def get_spectrum(force_constants: ForceConstants,
*,
bin_width: Quantity,
max_energy: Quantity,
q: Quantity = (0.1 * ureg('1/angstrom')),
npts: int = 1000,
npts_density: bool = False,
sampling: str = 'golden',
jitter: bool = True,
dos: bool = False,
smear_width: Optional[Quantity] = (1 * ureg('meV'))):
assert isinstance(q, Quantity)
if npts_density:
npts = int(np.ceil(npts * (q.to('1/angstrom').magnitude**2)))
energy_bins = np.arange(0,
(max_energy.to('meV').magnitude),
bin_width.to('meV').magnitude) * max_energy.units
if dos:
sampling_function = sample_sphere_dos
else:
sampling_function = sample_sphere_structure_factor
spectrum = sampling_function(force_constants, mod_q=q, npts=npts,
sampling=sampling, jitter=jitter,
energy_bins=energy_bins)
if smear_width is None:
return spectrum
else:
return spectrum.broaden(smear_width, shape='gauss')
class TestQpointPhononModesCalculateDos:
@pytest.mark.parametrize(
'material, qpt_ph_modes_file, expected_dos_json, ebins',
[('quartz', 'quartz-666-grid.phonon', 'quartz_666_dos.json',
np.arange(0, 155, 0.5) * ureg('meV')),
('CaHgO2', 'CaHgO2-666-grid.yaml', 'CaHgO2_666_dos.json',
np.arange(0, 95, 0.4) * ureg('meV'))])
def test_calculate_dos(self, material, qpt_ph_modes_file,
expected_dos_json, ebins):
if qpt_ph_modes_file.endswith('.phonon'):
qpt_ph_modes = QpointPhononModes.from_castep(
get_castep_path(material, qpt_ph_modes_file))
else:
qpt_ph_modes = QpointPhononModes.from_phonopy(
phonon_name=get_phonopy_path(material, qpt_ph_modes_file))
dos = qpt_ph_modes.calculate_dos(ebins)
expected_dos = get_expected_spectrum1d(expected_dos_json)
check_spectrum1d(dos, expected_dos)
def test_calculate_dos_with_0_inv_cm_bin_doesnt_raise_runtime_warn(self):
qpt_ph_modes = get_qpt_ph_modes('quartz')
ebins = np.arange(0, 1300, 4) * ureg('1/cm')
with pytest.warns(None) as warn_record:
dos = qpt_ph_modes.calculate_dos(ebins)
assert len(warn_record) == 0
def setUp(self):
# Test creation of BandsData object (which reads NaH.bands file in
# test/data dir). BandsData object will also read extra data (ion_r
# and ion_type) from the NaH.castep file
# Create trivial object so attributes can be assigned to it
expctd_data = type('', (), {})() # Expected data
expctd_data.cell_vec = np.array(
[[0.000000, 4.534397, 4.534397], [4.534397, 0.000000, 4.534397],
[4.534397, 4.534397, 0.000000]]) * ureg('bohr')
expctd_data.ion_r = np.array([[0.500000, 0.500000, 0.500000],
[0.000000, 0.000000, 0.000000]])
expctd_data.ion_type = np.array(['H', 'Na'])
expctd_data.qpts = np.array([[-0.45833333, -0.37500000, -0.45833333],
[-0.45833333, -0.37500000, -0.20833333]])
expctd_data.weights = np.array([0.00347222, 0.00694444])
expctd_data.freqs = np.array([[
-1.83230180, -0.83321119, -0.83021854, -0.83016941, -0.04792334
], [-1.83229571, -0.83248269, -0.83078961, -0.83036048, -0.05738470]
]) * ureg('hartree')
expctd_data.freq_down = np.array([]) * ureg('hartree')
expctd_data.fermi = np.array([-0.009615]) * ureg('hartree')
self.expctd_data = expctd_data
seedname = 'NaH'
path = 'data'
data = BandsData.from_castep(seedname, path=path)
self.data = data
def check_unit_conversion(obj, attr, unit):
"""
Utility function to check unit conversions in Euphonic objects
Parameters
----------
obj : Object
The object to check
attr : str
The name of the attribute to change the units of
unit : str
The unit to change attr to
"""
unit_attr = attr + '_unit'
original_attr_value = np.copy(getattr(obj, attr).magnitude) * getattr(
obj, attr).units
setattr(obj, unit_attr, unit)
# Check unit value (e.g. 'frequencies_unit') has changed
assert getattr(obj, unit_attr) == unit
# Check when returning the attrbute (e.g. 'frequencies') it is in
# the desired unit and has the correct magnitude
if attr == 'temperature':
assert str(getattr(obj, attr).units) == str(ureg(unit).units)
else:
assert getattr(obj, attr).units == ureg(unit)
npt.assert_allclose(
getattr(obj, attr).magnitude,
original_attr_value.to(unit).magnitude)
def test_get_default_bins(mocker, units):
qpm = mocker.MagicMock()
qpm.frequencies = np.array([-1., 0.3, (10 / 1.05), 4.2]) * ureg(units)
default_bins = _get_default_bins(qpm, nbins=10)
assert default_bins.units == ureg(units)
npt.assert_almost_equal(default_bins.magnitude,
[0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10.])
class TestSpectrum1DCollectionMethods:
@pytest.mark.parametrize(
'spectrum, split_kwargs, expected_spectra',
[(get_spectrum1dcollection('methane_pdos.json'), {
'indices': [50]
}, [
get_spectrum1dcollection(f'methane_pdos_split50_{i}.json')
for i in range(2)
])])
def test_split(self, spectrum, split_kwargs, expected_spectra):
spectra = spectrum.split(**split_kwargs)
for split, expected_split in zip(spectra, expected_spectra):
check_spectrum1dcollection(split, expected_split)
@pytest.mark.parametrize(
'spectrum_file, expected_bin_edges_file, expected_units',
[('gan_bands.json', 'gan_bands_bin_edges.npy', ureg('1/angstrom')),
('quartz_dos_collection.json', 'quartz_dos_collection_bin_edges.npy',
ureg('meV'))])
def test_get_bin_edges(self, spectrum_file, expected_bin_edges_file,
expected_units):
spec = get_spectrum1dcollection(spectrum_file)
bin_edges = spec.get_bin_edges()
expected_bin_edges = np.load(
os.path.join(get_spectrum_dir(), expected_bin_edges_file))
assert bin_edges.units == expected_units
assert_allclose(bin_edges.magnitude, expected_bin_edges)
@pytest.mark.parametrize(
'spectrum_file, expected_bin_centres_file, expected_units',
[('gan_bands.json', 'gan_bands_bin_centres.npy', ureg('1/angstrom')),
('quartz_dos_collection.json',
'quartz_dos_collection_bin_centres.npy', ureg('meV'))])
def test_get_bin_centres(self, spectrum_file, expected_bin_centres_file,
expected_units):
spec = get_spectrum1dcollection(spectrum_file)
bin_centres = spec.get_bin_centres()
expected_bin_centres = np.load(
os.path.join(get_spectrum_dir(), expected_bin_centres_file))
assert bin_centres.units == expected_units
assert_allclose(bin_centres.magnitude, expected_bin_centres)
def test_get_bin_edges_with_invalid_data_shape_raises_value_error(self):
spec = get_spectrum1dcollection('gan_bands.json')
spec._y_data = spec._y_data[:, :51]
with pytest.raises(ValueError):
spec.get_bin_edges()
def test_get_bin_centres_with_invalid_data_shape_raises_value_error(self):
spec = get_spectrum1dcollection('quartz_dos_collection.json')
spec._x_data = spec._x_data[:31]
with pytest.raises(ValueError):
spec.get_bin_centres()
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)
def get_mp_grid_spec(
self, spacing: Quantity = 0.1 * ureg('1/angstrom')
) -> Tuple[int, int, int]:
"""
Get suggested divisions for Monkhorst-Pack grid
Determine a mesh for even Monkhorst-Pack sampling of the reciprocal
cell
Parameters
----------
spacing
Scalar float quantity in 1/length units. Maximum
reciprocal-space distance between q-point samples
Returns
-------
grid_spec
The number of divisions for each reciprocal lattice vector
"""
recip_length_unit = spacing.units
lattice = self.reciprocal_cell().to(recip_length_unit)
grid_spec = np.linalg.norm(lattice.magnitude,
axis=1) / spacing.magnitude
# math.ceil is better than np.ceil because it returns ints
return tuple([ceil(x) for x in grid_spec])
def test_calculate_dos_with_0_inv_cm_bin_doesnt_raise_runtime_warn(self):
qpt_freqs = get_qpt_freqs('quartz',
'quartz_666_qpoint_frequencies.json')
ebins = np.arange(0, 1300, 4) * ureg('1/cm')
with pytest.warns(None) as warn_record:
dos = qpt_freqs.calculate_dos(ebins)
assert len(warn_record) == 0
def temperature(self):
if self._temperature is not None:
# See https://pint.readthedocs.io/en/latest/nonmult.html
return Quantity(self._temperature,
ureg('K')).to(self.temperature_unit)
else:
return None
def diff_1d(spectrum: Spectrum1D,
reference: Spectrum1D,
fractional: bool = False,
threshold: float = 1e-12) -> Quantity:
"""Compare the values of two Spectrum1D objects, returning an array
Args:
spectrum, reference: Spectra with same x-values for comparison
fractional:
Calculate relative difference by formula (S - R)/R. If False,
use the unscaled difference between values instead.
threshold:
Ignore error from values smaller than this threshold in reference
spectrum when fractional=True
Returns:
array Quantity:
Difference between spectra
"""
assert spectrum.x_data_unit == reference.x_data_unit
assert allclose(spectrum.x_data.magnitude, reference.x_data.magnitude)
diff = (spectrum.y_data.to(reference.y_data_unit).magnitude
- reference.y_data.magnitude)
if fractional:
ref_values = reference.y_data.magnitude
mask = absolute(ref_values) > threshold
diff = diff[mask] / ref_values[mask] * ureg(None)
else:
diff *= spectrum.y_data.units
return diff
def _check_unit_conversion(obj: object, attr_name: str, attr_value: Any,
unit_attrs: List[str]) -> None:
"""
If setting an attribute on an object that relates to the units of a
Quantity (e.g. 'frequencies_unit' in QpointPhononModes) check that
the unit conversion is valid before allowing the value to be set
Parameters
----------
obj
The object to check
attr_name
The name of the attribute that is being set
attr_value
The new value of the attribute
unit_attrs
Only check the unit conversion if the attribute is one of
unit_attrs
Raises
------
ValueError
If the unit conversion is not valid
"""
if hasattr(obj, attr_name):
if attr_name in unit_attrs:
try:
_ = ureg(getattr(obj, attr_name)).to(attr_value)
except DimensionalityError:
raise ValueError(
(f'"{attr_value}" is not a known dimensionally-consistent '
f'unit for "{attr_name}"'))
def setUp(self):
data = type('', (), {})()
# Input values
data._e_units = 'E_h'
data.dos = np.array([
2.30e-01, 1.82e-01, 8.35e-02, 3.95e-02, 2.68e-02, 3.89e-02,
6.15e-02, 6.75e-02, 6.55e-02, 5.12e-02, 3.60e-02, 2.80e-02,
5.22e-02, 1.12e-01, 1.52e-01, 1.37e-01, 9.30e-02, 6.32e-02,
7.92e-02, 1.32e-01, 1.53e-01, 8.88e-02, 2.26e-02, 2.43e-03,
1.08e-04, 2.00e-06, 8.11e-07, 4.32e-05, 9.63e-04, 8.85e-03,
3.35e-02, 5.22e-02, 3.35e-02, 8.85e-03, 9.63e-04, 4.32e-05,
7.96e-07, 6.81e-09, 9.96e-08, 5.40e-06, 1.21e-04, 1.13e-03,
4.71e-03, 1.19e-02, 2.98e-02, 6.07e-02, 6.91e-02, 3.79e-02,
9.33e-03, 9.85e-04, 4.40e-05, 2.24e-05, 4.82e-04, 4.43e-03,
1.67e-02, 2.61e-02, 1.67e-02, 4.43e-03, 4.82e-04, 2.16e-05,
3.98e-07
])
data.dos_down = np.array([
6.05e-09, 7.97e-07, 4.33e-05, 9.71e-04, 9.08e-03, 3.72e-02,
8.06e-02, 1.37e-01, 1.84e-01, 1.47e-01, 7.37e-02, 3.84e-02,
2.67e-02, 3.80e-02, 5.36e-02, 4.24e-02, 4.28e-02, 5.76e-02,
5.03e-02, 3.55e-02, 2.32e-02, 3.15e-02, 7.39e-02, 1.24e-01,
1.40e-01, 1.11e-01, 7.48e-02, 5.04e-02, 5.22e-02, 8.75e-02,
1.37e-01, 1.30e-01, 6.37e-02, 1.47e-02, 1.51e-03, 1.09e-04,
9.64e-04, 8.85e-03, 3.35e-02, 5.22e-02, 3.35e-02, 8.85e-03,
9.63e-04, 4.33e-05, 6.19e-06, 1.21e-04, 1.13e-03, 4.71e-03,
1.19e-02, 2.98e-02, 6.07e-02, 6.91e-02, 3.79e-02, 9.33e-03,
9.85e-04, 4.40e-05, 2.24e-05, 4.82e-04, 4.43e-03, 1.67e-02,
2.61e-02
])
data.dos_bins = np.array([
0.58, 0.78, 0.98, 1.18, 1.38, 1.58, 1.78, 1.98, 2.18, 2.38, 2.58,
2.78, 2.98, 3.18, 3.38, 3.58, 3.78, 3.98, 4.18, 4.38, 4.58, 4.78,
4.98, 5.18, 5.38, 5.58, 5.78, 5.98, 6.18, 6.38, 6.58, 6.78, 6.98,
7.18, 7.38, 7.58, 7.78, 7.98, 8.18, 8.38, 8.58, 8.78, 8.98, 9.18,
9.38, 9.58, 9.78, 9.98, 10.18, 10.38, 10.58, 10.78, 10.98, 11.18,
11.38, 11.58, 11.78, 11.98, 12.18, 12.38, 12.58, 12.78
]) * ureg('E_h')
data.fermi = np.array([4.71, 4.71]) * ureg('E_h')
self.data = data
self.title = 'Iron'
self.mirror = False
# Results
self.fig = plot_dos(self.data, self.title, self.mirror)
self.ax = self.fig.axes[0]
def test_qpts_cart_to_frac_trivial(trivial_crystal, trivial_qpts):
"""Check internal method for q-point conversion with trivial example"""
cart_qpts = np.asarray(trivial_qpts['cart'], dtype=float
) * ureg('1 / angstrom')
frac_qpts = np.asarray(trivial_qpts['frac'], dtype=float)
calc_frac_qpts = _qpts_cart_to_frac(cart_qpts, trivial_crystal)
npt.assert_almost_equal(calc_frac_qpts, frac_qpts)
def from_castep_phonon_dos(cls: SC, filename: str) -> SC:
"""
Reads total DOS and per-element PDOS from a CASTEP
.phonon_dos file
Parameters
----------
filename
The path and name of the .phonon_dos file to read
"""
data = read_phonon_dos_data(filename)
items = data['dos'].items()
metadata = {'line_data': [{'label': item[0]} for item in items]}
y_data = np.stack([item[1] for item in items])
return Spectrum1DCollection(data['dos_bins'] *
ureg(data['dos_bins_unit']),
y_data * ureg('dimensionless'),
metadata=metadata)
def test_qpts_cart_to_frac_roundtrip(random_qpts_array,
nontrivial_crystal):
frac_qpts = random_qpts_array
cart_qpts = frac_qpts.dot(nontrivial_crystal.reciprocal_cell()
.to('1 / angstrom').magnitude
) * ureg('1 / angstrom')
calc_frac_qpts = _qpts_cart_to_frac(cart_qpts, nontrivial_crystal)
npt.assert_almost_equal(calc_frac_qpts, frac_qpts)
def mock_crystal(self, mocker):
crystal = mocker.MagicMock()
crystal.configure_mock(
**{'reciprocal_cell.return_value': np.array([[1, 0, 0],
[0, 1, 0],
[0, 0, 1]])
* ureg('1 / angstrom'),
'get_mp_grid_spec.return_value': (2, 2, 2)})
return crystal
def test_sample_sphere_structure_factor(self, mocker, mock_crystal,
mock_fc, mock_qpm,
mock_s, mock_dw, random_qpts_array,
options):
# Make sure the same instance of mock DebyeWaller is used everywhere
if options['dw'] == 'mock_dw':
options['dw'] = mock_dw
# Fixed return values for dummy functions
return_bins = self._energy_bins
return_scattering_lengths = self._scattering_lengths
# Dummy out functions called by sample_sphere_structure_factor
# that are tested elsewhere
self.mock_get_default_bins(mocker, return_bins)
get_qpts_sphere = self.mock_get_qpts_sphere(mocker, random_qpts_array)
get_ref_data = self.mock_get_reference_data(mocker,
return_scattering_lengths)
assert (sample_sphere_structure_factor(
mock_fc, **options)
== 'calculate_1d_average_return_value')
# Check scattering lengths were looked up as expected
if isinstance(options['scattering_lengths'], str):
assert get_ref_data.call_args == (
(), {'physical_property': 'coherent_scattering_length',
'collection': 'Sears1992'})
else:
assert isinstance(options['scattering_lengths'], dict)
# Check qpts sphere called as expected
assert get_qpts_sphere.call_args == ((options['npts'],),
{'sampling': options['sampling'],
'jitter': options['jitter']})
# Check expected list of qpoints was passed to forceconstants
# (fractional q = cart q because the lattice vectors are unit cube)
npt.assert_almost_equal(
random_qpts_array * options['mod_q'].magnitude,
mock_fc.calculate_qpoint_phonon_modes.call_args[0][0])
# Check structure factor args were as expected
assert (mock_qpm.calculate_structure_factor.call_args
== (tuple(), {'scattering_lengths': self._scattering_lengths,
'dw': mock_dw}))
# Check auto grid was used if temperature given
if options.get('temperature') is not None:
assert (mock_qpm.calculate_debye_waller.call_args[0][0]
== options['temperature'])
assert (mock_crystal.get_mp_grid_spec.call_args[0][0]
== 0.025 * ureg('1/angstrom'))
# Check expected bins set for 1d averaging
assert mock_s.calculate_1d_average.call_args == ((return_bins,),)
def _grid_spec_from_args(crystal: Crystal,
grid: Optional[Sequence[int]] = None,
grid_spacing: Quantity = 0.1 * ureg('1/angstrom')
) -> Sequence[int]:
"""Get Monkorst-Pack mesh divisions from user arguments"""
if grid:
grid_spec = grid
else:
grid_spec = crystal.get_mp_grid_spec(spacing=grid_spacing)
return grid_spec
def _bose_corrected_structure_factor(
self,
e_bins: Quantity,
calc_bose: bool = True,
temperature: Optional[Quantity] = None) -> Quantity:
"""Bin structure factor in energy, return (Bose-populated) array
Parameters
----------
e_bins
Shape (n_e_bins + 1,) float Quantity. The energy bin edges
calc_bose
Whether to calculate and apply the Bose population factor
temperature
Temperature used to calculate the Bose factor. This is only
required if StructureFactor.temperature = None, otherwise
the temperature stored in StructureFactor will be used.
Returns
-------
intensities
Scattering intensities as array over (qpt, energy)
"""
# Convert units
freqs = self._frequencies
e_bins_internal = e_bins.to('hartree').magnitude
# Create initial sqw_map with an extra an energy bin either
# side, for any branches that fall outside the energy bin range
sqw_map = np.zeros((self.n_qpts, len(e_bins) + 1))
sf = self._structure_factors
p_intensity = sf
n_intensity = sf
if calc_bose:
try:
bose = self._bose_factor(temperature)
p_intensity = (1 + bose) * p_intensity
n_intensity = bose * n_intensity
except NoTemperatureError:
pass
p_bin = np.digitize(freqs, e_bins_internal)
n_bin = np.digitize(-freqs, e_bins_internal)
# Sum intensities into bins
first_index = np.transpose(
np.tile(range(self.n_qpts), (3 * self.crystal.n_atoms, 1)))
np.add.at(sqw_map, (first_index, p_bin), p_intensity)
np.add.at(sqw_map, (first_index, n_bin), n_intensity)
# Exclude values outside ebin range
sqw_map = sqw_map[:, 1:-1] * ureg('bohr**2').to(
self.structure_factors_unit)
return sqw_map
def calculate_dos(self, dos_bins: Quantity,
mode_widths: Optional[np.ndarray] = None,
mode_widths_min: Quantity = Quantity(0.01, 'meV')
) -> Spectrum1D:
"""
Calculates a density of states
Parameters
----------
dos_bins
Shape (n_e_bins + 1,) float Quantity. The energy bin edges
to use for calculating the DOS
mode_widths
Shape (n_qpts, n_branches) float Quantity in energy units.
The broadening width for each mode at each q-point, for
adaptive broadening
mode_widths_min
Scalar float Quantity in energy units. Sets a lower limit on
the mode widths, as mode widths of zero will result in
infinitely sharp peaks
Returns
-------
dos
A spectrum containing the energy bins on the x-axis and dos
on the y-axis
"""
freqs = self._frequencies
n_modes = self.frequencies.shape[1]
# dos_bins commonly contains a 0 bin, and converting from 0 1/cm
# to 0 hartree causes a RuntimeWarning, so suppress it
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=RuntimeWarning)
dos_bins_calc = dos_bins.to('hartree').magnitude
if mode_widths is not None:
from scipy.stats import norm
dos_bins_calc = Spectrum1D._bin_edges_to_centres(dos_bins_calc)
dos = np.zeros(len(dos_bins_calc))
mode_widths = mode_widths.to('hartree').magnitude
mode_widths = np.maximum(mode_widths,
mode_widths_min.to('hartree').magnitude)
for q in range(self.n_qpts):
for m in range(n_modes):
pdf = norm.pdf(dos_bins_calc, loc=freqs[q,m],
scale=mode_widths[q,m])
dos += pdf*self.weights[q]/n_modes
else:
weights = np.repeat(self.weights[:, np.newaxis],
n_modes,
axis=1)
dos, _ = np.histogram(freqs, dos_bins_calc, weights=weights, density=True)
return Spectrum1D(
dos_bins,
dos*ureg('dimensionless'))
def from_castep_phonon_dos(cls: S1D,
filename: str,
element: Optional[str] = None) -> S1D:
"""
Reads DOS from a CASTEP .phonon_dos file
Parameters
----------
filename
The path and name of the .phonon_dos file to read
element
Which element's PDOS to read. If not supplied reads
the total DOS.
"""
data = read_phonon_dos_data(filename)
if element is None:
element = 'Total'
return Spectrum1D(data['dos_bins'] * ureg(data['dos_bins_unit']),
data['dos'][element] * ureg('dimensionless'),
metadata={'label': element})
def test_calculate_dos_with_mode_widths(self, material, qpt_freqs_json,
mode_widths_json,
expected_dos_json, ebins):
qpt_freqs = get_qpt_freqs(material, qpt_freqs_json)
with open(os.path.join(get_fc_dir(), mode_widths_json), 'r') as fp:
modw_dict = json.load(fp)
mode_widths = modw_dict['mode_widths'] * ureg(
modw_dict['mode_widths_unit'])
dos = qpt_freqs.calculate_dos(ebins, mode_widths=mode_widths)
expected_dos = get_expected_spectrum1d(expected_dos_json)
check_spectrum1d(dos, expected_dos)
def cell_volume(self) -> Quantity:
"""
Calculates the cell volume
Returns
-------
volume
Scalar float quantity in length**3 units. The cell volume
"""
vol = self._cell_volume() * ureg.bohr**3
return vol.to(ureg(self.cell_vectors_unit)**3)
def broaden(self: S1D, x_width: Quantity, shape: str = 'gauss') -> S1D:
"""
Broaden y_data and return a new broadened spectrum object
Parameters
----------
x_width
Scalar float Quantity. The broadening FWHM
shape
One of {'gauss', 'lorentz'}. The broadening shape
Returns
-------
broadened_spectrum
A new Spectrum1D object with broadened y_data
Raises
------
ValueError
If shape is not one of the allowed strings
"""
if shape == 'gauss':
xsigma = self._gfwhm_to_sigma(x_width, self.get_bin_centres())
y_broadened = gaussian_filter1d(
self.y_data.magnitude, xsigma, mode='constant') * ureg(
self.y_data_unit)
elif shape == 'lorentz':
broadening = _distribution_1d(self.get_bin_centres().magnitude,
x_width.to(
self.x_data_unit).magnitude,
shape=shape)
y_broadened = correlate1d(self.y_data.magnitude,
broadening,
mode='constant') * ureg(self.y_data_unit)
else:
raise ValueError(f"Distribution shape '{shape}' not recognised")
return Spectrum1D(
np.copy(self.x_data.magnitude) * ureg(self.x_data_unit),
y_broadened, deepcopy(
(self.x_tick_labels)), deepcopy(self.metadata))
def _get_q_distance(length_unit_string: str, q_distance: float) -> Quantity:
"""
Parse user arguments to obtain reciprocal-length spacing Quantity
"""
try:
length_units = ureg(length_unit_string)
except UndefinedUnitError:
raise ValueError("Length unit not known. Euphonic uses Pint for units."
" Try 'angstrom' or 'bohr'. Metric prefixes "
"are also allowed, e.g 'nm'.")
recip_length_units = 1 / length_units
return q_distance * recip_length_units
def calculate_dos_map(modes: euphonic.QpointPhononModes,
ebins: euphonic.Quantity) -> euphonic.Spectrum2D:
from euphonic.util import _calc_abscissa
q_bins = _calc_abscissa(modes.crystal.reciprocal_cell(), modes.qpts)
bin_indices = np.digitize(modes.frequencies.magnitude, ebins.magnitude)
intensity_map = np.zeros((modes.n_qpts, len(ebins) + 1))
first_index = np.tile(range(modes.n_qpts),
(3 * modes.crystal.n_atoms, 1)).transpose()
np.add.at(intensity_map, (first_index, bin_indices), 1)
return euphonic.Spectrum2D(q_bins, ebins,
intensity_map[:, :-1] * ureg('dimensionless'))
class TestStructureFactorCalculate1dAverage:
@pytest.mark.parametrize(
'material, sf_json, expected_1d_json, ebins, kwargs',
[('quartz', 'quartz_666_300K_structure_factor.json',
'quartz_666_300K_sf_1d_average_with_weights.json',
np.arange(0, 156) * ureg('meV'), {}),
('quartz', 'quartz_666_300K_structure_factor_noweights.json',
'quartz_666_300K_sf_1d_average_with_weights.json',
np.arange(0, 156) * ureg('meV'), {
'weights':
np.load(
os.path.join(get_sf_dir('quartz'), 'quartz_666_weights.npy'))
}),
('quartz', 'quartz_666_300K_structure_factor_noweights.json',
'quartz_666_300K_sf_1d_average_noweights.json',
np.arange(0, 156) * ureg('meV'), {})])
def test_calculate_1d_average(self, material, sf_json, expected_1d_json,
ebins, kwargs):
sf = get_sf(material, sf_json)
sw = sf.calculate_1d_average(ebins, **kwargs)
expected_sw = get_expected_spectrum1d(expected_1d_json)
check_spectrum1d(sw, expected_sw)
def _qpts_cart_to_frac(qpts: Quantity,
crystal: Crystal) -> np.ndarray:
"""Convert set of q-points from Cartesian to fractional coordinates
Parameters
----------
qpts
Array of q-points in Cartesian coordinates.
crystal
Crystal structure determining reciprocal lattice
Returns
-------
np.ndarray
Dimensionless array of q-points in fractional coordinates
"""
lattice = crystal.reciprocal_cell()
return np.linalg.solve(lattice.to(ureg('1/bohr')).magnitude.T,
qpts.to(ureg('1/bohr')).magnitude.T
).T
def setUp(self):
# Test creation of BandsData object (which reads Fe.bands file in
# test/data dir). There is no Fe.castep file in test/data so the ion_r
# and ion_pos attributes shouldn't exist
# Create trivial function object so attributes can be assigned to it
expctd_data = type('', (), {})() # Expected data
expctd_data.cell_vec = np.array(
[[-2.708355, 2.708355, 2.708355], [2.708355, -2.708355, 2.708355],
[2.708355, 2.708355, -2.708355]]) * ureg('bohr')
expctd_data.qpts = np.array([[-0.37500000, -0.45833333, 0.29166667],
[-0.37500000, -0.37500000, 0.29166667]])
expctd_data.weights = np.array([0.01388889, 0.01388889])
expctd_data.freqs = np.array([[
0.02278248, 0.02644693, 0.12383402, 0.15398152, 0.17125020,
0.43252010
],
[
0.02760952, 0.02644911, 0.12442671,
0.14597457, 0.16728951, 0.35463529
]]) * ureg('hartree')
expctd_data.freq_down = np.array(
[[
0.08112495, 0.08345039, 0.19185076, 0.22763689, 0.24912308,
0.46511567
],
[
0.08778721, 0.08033338, 0.19288937, 0.21817779, 0.24476910,
0.39214129
]]) * ureg('hartree')
expctd_data.fermi = [0.173319, 0.173319] * ureg('hartree')
self.expctd_data = expctd_data
seedname = 'Fe'
path = 'data'
data = BandsData.from_castep(seedname, path=path)
self.data = data