def test_base(self):
"""Base tests for PhononBands"""
filename = abidata.ref_file("trf2_5.out_PHBST.nc")
phbands = PhononBands.from_file(filename)
print(phbands)
assert PhononBands.as_phbands(phbands) is phbands
assert np.array_equal(
PhononBands.as_phbands(filename).phfreqs, phbands.phfreqs)
self.serialize_with_pickle(phbands, protocols=[-1], test_eq=False)
self.assertEqual(phbands.minfreq, 0.0)
#self.assertEqual(phbands.maxfreq, 30)
# Test XYZ vib
_, filename = tempfile.mkstemp(text=True)
phbands.create_xyz_vib(iqpt=0,
filename=filename,
max_supercell=[4, 4, 4])
# Test convertion to eigenvectors. Verify that they are orthonormal
# Allow relatively large tolerance due to possible mismatching in the atomic masses between abinit and pmg
eig = phbands.dyn_mat_eigenvect
self.assertTrue(
np.allclose(np.dot(eig[0], eig[0].T),
np.eye(len(eig[0]), dtype=np.complex),
atol=1e-5,
rtol=1e-3))
def test_base(self):
"""Base tests for PhononBands"""
filename = abidata.ref_file("trf2_5.out_PHBST.nc")
phbands = PhononBands.from_file(filename)
print(phbands)
assert PhononBands.as_phbands(phbands) is phbands
assert np.array_equal(
PhononBands.as_phbands(filename).phfreqs, phbands.phfreqs)
self.serialize_with_pickle(phbands, protocols=[-1], test_eq=False)
self.assertEqual(phbands.minfreq, 0.0)
#self.assertEqual(phbands.maxfreq, 30)
# Test XYZ vib
phbands.create_xyz_vib(iqpt=0,
filename=self.get_tmpname(text=True),
max_supercell=[4, 4, 4])
# Test ascii file
phbands.create_ascii_vib(iqpts=0,
filename=self.get_tmpname(text=True),
pre_factor=1)
# Test phononwebsite file
phbands.create_phononwebsite_json(filename=self.get_tmpname(text=True),
name='test')
# Test xmgrace
phbands.to_xmgrace(self.get_tmpname(text=True))
# Test convertion to eigenvectors. Verify that they are orthonormal
# Allow relatively large tolerance due to possible mismatching in the atomic masses between abinit and pmg
eig = phbands.dyn_mat_eigenvect
assert np.allclose(np.dot(eig[0], eig[0].T),
np.eye(len(eig[0]), dtype=np.complex),
atol=1e-5,
rtol=1e-3)
if self.has_matplotlib():
phbands.plot(show=False)
phbands.plot_fatbands(show=False)
phbands.plot_colored_matched(show=False)
# Cannot compute PHDOS with q-path
with self.assertRaises(ValueError):
phdos = phbands.get_phdos()
# convert to pymatgen object
phbands.to_pymatgen()
def test_base(self):
"""Base tests for PhononBands"""
filename = abidata.ref_file("trf2_5.out_PHBST.nc")
phbands = PhononBands.from_file(filename)
print(phbands)
assert PhononBands.as_phbands(phbands) is phbands
assert np.array_equal(PhononBands.as_phbands(filename).phfreqs, phbands.phfreqs)
self.serialize_with_pickle(phbands, protocols=[-1], test_eq=False)
self.assertEqual(phbands.minfreq, 0.0)
#self.assertEqual(phbands.maxfreq, 30)
# Test XYZ vib
_, filename = tempfile.mkstemp(text=True)
phbands.create_xyz_vib(iqpt=0, filename=filename, max_supercell=[4,4,4])
# Test convertion to eigenvectors. Verify that they are orthonormal
# Allow relatively large tolerance due to possible mismatching in the atomic masses between abinit and pmg
eig = phbands.dyn_mat_eigenvect
self.assertTrue(np.allclose(np.dot(eig[0], eig[0].T), np.eye(len(eig[0]), dtype=np.complex), atol=1e-5, rtol=1e-3))
def test_base(self):
"""Base tests for PhononBands"""
filename = abidata.ref_file("trf2_5.out_PHBST.nc")
phbands = PhononBands.from_file(filename)
repr(phbands); str(phbands)
assert phbands.to_string(title="Title", with_structure=False, with_qpoints=True, verbose=1)
assert PhononBands.as_phbands(phbands) is phbands
with self.assertRaises(TypeError):
PhononBands.as_phbands({})
assert np.array_equal(PhononBands.as_phbands(filename).phfreqs, phbands.phfreqs)
with abilab.abiopen(abidata.ref_file("trf2_5.out_PHBST.nc")) as nc:
repr(nc); str(nc)
assert nc.to_string(verbose=1)
assert nc.params["nqpt"] == len(nc.qpoints)
assert nc.qpoints.is_path
assert any(q.name is not None for q in nc.qpoints)
same_phbands_nc = PhononBands.as_phbands(nc)
self.assert_equal(same_phbands_nc.phfreqs, phbands.phfreqs)
assert phbands.phdispl_cart.shape == (phbands.nqpt, phbands.num_branches, phbands.num_branches)
# a + b gives plotter
assert hasattr(same_phbands_nc + phbands, "combiplot")
self.serialize_with_pickle(phbands, protocols=[-1], test_eq=False)
# From pickle file.
tmp_path = self.get_tmpname(suffix=".pickle")
with open(tmp_path, "wb") as fh:
pickle.dump(phbands, fh)
same_phbands = PhononBands.as_phbands(tmp_path)
self.assert_equal(same_phbands.phfreqs, phbands.phfreqs)
# a + b + c gives plotter
p = phbands + same_phbands + same_phbands_nc
assert hasattr(p, "combiplot")
assert phbands.minfreq == 0.0
#self.assertEqual(phbands.maxfreq, 30)
assert phbands.phfactor_ev2units("eV") == abu.phfactor_ev2units("eV")
# Test XYZ vib
phbands.create_xyz_vib(iqpt=0, filename=self.get_tmpname(text=True), max_supercell=[4, 4, 4])
# Test ascii file
phbands.create_ascii_vib(iqpts=0, filename=self.get_tmpname(text=True), pre_factor=1)
# Test phononwebsite file
phbands.create_phononwebsite_json(filename=self.get_tmpname(text=True), name='test')
assert phbands.view_phononwebsite(verbose=1, dryrun=True) == 0
# Test xmgrace
phbands.to_xmgrace(self.get_tmpname(text=True))
#phbands.to_xmgrace(sys.stdout)
df = phbands.get_dataframe()
assert "freq" in df and "mode" in df
self.assert_almost_equal(df["freq"].values.min(), 0)
umodes = phbands.get_unstable_modes(below_mev=-1000)
assert len(umodes) == 0
acoustic_modes = phbands.acoustic_indices((0, 0, 0))
self.assertArrayEqual(acoustic_modes, [0, 1, 2])
asr_breaking = phbands.asr_breaking()
assert asr_breaking.absmax_break == 0
# Test convertion to eigenvectors. Verify that they are orthonormal
# Allow relatively large tolerance due to possible mismatching in the atomic masses between abinit and pmg
# (Note that amu is None here)
assert phbands.amu is None
eig = phbands.dyn_mat_eigenvect
assert len(eig) == phbands.nqpt
cidentity = np.eye(len(eig[0]), dtype=np.complex)
for iq in range(len(eig)):
#print("About to test iq", iq, np.dot(eig[iq], eig[iq].T))
#assert np.allclose(np.dot(eig[iq], eig[iq].T), cidentity , atol=1e-5, rtol=1e-3)
assert np.allclose(np.dot(eig[iq].conjugate().T, eig[iq]), cidentity , atol=1e-5, rtol=1e-3)
#self.assert_almost_equal(np.dot(eig[iq].conjugate().T, eig[iq]), cidentity)
# Mapping reduced coordinates -> labels
qlabels = {
(0,0,0): r"$\Gamma$",
(0.375, 0.375, 0.75): "K",
(0.5, 0.5, 1.0): "X",
(0.5, 0.5, 0.5): "L",
(0.5, 0.0, 0.5): "X",
(0.5, 0.25, 0.75): "W",
}
if self.has_matplotlib():
assert phbands.plot(units="Thz", show=False)
assert phbands.plot_fatbands(units="ha", qlabels=qlabels, show=False)
assert phbands.plot_fatbands(phdos_file=abidata.ref_file("trf2_5.out_PHDOS.nc"), units="thz", show=False)
assert phbands.plot_colored_matched(units="cm^-1", show=False)
assert phbands.plot_phdispl(qpoint=(0, 0, 0), units="cm^-1", hatches=None, show=False)
assert phbands.plot_phdispl(qpoint=(0, 0, 0), units="cm^-1", hatches=None, show=False, cart_dir="x+y")
assert phbands.plot_phdispl(qpoint=(0, 0, 0), units="cm^-1", hatches=None, show=False, use_sqrt=True,
normalize=False)
with self.assertRaises(ValueError):
# No LO-TO terms
assert phbands.plot_phdispl(qpoint=1, is_non_analytical_direction=True, show=False)
assert phbands.plot_phdispl_cartdirs(qpoint=0, units="cm^-1", show=False)
assert phbands.boxplot(units="ev", mode_range=[2, 4], show=False)
# Cannot compute PHDOS with q-path
with self.assertRaises(ValueError):
phdos = phbands.get_phdos()
# convert to pymatgen object
phbands.to_pymatgen()
# get frozen phonons
phbands.get_frozen_phonons((0.5, 0.5, 1.0), 1, eta=0.5, max_supercell=[5,5,5])
assert not phbands.has_linewidths
phbands.linewidths = np.ones(phbands.shape)
assert phbands.has_linewidths
def test_base(self):
"""Base tests for PhononBands"""
filename = abidata.ref_file("trf2_5.out_PHBST.nc")
phbands = PhononBands.from_file(filename)
repr(phbands)
str(phbands)
assert phbands.to_string(title="Title",
with_structure=False,
with_qpoints=True,
verbose=1)
assert PhononBands.as_phbands(phbands) is phbands
with self.assertRaises(TypeError):
PhononBands.as_phbands({})
assert np.array_equal(
PhononBands.as_phbands(filename).phfreqs, phbands.phfreqs)
with abilab.abiopen(abidata.ref_file("trf2_5.out_PHBST.nc")) as nc:
repr(nc)
str(nc)
assert nc.to_string(verbose=1)
assert nc.params["nqpt"] == len(nc.qpoints)
assert nc.qpoints.is_path
assert any(q.name is not None for q in nc.qpoints)
same_phbands_nc = PhononBands.as_phbands(nc)
self.assert_equal(same_phbands_nc.phfreqs, phbands.phfreqs)
assert phbands.phdispl_cart.shape == (phbands.nqpt,
phbands.num_branches,
phbands.num_branches)
# a + b gives plotter
assert hasattr(same_phbands_nc + phbands, "combiplot")
assert phbands.epsinf is None and phbands.zcart is None
self.serialize_with_pickle(phbands, protocols=[-1], test_eq=False)
# From pickle file.
tmp_path = self.get_tmpname(suffix=".pickle")
with open(tmp_path, "wb") as fh:
pickle.dump(phbands, fh)
same_phbands = PhononBands.as_phbands(tmp_path)
self.assert_equal(same_phbands.phfreqs, phbands.phfreqs)
# a + b + c gives plotter
p = phbands + same_phbands + same_phbands_nc
assert hasattr(p, "combiplot")
assert phbands.minfreq == 0.0
#self.assertEqual(phbands.maxfreq, 30)
assert phbands.phfactor_ev2units("eV") == abu.phfactor_ev2units("eV")
# Test XYZ vib
phbands.create_xyz_vib(iqpt=0,
filename=self.get_tmpname(text=True),
max_supercell=[4, 4, 4])
# Test ascii file
phbands.create_ascii_vib(iqpts=0,
filename=self.get_tmpname(text=True),
pre_factor=1)
# Test phononwebsite file
phbands.create_phononwebsite_json(filename=self.get_tmpname(text=True),
name='test')
assert phbands.view_phononwebsite(verbose=1, dryrun=True) == 0
# Test xmgrace
phbands.to_xmgrace(self.get_tmpname(text=True))
#phbands.to_xmgrace(sys.stdout)
df = phbands.get_dataframe()
assert "freq" in df and "mode" in df
self.assert_almost_equal(df["freq"].values.min(), 0)
umodes = phbands.get_unstable_modes(below_mev=-1000)
assert len(umodes) == 0
acoustic_modes = phbands.acoustic_indices((0, 0, 0))
self.assertArrayEqual(acoustic_modes, [0, 1, 2])
asr_breaking = phbands.asr_breaking()
assert asr_breaking.absmax_break == 0
# Test convertion to eigenvectors. Verify that they are orthonormal
# Allow relatively large tolerance due to possible mismatching in the atomic masses between abinit and pmg
# (Note that amu is None here)
assert phbands.amu is None
eig = phbands.dyn_mat_eigenvect
assert len(eig) == phbands.nqpt
cidentity = np.eye(len(eig[0]), dtype=np.complex)
for iq in range(len(eig)):
#print("About to test iq", iq, np.dot(eig[iq], eig[iq].T))
#assert np.allclose(np.dot(eig[iq], eig[iq].T), cidentity , atol=1e-5, rtol=1e-3)
assert np.allclose(np.dot(eig[iq].conjugate().T, eig[iq]),
cidentity,
atol=1e-5,
rtol=1e-3)
#self.assert_almost_equal(np.dot(eig[iq].conjugate().T, eig[iq]), cidentity)
# Mapping reduced coordinates -> labels
qlabels = {
(0, 0, 0): r"$\Gamma$",
(0.375, 0.375, 0.75): "K",
(0.5, 0.5, 1.0): "X",
(0.5, 0.5, 0.5): "L",
(0.5, 0.0, 0.5): "X",
(0.5, 0.25, 0.75): "W",
}
if self.has_matplotlib():
assert phbands.plot(units="Thz", show=False, temp=300)
assert phbands.plot_fatbands(units="ha",
qlabels=qlabels,
show=False)
assert phbands.plot_fatbands(
phdos_file=abidata.ref_file("trf2_5.out_PHDOS.nc"),
units="thz",
show=False)
assert phbands.plot_colored_matched(units="cm^-1", show=False)
assert phbands.plot_phdispl(qpoint=(0, 0, 0),
units="cm^-1",
hatches=None,
show=False)
assert phbands.plot_phdispl(qpoint=(0, 0, 0),
units="cm^-1",
hatches=None,
show=False,
cart_dir="x+y")
assert phbands.plot_phdispl(qpoint=(0, 0, 0),
units="cm^-1",
hatches=None,
show=False,
use_sqrt=True,
normalize=False)
with self.assertRaises(ValueError):
# No LO-TO terms
assert phbands.plot_phdispl(qpoint=1,
is_non_analytical_direction=True,
show=False)
assert phbands.plot_phdispl_cartdirs(qpoint=0,
units="cm^-1",
show=False)
assert phbands.boxplot(units="ev", mode_range=[2, 4], show=False)
# Cannot compute PHDOS with q-path
with self.assertRaises(ValueError):
phdos = phbands.get_phdos()
# convert to pymatgen object
phbands.to_pymatgen()
# get frozen phonons
phbands.get_frozen_phonons((0.5, 0.5, 1.0),
1,
eta=0.5,
max_supercell=[5, 5, 5])
assert not phbands.has_linewidths
phbands.linewidths = np.ones(phbands.shape)
assert phbands.has_linewidths