def create_from_castep(self, request):
material, phonon_file, json_file = request.param
qpt_freqs = QpointFrequencies.from_castep(
get_castep_path(material, phonon_file))
expected_qpt_freqs = ExpectedQpointFrequencies(
os.path.join(get_qpt_freqs_dir(material), json_file))
return qpt_freqs, expected_qpt_freqs
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_debye_waller(self, material, qpt_ph_modes_file,
expected_dw_json, temperature, kwargs):
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))
dw = qpt_ph_modes.calculate_debye_waller(temperature * ureg('K'),
**kwargs)
expected_dw = get_expected_dw(material, expected_dw_json)
check_debye_waller(dw, expected_dw, dw_atol=1e-12)
def test_read_data(self, material, phonon_dos_file, expected_data_file):
dos_data = read_phonon_dos_data(
get_castep_path(material, phonon_dos_file))
with open(get_filepath(expected_data_file), 'r') as fp:
expected_dos_data = json.loads(fp.read())
dos_crystal = ExpectedCrystal(dos_data.pop('crystal'))
expected_dos_crystal = ExpectedCrystal(
expected_dos_data.pop('crystal'))
check_crystal(dos_crystal, expected_dos_crystal)
def check_dict(dct, expected_dct):
for exp_key, exp_val in expected_dct.items():
if isinstance(exp_val, list):
npt.assert_allclose(dct[exp_key], np.array(exp_val))
elif isinstance(exp_val, dict):
check_dict(dct[exp_key], exp_val)
else:
assert dct[exp_key] == exp_val
check_dict(dos_data, expected_dos_data)
def create_from_castep_phonon_dos(self, request):
material, phonon_dos_file, json_file = request.param
spec = Spectrum1DCollection.from_castep_phonon_dos(
get_castep_path(material, phonon_dos_file))
expected_spec = get_expected_spectrum1dcollection(json_file)
return spec, expected_spec
def get_si2_qpt_ph_modes():
return QpointPhononModes.from_castep(
get_castep_path('Si2-sc-skew', 'Si2-sc-skew.phonon'))
def get_quartz_qpt_ph_modes():
return QpointPhononModes.from_castep(
get_castep_path('quartz', 'quartz_nosplit.phonon'))
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_create_from_castep_with_no_fc_raises_runtime_error(self):
with pytest.raises(RuntimeError):
ForceConstants.from_castep(
get_castep_path('h-BN', 'h-BN_no_force_constants.castep_bin'))
def get_si2_fc():
return ForceConstants.from_castep(
get_castep_path('Si2-sc-skew', 'Si2-sc-skew.castep_bin'))
def get_lzo_fc():
return ForceConstants.from_castep(
get_castep_path('LZO', 'La2Zr2O7.castep_bin'))
from unittest.mock import patch
import pytest
import numpy.testing as npt
# Required for mocking
import matplotlib.pyplot
from tests_and_analysis.test.utils import get_data_path, get_castep_path
from tests_and_analysis.test.script_tests.utils import (
get_script_test_data_path, get_current_plot_image_data, args_to_key)
import euphonic.cli.intensity_map
quartz_phonon_file = os.path.join(
get_data_path(), 'qpoint_phonon_modes', 'quartz',
'quartz_bandstructure_qpoint_phonon_modes.json')
lzo_phonon_file = get_castep_path('LZO', 'La2Zr2O7.phonon')
graphite_fc_file = get_castep_path('graphite', 'graphite.castep_bin')
intensity_map_output_file = os.path.join(get_script_test_data_path(),
'intensity-map.json')
intensity_map_params = [
[graphite_fc_file], [graphite_fc_file, '--v-min=0', '--v-max=1e-10'],
[graphite_fc_file, '--energy-unit=meV'],
[graphite_fc_file, '--weights=coherent', '--cmap=bone'],
[graphite_fc_file, '--weights=coherent', '--temperature=800'],
[graphite_fc_file, '-w', 'dos', '--y-label=DOS', '--title=DOS TITLE'],
[graphite_fc_file, '--e-min=50', '-u=cm^-1', '--x-label=wavenumber'],
[
graphite_fc_file, '--e-min=-100', '--e-max=1000', '--ebins=100',
'--energy-unit=cm^-1'
], [graphite_fc_file, '--energy-broadening=2e-3', '-u=eV'],
[
def create_from_castep_phonon_dos(self, request):
material, phonon_dos_file, kwargs, json_file = request.param
expected_spec1d = get_expected_spectrum1d(json_file)
spec1d = Spectrum1D.from_castep_phonon_dos(
get_castep_path(material, phonon_dos_file), **kwargs)
return spec1d, expected_spec1d
import os
import json
from unittest.mock import patch
import pytest
import numpy.testing as npt
# Required for mocking
import matplotlib.pyplot
from tests_and_analysis.test.utils import get_data_path, get_castep_path, get_phonopy_path
from tests_and_analysis.test.script_tests.utils import (
get_script_test_data_path, get_current_plot_image_data, args_to_key)
import euphonic.cli.powder_map
graphite_fc_file = get_castep_path('graphite', 'graphite.castep_bin')
nacl_prim_fc_file = get_phonopy_path('NaCl_prim', 'phonopy_nacl.yaml')
powder_map_output_file = os.path.join(get_script_test_data_path(),
'powder-map.json')
quick_calc_params = ['--npts=10', '--npts-min=10', '--q-spacing=1']
powder_map_params = [
[nacl_prim_fc_file], [nacl_prim_fc_file, *quick_calc_params],
[nacl_prim_fc_file, '--temperature=1000', *quick_calc_params],
[
nacl_prim_fc_file, '--temperature=1000', '--weights=coherent',
*quick_calc_params
], [nacl_prim_fc_file, '--v-min=0', '--v-max=1e-10', *quick_calc_params],
[nacl_prim_fc_file, '--energy-unit=meV', *quick_calc_params],
[nacl_prim_fc_file, '--weights=coherent', '--cmap=bone'],
[
graphite_fc_file, '-w', 'dos', '--y-label=DOS', '--title=DOS TITLE',
def get_quartz_fc():
return ForceConstants.from_castep(
get_castep_path('quartz', 'quartz.castep_bin'))
def create_from_castep(self, request):
material, castep_bin_file = request.param
expected_fc = get_expected_fc(material)
castep_filepath = get_castep_path(material, castep_bin_file)
fc = ForceConstants.from_castep(castep_filepath)
return fc, expected_fc
