def test_api(self):
"""Testing PhononDos API with fake data."""
dos = PhononDos(mesh=[1,2,3], values=[4,5,6])
assert dos.mesh.tolist() == [1,2,3] and dos.h == 1 and dos.values.tolist() == [4,5,6]
print(dos)
dos.idos
dos.plot(show=False)
h = dos.get_harmonic_thermo(1, 10)
assert h is not None
def test_api(self):
"""Testing PhononDos API with fake data."""
dos = PhononDos(mesh=[1, 2, 3], values=[4, 5, 6])
assert dos.mesh.tolist() == [
1, 2, 3
] and dos.h == 1 and dos.values.tolist() == [4, 5, 6]
print(dos)
dos.idos
assert PhononDos.as_phdos(dos, {}) is dos
assert dos.iw0 == 0
def test_api(self):
"""Testing PhononDos API with fake data."""
dos = PhononDos(mesh=[1, 2, 3], values=[4, 5, 6])
assert dos.mesh.tolist() == [
1, 2, 3
] and dos.h == 1 and dos.values.tolist() == [4, 5, 6]
print(dos)
dos.idos
dos.plot(show=False)
h = dos.get_harmonic_thermo(1, 10)
assert h is not None
def from_files(cls, gsr_files_paths, phdos_files_paths, ind_doses):
"""
Creates an instance of QHA from a list og GSR files and a list PHDOS.nc files.
The list should have the same size and the volumes should match.
Args:
gsr_files_paths: list of paths to GSR files.
phdos_files_paths: list of paths to three PHDOS.nc files.
ind_doses: list of three values indicating, for each of the three doses, the index of the
corresponding gsr_file in "gsr_files_paths".
Returns:
A new instance of QHA
"""
energies = []
structures = []
for gp in gsr_files_paths:
with GsrFile.from_file(gp) as g:
energies.append(g.energy)
structures.append(g.structure)
doses = [PhononDos.as_phdos(dp) for dp in phdos_files_paths]
return cls(structures, doses, energies, ind_doses)
def from_files(cls, gsr_files_paths, phdos_files_paths, ind_doses):
"""
Creates an instance of QHA from a list og GSR files and a list PHDOS.nc files.
The list should have the same size and the volumes should match.
Args:
gsr_files_paths: list of paths to GSR files.
phdos_files_paths: list of paths to three PHDOS.nc files.
ind_doses: list of three values indicating, for each of the three doses, the index of the
corresponding gsr_file in "gsr_files_paths".
Returns:
A new instance of QHA
"""
energies = []
structures = []
for gp in gsr_files_paths:
with GsrFile.from_file(gp) as g:
energies.append(g.energy)
structures.append(g.structure)
doses = [PhononDos.as_phdos(dp) for dp in phdos_files_paths]
return cls(structures, doses, energies, ind_doses)
def phdos(self):
"""
The |PhononDos| corresponding to iv0, if present in the file, None otherwise.
"""
if not self.doses:
return None
return PhononDos(self.doses['wmesh'], self.doses['gruns_wdos'][0])
def test_api(self):
"""Testing PhononDos API with fake data."""
phdos = PhononDos(mesh=[1, 2, 3], values=[4, 5, 6])
assert phdos.mesh.tolist() == [1, 2, 3] and phdos.h == 1 and phdos.values.tolist() == [4, 5, 6]
repr(phdos); str(phdos)
phdos.idos
with self.assertRaises(TypeError):
PhononDos.as_phdos({}, {})
assert PhononDos.as_phdos(phdos, {}) is phdos
assert phdos.iw0 == 0
# From pickle file.
tmp_path = self.get_tmpname(suffix=".pickle")
with open(tmp_path, "wb") as fh:
pickle.dump(phdos, fh)
same_phdos = PhononDos.as_phdos(tmp_path)
same_phdos == phdos
phdos.to_pymatgen()
def test_api(self):
"""Testing PhononDos API with fake data."""
phdos = PhononDos(mesh=[1, 2, 3], values=[4, 5, 6])
assert phdos.mesh.tolist() == [1, 2, 3] and phdos.h == 1 and phdos.values.tolist() == [4, 5, 6]
repr(phdos); str(phdos)
phdos.idos
with self.assertRaises(TypeError):
PhononDos.as_phdos({}, {})
assert PhononDos.as_phdos(phdos, {}) is phdos
assert phdos.iw0 == 0
# From pickle file.
tmp_path = self.get_tmpname(suffix=".pickle")
with open(tmp_path, "wb") as fh:
pickle.dump(phdos, fh)
same_phdos = PhononDos.as_phdos(tmp_path)
same_phdos == phdos
phdos.to_pymatgen()
def from_files(cls, gsr_files_paths, phdos_files_paths):
"""
Creates an instance of QHA from a list of GSR files and a list of PHDOS.nc files.
The list should have the same size and the volumes should match.
Args:
gsr_files_paths: list of paths to GSR files.
phdos_files_paths: list of paths to PHDOS.nc files.
Returns:
A new instance of QHA
"""
energies = []
structures = []
for gp in gsr_files_paths:
with GsrFile.from_file(gp) as g:
energies.append(g.energy)
structures.append(g.structure)
doses = [PhononDos.as_phdos(dp) for dp in phdos_files_paths]
return cls(structures, doses, energies)
def from_files(cls, gsr_files_paths, phdos_files_paths):
"""
Creates an instance of QHA from a list og GSR files and a list PHDOS.nc files.
The list should have the same size and the volumes should match.
Args:
gsr_files_paths: list of paths to GSR files.
phdos_files_paths: list of paths to PHDOS.nc files.
Returns:
A new instance of QHA
"""
energies = []
structures = []
for gp in gsr_files_paths:
with GsrFile.from_file(gp) as g:
energies.append(g.energy)
structures.append(g.structure)
doses = [PhononDos.as_phdos(dp) for dp in phdos_files_paths]
return cls(structures, doses, energies)
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_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()
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()