def build_flow(options):
"""
Create an `AbinitFlow` for phonon calculations:
1) One workflow for the GS run.
2) nqpt workflows for phonon calculations. Each workflow contains
nirred tasks where nirred is the number of irreducible phonon perturbations
for that particular q-point.
"""
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
# Instantiate the TaskManager.
manager = abilab.TaskManager.from_user_config() if not options.manager else \
abilab.TaskManager.from_file(options.manager)
all_inps = scf_ph_inputs()
scf_input, ph_inputs = all_inps[0], all_inps[1:]
flow = abilab.Flow(workdir, manager=manager)
from pymatgen.io.abinitio.works import build_oneshot_phononwork
work = build_oneshot_phononwork(scf_input, ph_inputs)
flow.register_work(work)
return flow.allocate()
def build_flow(options):
"""
Create an `AbinitFlow` for phonon calculations:
1) One workflow for the GS run.
2) nqpt workflows for phonon calculations. Each workflow contains
nirred tasks where nirred is the number of irreducible phonon perturbations
for that particular q-point.
"""
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
all_inps = scf_ph_inputs()
scf_input, ph_inputs = all_inps[0], all_inps[1:]
flow = abilab.Flow(workdir, manager=options.manager)
from pymatgen.io.abinitio.works import build_oneshot_phononwork
work = build_oneshot_phononwork(scf_input, ph_inputs)
flow.register_work(work)
return flow
def itest_oneshot_phonon_work(fwp):
"""
Test build_oneshot_phononwork i.e. computation of the phonon frequencies
for all modes in a single task.
"""
all_inps = scf_ph_inputs()
# SCF + one-shot for the first 2 qpoints.
scf_input, ph_inputs = all_inps[0], all_inps[1:3]
from pymatgen.io.abinitio.works import build_oneshot_phononwork
flow = abilab.Flow(fwp.workdir)
# rfdir and rfatpol are missing!
with pytest.raises(ValueError):
phon_work = build_oneshot_phononwork(scf_input, ph_inputs)
for phinp in ph_inputs: phinp.set_vars(rfdir=[1, 1, 1])
with pytest.raises(ValueError):
phon_work = build_oneshot_phononwork(scf_input, ph_inputs)
for phinp in ph_inputs: phinp.set_vars(rfatpol=[1, len(phinp.structure)])
# Now ph_inputs is ok
phon_work = build_oneshot_phononwork(scf_input, ph_inputs)
flow.register_work(phon_work)
assert flow.make_scheduler().start() == 0
flow.check_status(show=True, verbose=1)
assert all(work.finalized for work in flow)
assert flow.all_ok
# Read phonons from main output file.
phonons_list = phon_work.read_phonons()
assert len(phonons_list) == 2
ph0, ph1 = phonons_list[0], phonons_list[1]
assert ph0.qpt == [0, 0, 0]
assert ph1.qpt == [2.50000000E-01, 0.00000000E+00, 0.00000000E+00]
assert len(ph0.freqs) == 3 * len(scf_input.structure)
assert len(ph1.freqs) == 3 * len(scf_input.structure)
nptu.assert_almost_equal(ph0.freqs.to("Ha"),
[-1.219120E-05, -1.201501E-05, -1.198453E-05, 1.577646E-03, 1.577647E-03, 1.577647E-03])
nptu.assert_almost_equal(ph1.freqs.to("Ha"),
[2.644207E-04, 2.644236E-04, 6.420904E-04, 1.532696E-03, 1.532697E-03, 1.707196E-03])
def work_for_pseudo(self, pseudo, **kwargs):
"""
Create a :class:`Flow` for phonon calculations:
1) One workflow for the GS run.
2) nqpt workflows for phonon calculations. Each workflow contains
nirred tasks where nirred is the number of irreducible phonon perturbations
for that particular q-point.
the kwargs are passed to scf_hp_inputs
"""
try:
qpt = kwargs['qpt']
except IndexError:
raise ValueError('A phonon test needs to specify a qpoint.')
kwargs.pop('accuracy')
pseudo = Pseudo.as_pseudo(pseudo)
structure_or_cif = self.get_cif_path(pseudo.symbol)
if not isinstance(structure_or_cif, Structure):
# Assume CIF file
structure = Structure.from_file(structure_or_cif, primitive=False)
else:
structure = structure_or_cif
nat = len(structure)
report = pseudo.read_dojo_report()
ecut_str = '%.1f' % kwargs['ecut']
#print(ecut_str)
#print(report['deltafactor'][float(ecut_str)].keys())
try:
v0 = nat * report['deltafactor'][ecut_str]['v0']
except KeyError:
try:
v0 = nat * report['deltafactor'][float(ecut_str)]['v0']
except KeyError:
# the df calculation at this ecut is not done already so the phonon task can not be created
return None
structure.scale_lattice(v0)
all_inps = self.scf_ph_inputs(pseudos=[pseudo], structure=structure, **kwargs)
scf_input, ph_inputs = all_inps[0], all_inps[1:]
work = build_oneshot_phononwork(scf_input=scf_input, ph_inputs=ph_inputs, work_class=PhononDojoWork)
#print('after build_oneshot_phonon')
#print(work)
work.set_dojo_trial(qpt)
#print(scf_input.keys())
work.ecut = scf_input['ecut']
work._pseudo = pseudo
return work