWarning):
fc.calculate_qpoint_phonon_modes(get_test_qpts(), asr=asr)
class TestForceConstantsCalculateQPointPhononModes:
def get_lzo_fc():
return ForceConstants.from_castep(
get_castep_path('LZO', 'La2Zr2O7.castep_bin'))
lzo_params = [
(get_lzo_fc(), 'LZO', [get_test_qpts(),
{}], 'LZO_no_asr_qpoint_phonon_modes.json'),
(get_lzo_fc(), 'LZO', [get_test_qpts(), {
'asr': 'realspace'
}], 'LZO_realspace_qpoint_phonon_modes.json'),
(get_lzo_fc(), 'LZO', [get_test_qpts(), {
'asr': 'reciprocal'
}], 'LZO_reciprocal_qpoint_phonon_modes.json')
]
def get_si2_fc():
return ForceConstants.from_castep(
get_castep_path('Si2-sc-skew', 'Si2-sc-skew.castep_bin'))
si2_params = [
(get_si2_fc(), 'Si2-sc-skew', [get_test_qpts(), {}],
'Si2-sc-skew_no_asr_qpoint_phonon_modes.json'),
(get_si2_fc(), 'Si2-sc-skew', [get_test_qpts(), {
'asr': 'realspace'
}], 'Si2-sc-skew_realspace_qpoint_phonon_modes.json'),
(get_si2_fc(), 'Si2-sc-skew', [get_test_qpts(), {
'asr': 'reciprocal'
}], 'Si2-sc-skew_reciprocal_qpoint_phonon_modes.json')
]
def get_quartz_fc():
return ForceConstants.from_castep(
get_castep_path('quartz', 'quartz.castep_bin'))
quartz_params = [
(get_quartz_fc(), 'quartz',
[get_test_qpts(), {
'asr': 'reciprocal',
'splitting': False
}], 'quartz_reciprocal_qpoint_phonon_modes.json'),
(get_quartz_fc(), 'quartz', [
get_test_qpts(), {
'asr': 'reciprocal',
'splitting': False,
'eta_scale': 0.75
}
], 'quartz_reciprocal_qpoint_phonon_modes.json'),
(get_quartz_fc(), 'quartz', [
get_test_qpts('split'), {
'asr': 'reciprocal',
'splitting': True,
'insert_gamma': False
}
], 'quartz_split_reciprocal_qpoint_phonon_modes.json'),
(get_quartz_fc(), 'quartz', [
get_test_qpts('split_insert_gamma'), {
'asr': 'reciprocal',
'splitting': True,
'insert_gamma': True
}
], 'quartz_split_reciprocal_qpoint_phonon_modes.json')
]
nacl_params = [
(ForceConstants.from_phonopy(path=get_phonopy_path('NaCl', ''),
summary_name='phonopy_nacl.yaml'), 'NaCl',
[get_test_qpts(), {
'asr': 'reciprocal'
}], 'NaCl_reciprocal_qpoint_phonon_modes.json')
]
cahgo2_params = [
(ForceConstants.from_phonopy(path=get_phonopy_path('CaHgO2', ''),
summary_name='mp-7041-20180417.yaml'),
'CaHgO2', [get_test_qpts(), {
'asr': 'reciprocal'
}], 'CaHgO2_reciprocal_qpoint_phonon_modes.json')
]
@pytest.mark.parametrize(
'fc, material, all_args, expected_qpoint_phonon_modes_file',
lzo_params + quartz_params + nacl_params + si2_params + cahgo2_params)
@pytest.mark.parametrize('reduce_qpts, n_threads', [(False, 0), (True, 0),
(True, 1), (True, 2)])
def test_calculate_qpoint_phonon_modes(self, fc, material, all_args,
expected_qpoint_phonon_modes_file,
reduce_qpts, n_threads):
func_kwargs = all_args[1]
func_kwargs['reduce_qpts'] = reduce_qpts
if n_threads == 0:
func_kwargs['use_c'] = False
else:
func_kwargs['use_c'] = True
func_kwargs['n_threads'] = n_threads
qpoint_phonon_modes = fc.calculate_qpoint_phonon_modes(
all_args[0], **func_kwargs)
expected_qpoint_phonon_modes = ExpectedQpointPhononModes(
os.path.join(get_qpt_ph_modes_dir(material),
expected_qpoint_phonon_modes_file))
# Only give gamma-acoustic modes special treatment if the acoustic
# sum rule has been applied
if not 'asr' in func_kwargs.keys():
gamma_atol = None
else:
gamma_atol = 0.5
check_qpt_ph_modes(qpoint_phonon_modes,
expected_qpoint_phonon_modes,
frequencies_atol=1e-4,
frequencies_rtol=2e-5,
acoustic_gamma_atol=gamma_atol)
@pytest.mark.parametrize(
('fc, material, all_args, expected_qpoint_phonon_modes_file, '
'expected_modw_file'), [(get_quartz_fc(), 'quartz', [
mp_grid([5, 5, 4]), {
'asr': 'reciprocal',
'return_mode_widths': True
}
], 'quartz_554_full_qpoint_phonon_modes.json',
'quartz_554_full_mode_widths.json'),
(get_lzo_fc(), 'LZO', [
mp_grid([2, 2, 2]), {
'asr': 'reciprocal',
'return_mode_widths': True
}
], 'lzo_222_full_qpoint_phonon_modes.json',
'lzo_222_full_mode_widths.json')])
@pytest.mark.parametrize('n_threads', [0, 2])
def test_calculate_qpoint_phonon_modes_with_mode_widths(
self, fc, material, all_args, expected_qpoint_phonon_modes_file,
expected_modw_file, n_threads):
func_kwargs = all_args[1]
if n_threads == 0:
func_kwargs['use_c'] = False
else:
func_kwargs['use_c'] = True
func_kwargs['n_threads'] = n_threads
qpoint_phonon_modes, modw = fc.calculate_qpoint_phonon_modes(
all_args[0], **func_kwargs)
with open(os.path.join(get_fc_dir(), expected_modw_file), 'r') as fp:
modw_dict = json.load(fp)
expected_modw = modw_dict['mode_widths'] * ureg(
modw_dict['mode_widths_unit'])
expected_qpoint_phonon_modes = ExpectedQpointPhononModes(
os.path.join(get_qpt_ph_modes_dir(material),
expected_qpoint_phonon_modes_file))
# Only give gamma-acoustic modes special treatment if the acoustic
# sum rule has been applied
if not 'asr' in func_kwargs.keys():
gamma_atol = None
else:
gamma_atol = 0.5
check_qpt_ph_modes(qpoint_phonon_modes,
expected_qpoint_phonon_modes,
frequencies_atol=1e-4,
frequencies_rtol=2e-5,
acoustic_gamma_atol=gamma_atol)
assert modw.units == expected_modw.units
npt.assert_allclose(modw.magnitude,
expected_modw.magnitude,
atol=2e-4,
rtol=5e-5)
# ForceConstants stores some values (supercell image list, vectors
# for the Ewald sum) so check repeated calculations give the same
# result
def test_repeated_calculate_qpoint_phonon_modes_doesnt_change_result(self):
fc = get_fc('quartz')
qpt_ph_modes1 = fc.calculate_qpoint_phonon_modes(get_test_qpts(),
asr='realspace')
qpt_ph_modes2 = fc.calculate_qpoint_phonon_modes(get_test_qpts(),
asr='realspace')
check_qpt_ph_modes(qpt_ph_modes1, qpt_ph_modes2)
@pytest.mark.parametrize(
'fc, material, qpt, kwargs, expected_qpt_ph_modes_file',
[(get_fc('quartz'), 'quartz', np.array([[1., 1., 1.]]), {
'splitting': True
}, 'quartz_single_qpoint_phonon_modes.json')])
def test_calculate_qpoint_phonon_modes_single_qpt(
self, fc, material, qpt, kwargs, expected_qpt_ph_modes_file):
qpoint_phonon_modes = fc.calculate_qpoint_phonon_modes(qpt, **kwargs)
expected_qpoint_phonon_modes = ExpectedQpointPhononModes(
os.path.join(get_qpt_ph_modes_dir(material),
expected_qpt_ph_modes_file))
check_qpt_ph_modes(qpoint_phonon_modes,
expected_qpoint_phonon_modes,
frequencies_atol=1e-4,
frequencies_rtol=2e-5)
weights = np.array([0.1, 0.05, 0.05, 0.2, 0.2, 0.15, 0.15, 0.2, 0.1])
weights_output_split_gamma = np.array([
0.1, 0.05, 0.025, 0.025, 0.2, 0.1, 0.1, 0.075, 0.075, 0.075, 0.075,
0.2, 0.1
])
@pytest.mark.parametrize(
'fc, qpts, weights, expected_weights, kwargs',
[(get_fc('quartz'), get_test_qpts(), weights, weights, {}),
(get_fc('quartz'), get_test_qpts('split_insert_gamma'), weights,
weights_output_split_gamma, {
'insert_gamma': True
})])
def test_calculate_qpoint_phonon_modes_with_weights_sets_weights(
self, fc, qpts, weights, expected_weights, kwargs):
qpt_ph_modes_weighted = fc.calculate_qpoint_phonon_modes(
qpts, weights=weights, **kwargs)
npt.assert_allclose(qpt_ph_modes_weighted.weights, expected_weights)
@pytest.mark.parametrize(
'fc, qpts, weights, expected_weights, kwargs',
[(get_fc('quartz'), get_test_qpts(), weights, weights, {}),
(get_fc('quartz'), get_test_qpts('split_insert_gamma'), weights,
weights_output_split_gamma, {
'insert_gamma': True
})])
def test_calculate_qpoint_phonon_modes_with_weights_doesnt_change_result(
self, fc, qpts, weights, expected_weights, kwargs):
qpt_ph_modes_weighted = fc.calculate_qpoint_phonon_modes(
qpts, weights=weights, **kwargs)
qpt_ph_modes_unweighted = fc.calculate_qpoint_phonon_modes(
qpts, **kwargs)
qpt_ph_modes_unweighted.weights = expected_weights
check_qpt_ph_modes(qpt_ph_modes_weighted, qpt_ph_modes_unweighted)
@pytest.mark.parametrize('asr', ['realspace', 'reciprocal'])
def test_calc_qpt_ph_mds_asr_with_nonsense_fc_raises_warning(self, asr):
fc = ForceConstants.from_json_file(
os.path.join(get_fc_dir(), 'quartz_random_force_constants.json'))
with pytest.warns(UserWarning):
fc.calculate_qpoint_phonon_modes(get_test_qpts(), asr=asr)
class TestForceConstantsCalculateQPointFrequencies:
def get_lzo_fc():
return ForceConstants.from_castep(
get_castep_path('LZO', 'La2Zr2O7.castep_bin'))
lzo_params = [
(get_lzo_fc(), 'LZO', [get_test_qpts(),
{}], 'LZO_no_asr_qpoint_frequencies.json'),
(get_lzo_fc(), 'LZO', [get_test_qpts(), {
'asr': 'realspace'
}], 'LZO_realspace_qpoint_frequencies.json')
]
def get_quartz_fc():
return ForceConstants.from_castep(
get_castep_path('quartz', 'quartz.castep_bin'))
quartz_params = [
(get_quartz_fc(), 'quartz',
[get_test_qpts(), {
'asr': 'reciprocal',
'splitting': False
}], 'quartz_reciprocal_qpoint_frequencies.json'),
(get_quartz_fc(), 'quartz', [
get_test_qpts(), {
'asr': 'reciprocal',
'splitting': False,
'eta_scale': 0.75
}
], 'quartz_reciprocal_qpoint_frequencies.json'),
(get_quartz_fc(), 'quartz', [
get_test_qpts('split'), {
'asr': 'reciprocal',
'splitting': True,
'insert_gamma': False
}
], 'quartz_split_reciprocal_qpoint_frequencies.json'),
(get_quartz_fc(), 'quartz', [
get_test_qpts('split_insert_gamma'), {
'asr': 'reciprocal',
'splitting': True,
'insert_gamma': True
}
], 'quartz_split_reciprocal_qpoint_frequencies.json')
]
@pytest.mark.parametrize(
'fc, material, all_args, expected_qpoint_frequencies_file',
lzo_params + quartz_params)
@pytest.mark.parametrize('reduce_qpts, n_threads', [(False, 0), (True, 0),
(True, 1), (True, 2)])
def test_calculate_qpoint_frequencies(self, fc, material, all_args,
expected_qpoint_frequencies_file,
reduce_qpts, n_threads):
func_kwargs = all_args[1]
func_kwargs['reduce_qpts'] = reduce_qpts
if n_threads == 0:
func_kwargs['use_c'] = False
else:
func_kwargs['use_c'] = True
func_kwargs['n_threads'] = n_threads
qpt_freqs = fc.calculate_qpoint_frequencies(all_args[0], **func_kwargs)
expected_qpt_freqs = get_expected_qpt_freqs(
material, expected_qpoint_frequencies_file)
# Only give gamma-acoustic modes special treatment if the acoustic
# sum rule has been applied
if not 'asr' in func_kwargs.keys():
gamma_atol = None
else:
gamma_atol = 0.5
check_qpt_freqs(qpt_freqs,
expected_qpt_freqs,
frequencies_atol=1e-4,
frequencies_rtol=2e-5,
acoustic_gamma_atol=gamma_atol)
@pytest.mark.parametrize(
('fc, material, all_args, expected_qpoint_frequencies_file, '
'expected_modw_file'), [(get_quartz_fc(), 'quartz', [
mp_grid([5, 5, 4]), {
'asr': 'reciprocal',
'return_mode_widths': True
}
], 'quartz_554_full_qpoint_frequencies.json',
'quartz_554_full_mode_widths.json'),
(get_lzo_fc(), 'LZO', [
mp_grid([2, 2, 2]), {
'asr': 'reciprocal',
'return_mode_widths': True
}
], 'lzo_222_full_qpoint_frequencies.json',
'lzo_222_full_mode_widths.json')])
@pytest.mark.parametrize('n_threads', [0, 2])
def test_calculate_qpoint_frequencies_with_mode_widths(
self, fc, material, all_args, expected_qpoint_frequencies_file,
expected_modw_file, n_threads):
func_kwargs = all_args[1]
if n_threads == 0:
func_kwargs['use_c'] = False
else:
func_kwargs['use_c'] = True
func_kwargs['n_threads'] = n_threads
qpt_freqs, modw = fc.calculate_qpoint_frequencies(
all_args[0], **func_kwargs)
with open(os.path.join(get_fc_dir(), expected_modw_file), 'r') as fp:
modw_dict = json.load(fp)
expected_modw = modw_dict['mode_widths'] * ureg(
modw_dict['mode_widths_unit'])
expected_qpt_freqs = get_expected_qpt_freqs(
material, expected_qpoint_frequencies_file)
# Only give gamma-acoustic modes special treatment if the acoustic
# sum rule has been applied
if not 'asr' in func_kwargs.keys():
gamma_atol = None
else:
gamma_atol = 0.5
check_qpt_freqs(qpt_freqs,
expected_qpt_freqs,
frequencies_atol=1e-4,
frequencies_rtol=2e-5,
acoustic_gamma_atol=gamma_atol)
assert modw.units == expected_modw.units
npt.assert_allclose(modw.magnitude,
expected_modw.magnitude,
atol=2e-4,
rtol=5e-5)
weights = np.array([0.1, 0.05, 0.05, 0.2, 0.2, 0.15, 0.15, 0.2, 0.1])
weights_output_split_gamma = np.array([
0.1, 0.05, 0.025, 0.025, 0.2, 0.1, 0.1, 0.075, 0.075, 0.075, 0.075,
0.2, 0.1
])
@pytest.mark.parametrize(
'fc, qpts, weights, expected_weights, kwargs',
[(get_fc('quartz'), get_test_qpts(), weights, weights, {}),
(get_fc('quartz'), get_test_qpts('split_insert_gamma'), weights,
weights_output_split_gamma, {
'insert_gamma': True
})])
def test_calculate_qpoint_frequencies_with_weights_sets_weights(
self, fc, qpts, weights, expected_weights, kwargs):
qpt_freqs_weighted = fc.calculate_qpoint_frequencies(qpts,
weights=weights,
**kwargs)
npt.assert_allclose(qpt_freqs_weighted.weights, expected_weights)