def run_anaddb(self, item, workdir):
"""
Runs anaddb an reads the outputs
"""
anaddb_inp, labels_list = self.get_anaddb_input(item)
#TODO should this be an input?
tm = TaskManager.from_user_config()
ddb_path = item["ddb_path"]
task = AnaddbTask.temp_shell_task(anaddb_inp, ddb_node=ddb_path, workdir=workdir, manager=tm)
# Run the task here.
task.start_and_wait(autoparal=False)
report = task.get_event_report()
if not report.run_completed:
raise AnaddbError(task=task, report=report)
phbst_file = task.open_phbst()
phdos_file = task.open_phdos()
ananc_file = AnaddbNcFile.from_file(os.path.join(workdir, "anaddb.nc"))
return phbst_file, phdos_file, ananc_file, labels_list
def test_base(self):
"""Testing DielectricTensor"""
anaddbnc_fname = abidata.ref_file("AlAs_nl_dte_anaddb.nc")
phbstnc_fname = abidata.ref_file("AlAs_nl_dte_PHBST.nc")
d = DielectricTensorGenerator.from_files(phbstnc_fname, anaddbnc_fname)
assert d.eps0.shape == (3, 3)
df = d.epsinf.get_dataframe()
assert d.epsinf._repr_html_()
repr(d); str(d)
assert d.to_string(verbose=2)
df = d.get_oscillator_dataframe(reim="all", tol=1e-8)
df = d.get_oscillator_dataframe(reim="im", tol=1e-8)
df = d.get_oscillator_dataframe(reim="re", tol=1e-8)
self.assertAlmostEqual(d.tensor_at_frequency(0.001, units='Ha', gamma_ev=0.0)[0, 0], 11.917178540635028)
d = DielectricTensorGenerator.from_objects(PhononBands.from_file(phbstnc_fname),
AnaddbNcFile.from_file(anaddbnc_fname))
self.assertAlmostEqual(d.tensor_at_frequency(0.001, units='Ha', gamma_ev=0.0)[0, 0], 11.917178540635028)
if self.has_matplotlib():
assert d.plot_vs_w(w_min=0.0001, w_max=0.01, num=10, units="Ha", show=False)
assert d.plot_vs_w(w_min=0, w_max=None, num=10, units="cm-1", show=False)
for comp in ["diag", "all", "diag_av"]:
assert d.plot_vs_w(num=10, component=comp, units="cm-1", show=False)
def test_base(self):
"""Testing DielectricTensor"""
anaddbnc_fname = abidata.ref_file("AlAs_nl_dte_anaddb.nc")
phbstnc_fname = abidata.ref_file("AlAs_nl_dte_PHBST.nc")
d = DielectricTensorGenerator.from_files(phbstnc_fname, anaddbnc_fname)
repr(d)
str(d)
self.assertAlmostEqual(
d.tensor_at_frequency(0.001, units='Ha')[0, 0], 11.917178540635028)
d = DielectricTensorGenerator.from_objects(
PhononBands.from_file(phbstnc_fname),
AnaddbNcFile.from_file(anaddbnc_fname))
self.assertAlmostEqual(
d.tensor_at_frequency(0.001, units='Ha')[0, 0], 11.917178540635028)
if self.has_matplotlib():
assert d.plot_vs_w(w_min=0.0001,
w_max=0.01,
num=10,
units="Ha",
show=False)
assert d.plot_vs_w(w_min=0,
w_max=None,
num=10,
units="cm-1",
show=False)
for comp in ["diag", "all", "diag_av"]:
assert d.plot_vs_w(num=10,
component=comp,
units="cm-1",
show=False)
def test_base(self):
"""Base tests for AnaddbNcFile"""
anaddbnc_fname = abidata.ref_file("AlAs_nl_dte_anaddb.nc")
with AnaddbNcFile(anaddbnc_fname) as anc:
repr(anc)
str(anc)
anc.to_string(verbose=2)
assert anc.structure.formula == "Al1 As1"
assert anc.becs is not None
assert anc.emacro is not None
assert anc.emacro_rlx is not None
assert anc.dchidt is not None
assert anc.dchide is not None
assert anc.oscillator_strength is not None
assert anc.ifc is None
assert not anc.params
if self.has_nbformat():
anc.write_notebook(nbpath=self.get_tmpname(text=True))
def test_base(self):
"""Testing AnaddbNcFile API"""
anaddbnc_fname = abidata.ref_file("AlAs_nl_dte_anaddb.nc")
with AnaddbNcFile(anaddbnc_fname) as anc:
repr(anc)
str(anc)
anc.to_string(verbose=2)
assert anc.structure.formula == "Al1 As1"
assert not anc.has_elastic_data
assert not anc.has_piezoelectric_data
assert anc.becs is not None
assert anc.epsinf is not None
assert anc.eps0 is not None
assert anc.dchidt is not None
assert anc.dchide is not None
assert anc.oscillator_strength is not None
assert anc.ifc is None
assert anc.params["chneut"] == 1
if self.has_nbformat():
assert anc.write_notebook(nbpath=self.get_tmpname(text=True))