def test_alas_ddb_444_nobecs(self):
"""Testing DDB for AlAs on a 4x4x4x q-mesh without Born effective charges."""
ddb = DdbFile(os.path.join(test_dir, "AlAs_444_nobecs_DDB"))
print(ddb)
print(ddb.header)
ref_qpoints = np.reshape([
0.00000000E+00, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 0.00000000E+00, 0.00000000E+00,
5.00000000E-01, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 2.50000000E-01, 0.00000000E+00,
5.00000000E-01, 2.50000000E-01, 0.00000000E+00,
-2.50000000E-01, 2.50000000E-01, 0.00000000E+00,
5.00000000E-01, 5.00000000E-01, 0.00000000E+00,
-2.50000000E-01, 5.00000000E-01, 2.50000000E-01,
], (-1, 3))
assert len(ddb.qpoints) == 8
for qpt, ref_qpt in zip(ddb.qpoints, ref_qpoints):
assert qpt == ref_qpt
for qpoint in ddb.qpoints:
phbands = ddb.anaget_phmodes_at_qpoint(qpoint=qpoint)
assert phbands is not None and hasattr(phbands, "phfreqs")
assert np.all(ddb.guessed_ngqpt == [4, 4, 4])
# Get bands and Dos
phbands_file, phdos_file = ddb.anaget_phbst_and_phdos_files()
phbands, phdos = phbands_file.phbands, phdos_file.phdos
if self.has_matplotlib():
phbands.plot_with_phdos(phdos, title="Phonon bands and DOS of %s" % phbands.structure.formula, show=False)
# Thermodinamics in the Harmonic approximation
harmo = phdos.get_harmonic_thermo(tstart=10, tstop=50)
if self.has_matplotlib():
harmo.plot(show=False)
self.assert_almost_equal(phdos.idos.values[-1], 3 * len(ddb.structure), decimal=1)
phbands_file.close()
phdos_file.close()
c = ddb.anacompare_phdos(nqsmalls=[2, 4, 6], num_cpus=None)
if self.has_matplotlib():
c.plotter.plot(show=False)
ddb.close()
def test_alas_ddb_444_nobecs(self):
"""Testing DDB for AlAs on a 4x4x4x q-mesh without Born effective charges."""
ddb = DdbFile(os.path.join(test_dir, "AlAs_444_nobecs_DDB"))
print(ddb)
print(ddb.header)
ref_qpoints = np.reshape([
0.00000000E+00, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 0.00000000E+00, 0.00000000E+00,
5.00000000E-01, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 2.50000000E-01, 0.00000000E+00,
5.00000000E-01, 2.50000000E-01, 0.00000000E+00,
-2.50000000E-01, 2.50000000E-01, 0.00000000E+00,
5.00000000E-01, 5.00000000E-01, 0.00000000E+00,
-2.50000000E-01, 5.00000000E-01, 2.50000000E-01,
], (-1, 3))
assert len(ddb.qpoints) == 8
for qpt, ref_qpt in zip(ddb.qpoints, ref_qpoints):
assert qpt == ref_qpt
for qpoint in ddb.qpoints:
phbands = ddb.anaget_phmodes_at_qpoint(qpoint=qpoint)
assert phbands is not None and hasattr(phbands, "phfreqs")
assert np.all(ddb.guessed_ngqpt == [4, 4, 4])
# Get bands and Dos
phbands_file, phdos_file = ddb.anaget_phbst_and_phdos_files()
phbands, phdos = phbands_file.phbands, phdos_file.phdos
if have_matplotlib:
phbands.plot_with_phdos(phdos, title="Phonon bands and DOS of %s" % phbands.structure.formula, show=False)
# Thermodinamics in the Harmonic approximation
harmo = phdos.get_harmonic_thermo(tstart=10, tstop=50)
harmo.plot(show=False)
self.assert_almost_equal(phdos.idos.values[-1], 3 * len(ddb.structure), decimal=1)
phbands_file.close()
phdos_file.close()
c = ddb.anacompare_phdos(nqsmalls=[2, 4, 6], num_cpus=None)
c.plotter.plot(show=False)
ddb.close()
def test_alas_ddb_444_nobecs(self):
"""Testing DDB for AlAs on a 4x4x4x q-mesh without Born effective charges."""
ddb = DdbFile(os.path.join(test_dir, "AlAs_444_nobecs_DDB"))
repr(ddb)
str(ddb)
assert str(ddb.header)
assert ddb.to_string(verbose=2)
assert ddb.header["nkpt"] == 256
assert ddb.header.nsym == 24 and ddb.header.ntypat == 2
self.assert_equal(ddb.header.znucl, [13, 33])
self.assert_equal(ddb.header.acell, [1, 1, 1])
self.assert_equal(ddb.header.ngfft, [10, 10, 10])
self.assert_equal(ddb.header.spinat, 0.0)
#assert ddb.header.occ.shape = (ddb.header.nsppol, ddb.header.nkpt, ddb.header.nsppol)
assert not ddb.has_qpoint([0.345, 0.456, 0.567])
assert ddb.has_qpoint([0, 0, 0])
for qpoint in ddb.qpoints:
assert ddb.has_qpoint(qpoint)
assert ddb.has_qpoint(qpoint.frac_coords)
assert qpoint in ddb.computed_dynmat
assert len(ddb.computed_dynmat[qpoint].index[0]) == 4
assert ddb.has_bec_terms(select="at_least_one")
assert not ddb.has_bec_terms(select="all")
assert not ddb.has_epsinf_terms()
assert not ddb.has_lo_to_data()
assert not ddb.has_internalstrain_terms()
assert not ddb.has_piezoelectric_terms()
assert not ddb.has_strain_terms()
assert ddb.has_at_least_one_atomic_perturbation()
ref_qpoints = np.reshape([
0.00000000E+00,
0.00000000E+00,
0.00000000E+00,
2.50000000E-01,
0.00000000E+00,
0.00000000E+00,
5.00000000E-01,
0.00000000E+00,
0.00000000E+00,
2.50000000E-01,
2.50000000E-01,
0.00000000E+00,
5.00000000E-01,
2.50000000E-01,
0.00000000E+00,
-2.50000000E-01,
2.50000000E-01,
0.00000000E+00,
5.00000000E-01,
5.00000000E-01,
0.00000000E+00,
-2.50000000E-01,
5.00000000E-01,
2.50000000E-01,
], (-1, 3))
assert len(ddb.qpoints) == 8
for qpt, ref_qpt in zip(ddb.qpoints, ref_qpoints):
assert qpt == ref_qpt
for qpoint in ddb.qpoints:
phbands = ddb.anaget_phmodes_at_qpoint(qpoint=qpoint, verbose=1)
assert phbands is not None and hasattr(phbands, "phfreqs")
assert np.all(ddb.guessed_ngqpt == [4, 4, 4])
# Get bands and Dos
phbands_file, phdos_file = ddb.anaget_phbst_and_phdos_files(verbose=1)
phbands, phdos = phbands_file.phbands, phdos_file.phdos
assert ddb.view_phononwebsite(verbose=1, dryrun=True) == 0
if self.has_matplotlib():
assert phbands.plot_with_phdos(phdos,
show=False,
title="Phonon bands and DOS of %s" %
phbands.structure.formula)
assert phbands_file.plot_phbands(show=False)
# Get epsinf and becs
r = ddb.anaget_epsinf_and_becs(chneut=1, verbose=1)
epsinf, becs = r.epsinf, r.becs
assert np.all(becs.values == 0)
repr(becs)
str(becs)
assert becs.to_string(verbose=2)
self.assert_almost_equal(phdos.idos.values[-1],
3 * len(ddb.structure),
decimal=1)
phbands_file.close()
phdos_file.close()
# Test DOS computation via anaddb.
c = ddb.anacompare_phdos(nqsmalls=[2, 3, 4],
dipdip=0,
num_cpus=1,
verbose=2)
assert c.phdoses and c.plotter is not None
if self.has_matplotlib():
assert c.plotter.combiplot(show=False)
# Use threads and gaussian DOS.
c = ddb.anacompare_phdos(nqsmalls=[2, 3, 4],
dos_method="gaussian",
dipdip=0,
asr=0,
num_cpus=2,
verbose=2)
assert c.phdoses and c.plotter is not None
# Execute anaddb to compute the interatomic force constants.
ifc = ddb.anaget_ifc()
str(ifc)
repr(ifc)
assert ifc.to_string(verbose=2)
assert ifc.structure == ddb.structure
assert ifc.number_of_atoms == len(ddb.structure)
if self.has_matplotlib():
assert ifc.plot_longitudinal_ifc(show=False)
assert ifc.plot_longitudinal_ifc_short_range(show=False)
assert ifc.plot_longitudinal_ifc_ewald(show=False)
# Test get_coarse.
coarse_ddb = ddb.get_coarse([2, 2, 2])
# Check whether anaddb can read the coarse DDB.
coarse_phbands_file, coarse_phdos_file = coarse_ddb.anaget_phbst_and_phdos_files(
nqsmall=4, ndivsm=1, verbose=1)
coarse_phbands_file.close()
coarse_phdos_file.close()
coarse_ddb.close()
ddb.close()
def test_alas_ddb_444_nobecs(self):
"""Testing DDB for AlAs on a 4x4x4x q-mesh without Born effective charges."""
ddb = DdbFile(os.path.join(test_dir, "AlAs_444_nobecs_DDB"))
print(ddb)
print(ddb.header)
ref_qpoints = np.reshape([
0.00000000E+00,
0.00000000E+00,
0.00000000E+00,
2.50000000E-01,
0.00000000E+00,
0.00000000E+00,
5.00000000E-01,
0.00000000E+00,
0.00000000E+00,
2.50000000E-01,
2.50000000E-01,
0.00000000E+00,
5.00000000E-01,
2.50000000E-01,
0.00000000E+00,
-2.50000000E-01,
2.50000000E-01,
0.00000000E+00,
5.00000000E-01,
5.00000000E-01,
0.00000000E+00,
-2.50000000E-01,
5.00000000E-01,
2.50000000E-01,
], (-1, 3))
assert len(ddb.qpoints) == 8
for qpt, ref_qpt in zip(ddb.qpoints, ref_qpoints):
assert qpt == ref_qpt
for qpoint in ddb.qpoints:
phbands = ddb.anaget_phmodes_at_qpoint(qpoint=qpoint, verbose=1)
assert phbands is not None and hasattr(phbands, "phfreqs")
assert np.all(ddb.guessed_ngqpt == [4, 4, 4])
# Get bands and Dos
phbands_file, phdos_file = ddb.anaget_phbst_and_phdos_files(verbose=1)
phbands, phdos = phbands_file.phbands, phdos_file.phdos
if self.has_matplotlib():
phbands.plot_with_phdos(phdos,
title="Phonon bands and DOS of %s" %
phbands.structure.formula,
show=False)
# Get emacro and becs
emacro, becs = ddb.anaget_emacro_and_becs(chneut=1, verbose=1)
assert np.all(becs.values == 0)
assert np.all(becs.becs == 0)
print(becs)
self.assert_almost_equal(phdos.idos.values[-1],
3 * len(ddb.structure),
decimal=1)
phbands_file.close()
phdos_file.close()
# Test DOS computation via anaddb.
c = ddb.anacompare_phdos(nqsmalls=[2, 4, 6], num_cpus=None)
if self.has_matplotlib():
c.plotter.plot(show=False)
# Execute anaddb to compute the interatomic forces.
ifc = ddb.anaget_ifc()
assert ifc.structure == ddb.structure
assert ifc.number_of_atoms == len(ddb.structure)
if self.has_matplotlib():
ifc.plot_longitudinal_ifc(show=False)
ifc.plot_longitudinal_ifc_short_range(show=False)
ifc.plot_longitudinal_ifc_ewald(show=False)
ddb.close()
def test_alas_ddb_444_nobecs(self):
"""Testing DDB for AlAs on a 4x4x4x q-mesh without Born effective charges."""
ddb = DdbFile(os.path.join(test_dir, "AlAs_444_nobecs_DDB"))
repr(ddb); str(ddb)
assert str(ddb.header)
assert ddb.to_string(verbose=2)
assert ddb.header["nkpt"] == 256
assert ddb.header.nsym == 24 and ddb.header.ntypat == 2
self.assert_equal(ddb.header.znucl, [13, 33])
self.assert_equal(ddb.header.acell, [1, 1, 1])
self.assert_equal(ddb.header.ngfft, [10, 10, 10])
self.assert_equal(ddb.header.spinat, 0.0)
#assert ddb.header.occ.shape = (ddb.header.nsppol, ddb.header.nkpt, ddb.header.nsppol)
assert not ddb.has_qpoint([0.345, 0.456, 0.567])
assert ddb.has_qpoint([0, 0, 0])
for qpoint in ddb.qpoints:
assert ddb.has_qpoint(qpoint)
assert ddb.has_qpoint(qpoint.frac_coords)
assert qpoint in ddb.computed_dynmat
assert len(ddb.computed_dynmat[qpoint].index[0]) == 4
assert ddb.has_bec_terms(select="at_least_one")
assert not ddb.has_bec_terms(select="all")
assert not ddb.has_epsinf_terms()
assert not ddb.has_lo_to_data()
assert not ddb.has_internalstrain_terms()
assert not ddb.has_piezoelectric_terms()
assert not ddb.has_strain_terms()
assert ddb.has_at_least_one_atomic_perturbation()
ref_qpoints = np.reshape([
0.00000000E+00, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 0.00000000E+00, 0.00000000E+00,
5.00000000E-01, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 2.50000000E-01, 0.00000000E+00,
5.00000000E-01, 2.50000000E-01, 0.00000000E+00,
-2.50000000E-01, 2.50000000E-01, 0.00000000E+00,
5.00000000E-01, 5.00000000E-01, 0.00000000E+00,
-2.50000000E-01, 5.00000000E-01, 2.50000000E-01,
], (-1, 3))
assert len(ddb.qpoints) == 8
for qpt, ref_qpt in zip(ddb.qpoints, ref_qpoints):
assert qpt == ref_qpt
for qpoint in ddb.qpoints:
phbands = ddb.anaget_phmodes_at_qpoint(qpoint=qpoint, verbose=1)
assert phbands is not None and hasattr(phbands, "phfreqs")
assert np.all(ddb.guessed_ngqpt == [4, 4, 4])
# Get bands and Dos
phbands_file, phdos_file = ddb.anaget_phbst_and_phdos_files(verbose=1)
phbands, phdos = phbands_file.phbands, phdos_file.phdos
assert ddb.view_phononwebsite(verbose=1, dryrun=True) == 0
if self.has_matplotlib():
assert phbands.plot_with_phdos(phdos, show=False,
title="Phonon bands and DOS of %s" % phbands.structure.formula)
assert phbands_file.plot_phbands(show=False)
# Get emacro and becs
emacro, becs = ddb.anaget_emacro_and_becs(chneut=1, verbose=1)
assert np.all(becs.values == 0)
#assert np.all(emacro.values == 0)
repr(becs); str(becs)
assert becs.to_string(verbose=2)
self.assert_almost_equal(phdos.idos.values[-1], 3 * len(ddb.structure), decimal=1)
phbands_file.close()
phdos_file.close()
# Test DOS computation via anaddb.
c = ddb.anacompare_phdos(nqsmalls=[2, 3, 4], dipdip=0, num_cpus=1, verbose=2)
assert c.phdoses and c.plotter is not None
if self.has_matplotlib():
assert c.plotter.combiplot(show=False)
# Use threads and gaussian DOS.
c = ddb.anacompare_phdos(nqsmalls=[2, 3, 4], dos_method="gaussian", dipdip=0, asr=0,
num_cpus=2, verbose=2)
assert c.phdoses and c.plotter is not None
# Execute anaddb to compute the interatomic forces.
ifc = ddb.anaget_ifc()
str(ifc); repr(ifc)
#assert ifc.to_string(verbose=2)
assert ifc.structure == ddb.structure
assert ifc.number_of_atoms == len(ddb.structure)
if self.has_matplotlib():
assert ifc.plot_longitudinal_ifc(show=False)
assert ifc.plot_longitudinal_ifc_short_range(show=False)
assert ifc.plot_longitudinal_ifc_ewald(show=False)
ddb.close()