def test_phonon_computation(self):
"""Testing if pjdoses compute by anaddb integrate to 3*natom"""
path = os.path.join(abidata.dirpath, "refs", "mgb2_phonons_nkpt_tsmear", "mgb2_121212k_0.04tsmear_DDB")
ddb = abilab.abiopen(path)
for dos_method in ("tetra", "gaussian"):
# Get phonon bands and Dos with anaddb.
phbands_file, phdos_file = ddb.anaget_phbst_and_phdos_files(nqsmall=4, ndivsm=2,
dipdip=0, chneut=0, dos_method=dos_method, lo_to_splitting=False, verbose=1)
phbands, phdos = phbands_file.phbands, phdos_file.phdos
natom3 = len(phbands.structure) * 3
# Test that amu is present with correct values.
assert phbands.amu is not None
self.assert_almost_equal(phbands.amu[12.0], 0.24305e+02)
self.assert_almost_equal(phbands.amu[5.0], 0.10811e+02)
self.assert_almost_equal(phbands.amu_symbol["Mg"], phbands.amu[12.0])
self.assert_almost_equal(phbands.amu_symbol["B"], phbands.amu[5.0])
# Total PHDOS should integrate to 3 * natom
# Note that anaddb does not renormalize the DOS so we have to increate the tolerance.
#E Arrays are not almost equal to 2 decimals
#E ACTUAL: 8.9825274146312282
#E DESIRED: 9
self.assert_almost_equal(phdos.integral_value, natom3, decimal=1)
# Test convertion to eigenvectors. Verify that they are orthonormal
cidentity = np.eye(natom3, dtype=np.complex)
eig = phbands.dyn_mat_eigenvect
for iq in range(phbands.nqpt):
#print("About to test iq", iq, np.dot(eig[iq].T.conjugate(), eig[iq]))
#assert np.allclose(np.dot(eig[iq], eig[iq].T), cidentity , atol=1e-5, rtol=1e-3)
self.assert_almost_equal(np.dot(eig[iq].conjugate().T, eig[iq]), cidentity) #, decimal=1)
# Summing projected DOSes over types should give the total DOS.
pj_sum = sum(pjdos.integral_value for pjdos in phdos_file.pjdos_symbol.values())
self.assert_almost_equal(phdos.integral_value, pj_sum)
# Summing projected DOSes over types and directions should give the total DOS.
# phdos_rc_type[ntypat, 3, nomega]
values = phdos_file.reader.read_value("pjdos_rc_type").sum(axis=(0, 1))
tot_dos = abilab.Function1D(phdos.mesh, values)
self.assert_almost_equal(phdos.integral_value, tot_dos.integral_value)
phbands_file.close()
phdos_file.close()
ddb.close()
def test_from_phdosfile(self):
"""Testing PHDOS from netcdf file."""
ncfile = PhdosFile(abidata.ref_file("trf2_5.out_PHDOS.nc"))
repr(ncfile)
str(ncfile)
assert ncfile.to_string(verbose=1)
assert hasattr(ncfile, "structure")
nw = len(ncfile.wmesh)
assert nw == 461
natom3 = len(ncfile.structure) * 3
# Read PJDOSes
assert list(ncfile.pjdos_symbol.keys()) == ["Al", "As"]
od = ncfile.reader.read_pjdos_symbol_xyz_dict()
assert list(od.keys()) == ["Al", "As"]
assert all(v.shape == (3, nw) for v in od.values())
arr = ncfile.reader.read_pjdos_atdir()
assert arr.shape == (len(ncfile.structure), 3, nw)
phdos = ncfile.phdos
# Test integrals of DOS (the tolerance is a bit low likely due to too coarse meshes)
self.assert_almost_equal(phdos.integral_value, natom3, decimal=1)
# Summing projected DOSes over types should give the total DOS.
pj_sum = sum(pjdos.integral_value
for pjdos in ncfile.pjdos_symbol.values())
self.assert_almost_equal(phdos.integral_value, pj_sum)
# Summing projected DOSes over types and directions should give the total DOS.
# phdos_rc_type[ntypat, 3, nomega]
values = ncfile.reader.read_value("pjdos_rc_type").sum(axis=(0, 1))
tot_dos = abilab.Function1D(phdos.mesh, values)
self.assert_almost_equal(phdos.integral_value, tot_dos.integral_value)
assert phdos == PhononDos.as_phdos(
abidata.ref_file("trf2_5.out_PHDOS.nc"))
# Test Thermodinamics in the Harmonic approximation
self.assert_almost_equal(phdos.zero_point_energy.to("Ha"),
0.0030872835637731303)
u = phdos.get_internal_energy()
self.assert_almost_equal(u.values[0], 0.084009326574073395)
self.assert_almost_equal(u.values[-1], 0.17270110252071791)
s = phdos.get_entropy()
self.assert_almost_equal(s.values[0], 1.6270193052583423e-08)
self.assert_almost_equal(s.values[-1], 0.00058238779354717)
cv = phdos.get_cv()
self.assert_almost_equal(cv.values[0], 5.3715488328604253e-08)
self.assert_almost_equal(cv.values[-1], 0.00045871909188672578)
f = phdos.get_free_energy()
self.assert_almost_equal(f.values, (u - s.mesh * s.values).values)
self.assertAlmostEqual(phdos.debye_temp, 469.01524830328606)
self.assertAlmostEqual(
phdos.get_acoustic_debye_temp(len(ncfile.structure)),
372.2576492728813)
assert ncfile.to_pymatgen()
if self.has_matplotlib():
assert ncfile.plot_pjdos_type(show=False)
assert ncfile.plot_pjdos_type(units="cm-1",
stacked=False,
colormap="viridis",
show=False)
assert ncfile.plot_pjdos_type(units="eV",
stacked=True,
colormap="jet",
exchange_xy=True,
fontsize=8,
show=False)
assert ncfile.plot_pjdos_cartdirs_type(units="Thz",
stacked=True,
show=False)
assert ncfile.plot_pjdos_cartdirs_type(units="meV",
stacked=False,
alpha=0.5,
show=False)
assert ncfile.plot_pjdos_cartdirs_site(units="meV",
stacked=False,
alpha=0.5,
show=False)
assert ncfile.plot_pjdos_cartdirs_site(units="meV",
view="all",
stacked=True,
alpha=0.5,
show=False)
assert phdos.plot(units="cm-1", show=False)
assert phdos.plot_harmonic_thermo(tstar=20,
tstop=350,
units="eV",
formula_units=1,
show=False)
assert phdos.plot_harmonic_thermo(tstar=20,
tstop=350,
units="Jmol",
formula_units=2,
show=False)
# Test notebook
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
ncfile.close()