def test_task_history_and_events(self):
si = abilab.Structure.from_file(abidata.cif_file("si.cif"))
si_relax_input = ion_ioncell_relax_input(si, abidata.pseudos("14si.pspnc"), ecut=2).split_datasets()[1]
th = TaskHistory()
th.log_initialization(task=RelaxFWTask(si_relax_input), initialization_info={"test_info": 1})
th.log_autoparal({u'time': u'12:0:0', u'ntasks': 15, u'partition': 'defq', u'nodes': 1, u'mem_per_cpu': 3000})
th.log_finalized(final_input=si_relax_input)
th.log_restart(RestartInfo(os.path.abspath('.'), reset=True, num_restarts=2))
th.log_unconverged()
th.log_corrections([events.Correction(events.DilatmxErrorHandler(), {}, events.DilatmxError('', '', '',), )])
th.log_abinit_stop(run_time=100)
try:
raise AbinitRuntimeError("test error")
except AbinitRuntimeError as exc:
th.log_error(exc)
try:
raise RuntimeError("test error")
except RuntimeError as exc:
th.log_error(exc)
th.log_converge_params({'dilatmx': 1.03}, si_relax_input)
self.assertMSONable(th)
for te in th:
self.assertMSONable(te)
def inputs_relax_si_low():
pseudos = abidata.pseudos("14si.pspnc")
cif_file = abidata.cif_file("si.cif")
structure = abilab.Structure.from_file(cif_file)
structure.apply_strain(0.005)
structure.translate_sites(0, [0.001, -0.003, 0.005])
structure.translate_sites(1, [0.007, 0.006, -0.005])
return ion_ioncell_relax_input(structure, pseudos, kppa=100, ecut=4).split_datasets()
def inputs_relax_si_low():
pseudos = abidata.pseudos("14si.pspnc")
structure = get_si_structure()
# negative strain. This will allow to trigger dilatmx error
structure.apply_strain(-0.005)
structure.translate_sites(0, [0.001, -0.003, 0.005])
structure.translate_sites(1, [0.007, 0.006, -0.005])
return ion_ioncell_relax_input(structure, pseudos, kppa=100, ecut=4, spin_mode="unpolarized",
accuracy="low", smearing=None).split_datasets()
def inputs_relax_si_low():
pseudos = abidata.pseudos("14si.pspnc")
structure = get_si_structure()
# negative strain. This will allow to trigger dilatmx error
structure.apply_strain(-0.005)
structure.translate_sites(0, [0.001, -0.003, 0.005])
structure.translate_sites(1, [0.007, 0.006, -0.005])
return ion_ioncell_relax_input(structure, pseudos, kppa=100, ecut=4, spin_mode="unpolarized",
accuracy="low", smearing=None).split_datasets()
def from_factory(cls, structure, pseudos, kppa=None, nband=None, ecut=None, pawecutdg=None, accuracy="normal",
spin_mode="polarized", smearing="fermi_dirac:0.1 eV", charge=0.0, scf_algorithm=None,
extra_abivars={}, decorators=[], autoparal=False, spec={}, initialization_info={},
target_dilatmx=None):
ion_input = ion_ioncell_relax_input(structure=structure, pseudos=pseudos, kppa=kppa, nband=nband, ecut=ecut,
pawecutdg=pawecutdg, accuracy=accuracy, spin_mode=spin_mode,
smearing=smearing, charge=charge, scf_algorithm=scf_algorithm)[0]
ioncell_fact = IoncellRelaxFromGsFactory(accuracy=accuracy)
return cls(ion_input, ioncell_fact, autoparal=autoparal, spec=spec, initialization_info=initialization_info,
target_dilatmx=target_dilatmx)
def test_task_history_and_events(self):
si = abilab.Structure.from_file(abidata.cif_file("si.cif"))
si_relax_input = ion_ioncell_relax_input(si,
abidata.pseudos("14si.pspnc"),
ecut=2).split_datasets()[1]
th = TaskHistory()
th.log_initialization(task=RelaxFWTask(si_relax_input),
initialization_info={"test_info": 1})
th.log_autoparal({
u'time': u'12:0:0',
u'ntasks': 15,
u'partition': 'defq',
u'nodes': 1,
u'mem_per_cpu': 3000
})
th.log_finalized(final_input=si_relax_input)
th.log_restart(
RestartInfo(os.path.abspath('.'), reset=True, num_restarts=2))
th.log_unconverged()
th.log_corrections([
events.Correction(
events.DilatmxErrorHandler(),
{},
events.DilatmxError(
'',
'',
'',
),
)
])
th.log_abinit_stop(run_time=100)
try:
raise AbinitRuntimeError("test error")
except AbinitRuntimeError as exc:
th.log_error(exc)
try:
raise RuntimeError("test error")
except RuntimeError as exc:
th.log_error(exc)
th.log_converge_params({'dilatmx': 1.03}, si_relax_input)
self.assertMSONable(th)
for te in th:
self.assertMSONable(te)
def work_for_pseudo(self, pseudo, kppa=1000, ecut=None, pawecutdg=None,
smearing="fermi_dirac:0.1 eV", include_soc=False,
workdir=None, manager=None):
"""
Create and return a :class:`RelaxAndAddPhGammaWork` object.
Args:
pseudo: filepath or :class:`Pseudo` object.
kppa: Number of k-points per reciprocal atom.
ecut: Cutoff energy in Hartree
pawecutdg: Cutoff energy of the fine grid (PAW only)
smearing: Smearing technique.
include_soc=True of SOC should be included.
workdir: Working directory.
manager: :class:`TaskManager` object.
"""
symbol = pseudo.symbol
if pseudo.ispaw and pawecutdg is None:
raise ValueError("pawecutdg must be specified for PAW calculations.")
if pseudo.xc != self._dfdb.xc:
raise ValueError(
"Pseudo xc differs from the XC used to instantiate the factory\n"
"Pseudo: %s, Database: %s" % (pseudo.xc, self._dfdb.xc))
qpt = np.zeros(3)
self.include_soc = include_soc
try:
cif_path = self.get_cif_path(pseudo.symbol)
except Exception as exc:
raise self.Error(str(exc))
# DO NOT CHANGE THE STRUCTURE REPORTED IN THE CIF FILE.
structure = Structure.from_file(cif_path, primitive=False)
# Get spinat and spin_mode from df database.
spinat, spin_mode = self._dfdb.spinat_spinmode_for_symbol(symbol)
# DFPT with AFM is not supported. Could try AFM in Relax and then polarized
# in WFK + DFPT but this one is safer.
if spin_mode == "afm": spin_mode = "polarized"
if include_soc: spin_mode = "spinor"
# Build inputs for structural relaxation.
multi = ion_ioncell_relax_input(
structure, pseudo,
kppa=kppa, nband=None,
ecut=ecut, pawecutdg=pawecutdg, accuracy="normal", spin_mode=spin_mode,
smearing=smearing)
# Set spinat from internal database.
multi.set_vars(chkprim=0, mem_test=0, spinat=spinat)
# Construct a *specialized" work for structural relaxation
# This work will create a new workflow for phonon calculations
# with the final relaxed structure (see on_all_ok below).
work = RelaxAndAddPhGammaWork(ion_input=multi[0], ioncell_input=multi[1])
# Monkey patch work
work.dojo_kppa = kppa
work.dojo_qpt = qpt
work.ecut = ecut
work.dojo_pawecutdg = pawecutdg
work.dojo_include_soc = include_soc
work._dojo_trial = "phgamma" if not include_soc else "phgamma_soc"
work.dojo_pseudo = pseudo
return work
