def test_run_second_order_phonons(self):
N2_ref = """\
2 angstroem
free
N 3.571946174 3.571946174 3.620526682
N 3.571946174 3.571946174 4.71401439"""
ref_pos = Posinp.from_string(N2_ref)
gs = Job(posinp=ref_pos, name='N2', run_dir='tests/phonons_N2')
phonons = Phonons(gs, order=2)
raman = RamanSpectrum(phonons)
assert not phonons.is_completed
assert not raman.is_completed
raman.run(nmpi=2, nomp=2)
assert phonons.is_completed
assert raman.is_completed
# Test the only physically relevant phonon energy
np.testing.assert_almost_equal(
max(raman.energies), 2386.9463343478246, decimal=6)
# Test the only physically relevant intensity
np.testing.assert_almost_equal(
max(raman.intensities), 22.564457304830206)
# Test the only physically relevant depolarization ratio
i = np.argmax(raman.energies)
np.testing.assert_almost_equal(
raman.depolarization_ratios[i], 0.09412173797731693)
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
phonons.run()
with pytest.warns(UserWarning):
raman.run()
def single_phonon_calculation(
nmpi=1,
nomp=1,
preparation=True,
savefile=True,
pseudos=False,
verbose=False,
optimization=True,
):
if preparation:
base_inp, ref_pos, jobname = utils.prepare_calculations()
if optimization:
base_job = Job(
posinp=ref_pos,
inputparams=base_inp,
name=jobname,
run_dir="geopt/",
pseudos=pseudos,
)
geopt = Geopt(base_job, forcemax=2e-5, ncount_cluster_x=50)
geopt.run(nmpi=nmpi, nomp=nomp, restart_if_incomplete=True)
relaxed_pos = geopt.final_posinp
else:
relaxed_pos = ref_pos
if "output" in base_inp:
del base_inp["output"]
ground_state = Job(
name=jobname,
posinp=relaxed_pos,
inputparams=base_inp,
run_dir="phonons/",
ref_data_dir=(geopt.queue[0].data_dir if optimization else None),
pseudos=pseudos,
)
phonons = Phonons(ground_state)
phonons.run(nmpi=nmpi, nomp=nomp, restart_if_incomplete=True)
if verbose:
for i in range(len(phonons.energies)):
print(f"Mode {i} :")
print("Energy : ", phonons.energies[i])
print("Mode : ", phonons.normal_modes[:, i], "\n")
if savefile:
save("phonons/ph_energies.npy", phonons.energies)
save("phonons/ph_normal_modes.npy", phonons.normal_modes)
def test_run_first_order(self):
N2_ref = """\
2 angstroem
free
N 3.571946174 3.571946174 3.620526682
N 3.571946174 3.571946174 4.71401439"""
ref_pos = Posinp.from_string(N2_ref)
gs = Job(posinp=ref_pos, name='N2', run_dir='tests/phonons_N2')
ph = Phonons(gs, order=1)
assert not ph.is_completed
ph.run(nmpi=2, nomp=2)
assert ph.is_completed
# Test the only physically relevant phonon energy
np.testing.assert_almost_equal(
max(ph.energies), 2386.9850607523636, decimal=6)
def test_run(self):
atoms = [Atom('N', [3.571946174, 3.571946174, 3.620526682]),
Atom('N', [3.571946174, 3.571946174, 4.71401439])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
gs = Job(posinp=pos, name='N2', run_dir='tests/phonons_N2')
ph = Phonons(gs)
ir = InfraredSpectrum(ph)
assert not ir.is_completed
ir.run()
assert ir.is_completed
# Test the only physically relevant infrared intensity
i = np.argmax(ir.energies)
np.testing.assert_almost_equal(ir.intensities[i], 1.100446469749e-06)
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
ir.run()
def test_run(self):
atoms = [Atom('N', [3.571946174, 3.571946174, 3.620526682]),
Atom('N', [3.571946174, 3.571946174, 4.71401439])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
gs = Job(posinp=pos, name='N2', run_dir='tests/phonons_N2')
ph = Phonons(gs)
ir = InfraredSpectrum(ph)
vpt = VibPolTensor(ir)
assert not vpt.is_completed
vpt.run()
assert vpt.is_completed
# Test the mean vibrational polarizability
np.testing.assert_almost_equal(vpt.mean_polarizability,
1.092296473682357e-08)
# Changing the value of e_cut changes the value of the mean
# vibrational polarizability
vpt.e_cut = 0
np.testing.assert_almost_equal(vpt.mean_polarizability,
0.0007775548377767935)
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
vpt.run()
class TestRamanSpectrum:
gs = Job(posinp=pos, name='N2', run_dir='tests/phonons_N2')
ph = Phonons(gs)
def test_run_first_order_phonons(self):
N2_ref = """\
2 angstroem
free
N 3.571946174 3.571946174 3.620526682
N 3.571946174 3.571946174 4.71401439"""
ref_pos = Posinp.from_string(N2_ref)
gs = Job(posinp=ref_pos, name='N2', run_dir='tests/phonons_N2')
phonons = Phonons(gs, order=1)
raman = RamanSpectrum(phonons)
assert not phonons.is_completed
assert not raman.is_completed
raman.run(nmpi=2, nomp=2)
assert phonons.is_completed
assert raman.is_completed
# Test the only physically relevant phonon energy
np.testing.assert_almost_equal(
max(raman.energies), 2386.9850607466974, decimal=6)
# Test the only physically relevant intensity
np.testing.assert_almost_equal(
max(raman.intensities), 22.561427637014187)
# Test the only physically relevant depolarization ratio
i = np.argmax(raman.energies)
np.testing.assert_almost_equal(
raman.depolarization_ratios[i], 0.09412532271275614)
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
phonons.run()
with pytest.warns(UserWarning):
raman.run()
def test_run_second_order_phonons(self):
N2_ref = """\
2 angstroem
free
N 3.571946174 3.571946174 3.620526682
N 3.571946174 3.571946174 4.71401439"""
ref_pos = Posinp.from_string(N2_ref)
gs = Job(posinp=ref_pos, name='N2', run_dir='tests/phonons_N2')
phonons = Phonons(gs, order=2)
raman = RamanSpectrum(phonons)
assert not phonons.is_completed
assert not raman.is_completed
raman.run(nmpi=2, nomp=2)
assert phonons.is_completed
assert raman.is_completed
# Test the only physically relevant phonon energy
np.testing.assert_almost_equal(
max(raman.energies), 2386.9463343478246, decimal=6)
# Test the only physically relevant intensity
np.testing.assert_almost_equal(
max(raman.intensities), 22.564457304830206)
# Test the only physically relevant depolarization ratio
i = np.argmax(raman.energies)
np.testing.assert_almost_equal(
raman.depolarization_ratios[i], 0.09412173797731693)
# Test that running the workflow again warns a UserWarning
with pytest.warns(UserWarning):
phonons.run()
with pytest.warns(UserWarning):
raman.run()
@pytest.mark.parametrize("to_evaluate", [
"RamanSpectrum(self.ph, ef_amplitudes=1)",
"RamanSpectrum(self.ph, ef_amplitudes=[3]*2)",
"RamanSpectrum(self.ph, ef_amplitudes=[3]*4)",
])
def test_init_raises_ValueError(self, to_evaluate):
with pytest.raises(ValueError):
eval(to_evaluate)
def test_init_raises_NotImplementedError(self):
with pytest.raises(NotImplementedError):
Phonons(self.gs, order=-1)