def setUp(self):
# Si ebands
self.si_structure = abidata.structure_from_cif("si.cif")
self.si_pseudo = abidata.pseudos("14si.pspnc")
self.gan_structure = abidata.structure_from_cif("gan.cif")
self.n_pseudo = abidata.pseudos("7n.pspnc")
self.ga_pseudo = abidata.pseudos("31ga.pspnc")
def setUp(self):
# Si ebands
self.si_structure = abidata.structure_from_cif("si.cif")
self.si_pseudo = abidata.pseudos("14si.pspnc")
self.gan_structure = abidata.structure_from_cif("gan.cif")
self.n_pseudo = abidata.pseudos("7n.pspnc")
self.ga_pseudo = abidata.pseudos("31ga.pspnc")
def test_effmassline_work(self):
"""Testing EffMassLineWork."""
si_structure = abidata.structure_from_cif("si.cif")
scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized")
flow = flowtk.Flow.temporary_flow()
with self.assertRaises(ValueError):
work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=2)
# Run SCF from scratch.
work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=9)
t0, t1 = work[0], work[1]
assert t1.depends_on(t0)
assert t1.input["kptopt"] == 0
assert t1.input["iscf"] == -2
flow.register_work(work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
# From DEN file
flow = flowtk.Flow.temporary_flow()
work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=10,
red_dirs=(1, 0, 0),
cart_dirs=[(1, 0, 0), (1, 1, 0)],
den_node=abidata.ref_file("si_DEN.nc"))
flow.register_work(work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def test_gruneisen_work(self):
"""Testing GruneisenWork."""
si_structure = abidata.structure_from_cif("si.cif")
gs_inp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
ecut=4,
spin_mode="unpolarized")
flow = flowtk.Flow.temporary_flow()
voldelta = gs_inp.structure.volume * 0.02
work = GruneisenWork.from_gs_input(gs_inp,
voldelta,
ngqpt=[2, 2, 2],
with_becs=False)
flow.register_work(work)
assert len(work.relax_tasks) == 3
assert all(t.input["optcell"] == 3 for t in work)
assert all(t.input["ionmov"] == 3 for t in work)
assert all(t.input["ecutsm"] == 0.5 for t in work)
assert all(t.input["dilatmx"] == 1.05 for t in work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
with self.assertRaises(ValueError):
GruneisenWork.from_gs_input(gs_inp,
voldelta,
ngqpt=[3, 3, 3],
with_becs=False)
def test_phonopy_work(self):
"""Testing PhononWork."""
self.skip_if_not_phonopy()
si_structure = abidata.structure_from_cif("si.cif")
same_structure = abiph.structure_from_atoms(abiph.atoms_from_structure(si_structure))
assert si_structure == same_structure
# TODO: Spin
gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized")
#gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="polarized")
flow = flowtk.Flow.temporary_flow()
scdims = [2, 2, 2]
phpy_work = abiph.PhonopyWork.from_gs_input(gsinp, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None)
flow.register_work(phpy_work)
self.assert_equal(scdims, phpy_work.scdims)
assert hasattr(phpy_work, "phonon")
assert len(phpy_work.phonopy_tasks) == len(phpy_work)
assert len(phpy_work.phonopy_tasks) == 1
assert len(phpy_work.bec_tasks) == 0
# Gruneisen with phonopy
grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp, voldelta=0.1, scdims=scdims,
phonopy_kwargs=None, displ_kwargs=None)
flow.register_work(grun_work)
self.assert_equal(scdims, grun_work.scdims)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def itest_phonopy_flow(fwp, tvars):
"""
Testing phonopy flow with the scheduler.
"""
if not has_phonopy():
raise unittest.SkipTest("This test requires phonopy")
#print("tvars:\n %s" % str(tvars))
si_structure = abidata.structure_from_cif("si.cif")
gsinp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
kppa=10,
ecut=2,
spin_mode="unpolarized")
gsinp["paral_kgb"] = tvars.paral_kgb
flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager)
scdims = [2, 2, 2]
phpy_work = abiph.PhonopyWork.from_gs_input(gsinp,
scdims=scdims,
phonopy_kwargs=None,
displ_kwargs=None)
flow.register_work(phpy_work)
assert hasattr(phpy_work, "phonon")
assert len(phpy_work.phonopy_tasks) == len(phpy_work)
assert len(phpy_work.phonopy_tasks) == 1
assert len(phpy_work.bec_tasks) == 0
nptu.assert_equal(scdims, phpy_work.scdims)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
scheduler = flow.make_scheduler()
assert scheduler.start() == 0
assert not scheduler.exceptions
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
for task in flow[0]:
assert not task.outdir.has_abiext("WFK")
out_filenames = set(
[os.path.basename(f) for f in phpy_work.outdir.list_filepaths()])
nmiss = 0
for f in [
"POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf",
"band-dos.conf", "README.md"
]:
if f not in out_filenames:
nmiss += 1
print("Cannot find %s in work.outdir" % f)
assert nmiss == 0
def itest_phonopy_flow(fwp, tvars):
"""
Testing phonopy Gruneisen flow with the scheduler.
"""
if not has_phonopy():
raise unittest.SkipTest("This test requires phonopy")
#print("tvars:\n %s" % str(tvars))
si_structure = abidata.structure_from_cif("si.cif")
gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), kppa=10, ecut=2, spin_mode="unpolarized")
gsinp["paral_kgb"] = tvars.paral_kgb
flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager)
scdims = [2, 2, 2]
# Grunesein with phonopy
grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp, voldelta=0.1, scdims=scdims,
phonopy_kwargs=None, displ_kwargs=None)
flow.register_work(grun_work)
assert len(grun_work) == 3
nptu.assert_equal(scdims, grun_work.scdims)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
scheduler = flow.make_scheduler()
assert scheduler.start() == 0
assert not scheduler.exceptions
flow.show_status()
assert flow.all_ok
# Initialial work + 3 phonopy works.
assert len(flow) == 4
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
# FIXME: This does not work because new works that have been created.
#for task in flow.iflat_tasks():
# assert not task.outdir.has_abiext("WFK")
for work in flow[1:]:
out_filenames = set([os.path.basename(f) for f in work.outdir.list_filepaths()])
nmiss = 0
for f in ["POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf", "band-dos.conf", "README.md"]:
if f not in out_filenames:
nmiss += 1
print("Cannot find %s in work.outdir" % f)
assert nmiss == 0
def test_infinite_flow(self):
si_structure = abidata.structure_from_cif("si.cif")
gsinp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
ecut=4)
flow = flowtk.Flow.temporary_flow()
work = flowtk.Work()
gstask = work.register_scf_task(gsinp)
flow.register_work(work)
flow.allocate()
mocks.infinite_flow(flow)
flow.check_status()
assert (t.status == flow.S_INIT for t in flow)
mocks.change_task_start(gstask, mocked_status="Error")
assert gstask.start() == 1 and gstask.status == gstask.S_ERROR
def test_effmass_autodfpt_work(self):
"""Testing EffMassAutoDFPTWork."""
si_structure = abidata.structure_from_cif("si.cif")
scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized")
flow = flowtk.Flow.temporary_flow()
# Run SCF from scratch.
work = EffMassAutoDFPTWork.from_scf_input(scf_input)
assert len(work) == 2
assert work[1].depends_on(work[0])
flow.register_work(work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def test_data_api(self):
"""Testing abipy.data API."""
ncpseudo_h = abidata.pseudo("01h.pspgth")
assert ncpseudo_h.isnc
paw_table = abidata.pseudos("1h.paw", "28ni.paw")
assert paw_table.allpaw
assert os.path.isfile(abidata.cif_file("al.cif"))
assert os.path.isfile(abidata.pyscript("plot_bz.py"))
d = abidata.get_mp_structures_dict()
assert isinstance(d, dict) and d is abidata.get_mp_structures_dict()
structure = abidata.structure_from_cif("gan2.cif")
assert hasattr(structure, "to_abivars")
structure = abidata.structure_from_mpid("mp-4820")
assert hasattr(structure, "to_abivars")
with self.assertRaises(KeyError):
abidata.structure_from_mpid("foobar")
def test_phonopy_work(self):
"""Testing PhononWork."""
self.skip_if_not_phonopy()
si_structure = abidata.structure_from_cif("si.cif")
same_structure = abiph.structure_from_atoms(
abiph.atoms_from_structure(si_structure))
assert si_structure == same_structure
# TODO: Spin
gsinp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
ecut=4,
spin_mode="unpolarized")
#gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="polarized")
flow = flowtk.Flow.temporary_flow()
scdims = [2, 2, 2]
phpy_work = abiph.PhonopyWork.from_gs_input(gsinp,
scdims=scdims,
phonopy_kwargs=None,
displ_kwargs=None)
flow.register_work(phpy_work)
self.assert_equal(scdims, phpy_work.scdims)
assert hasattr(phpy_work, "phonon")
assert len(phpy_work.phonopy_tasks) == len(phpy_work)
assert len(phpy_work.phonopy_tasks) == 1
assert len(phpy_work.bec_tasks) == 0
# Gruneisen with phonopy
grun_work = abiph.PhonopyGruneisenWork.from_gs_input(
gsinp,
voldelta=0.1,
scdims=scdims,
phonopy_kwargs=None,
displ_kwargs=None)
flow.register_work(grun_work)
self.assert_equal(scdims, grun_work.scdims)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def test_data_api(self):
"""Testing abipy.data API."""
ncpseudo_h = abidata.pseudo("01h.pspgth")
assert ncpseudo_h.isnc
paw_table = abidata.pseudos("1h.paw", "28ni.paw")
assert paw_table.allpaw
assert os.path.isfile(abidata.cif_file("al.cif"))
assert os.path.isfile(abidata.pyscript("plot_bz.py"))
d = abidata.get_mp_structures_dict()
assert isinstance(d, dict) and d is abidata.get_mp_structures_dict()
structure = abidata.structure_from_cif("gan2.cif")
assert hasattr(structure, "to_abivars")
structure = abidata.structure_from_mpid("mp-4820")
assert hasattr(structure, "to_abivars")
with self.assertRaises(KeyError):
abidata.structure_from_mpid("foobar")
def test_effmass_dfpt_work(self):
"""Testing EffMassDFPTWork."""
si_structure = abidata.structure_from_cif("si.cif")
scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized")
flow = flowtk.Flow.temporary_flow()
# Run SCF from scratch.
work = EffMassDFPTWork.from_scf_input(scf_input, k0_list=(0, 0, 0), effmass_bands_f90=[2, 4])
assert len(work) == 3
t0, t1, t2 = work
assert t1.input["iscf"] == -2
assert t2.input["kptopt"] == 0
assert t2.input["efmas"] == 1 and t2.input["rfelfd"] == 2
assert t2.depends_on(t1)
flow.register_work(work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def itest_phonopy_gruneisen_flow(fwp, tvars):
"""
Testing phonopy Gruneisen flow with the scheduler.
"""
if not has_phonopy():
raise unittest.SkipTest("This test requires phonopy")
#print("tvars:\n %s" % str(tvars))
si_structure = abidata.structure_from_cif("si.cif")
gsinp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
kppa=10,
ecut=2,
spin_mode="unpolarized")
gsinp["paral_kgb"] = tvars.paral_kgb
flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager)
scdims = [2, 2, 2]
# Grunesein with phonopy
grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp,
voldelta=0.1,
scdims=scdims,
phonopy_kwargs=None,
displ_kwargs=None)
flow.register_work(grun_work)
assert len(grun_work) == 3
nptu.assert_equal(scdims, grun_work.scdims)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
scheduler = flow.make_scheduler()
assert scheduler.start() == 0
assert not scheduler.exceptions
flow.show_status()
if not flow.all_ok:
flow.debug()
raise RuntimeError()
# Initialial work + 3 phonopy works.
assert len(flow) == 4
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
# FIXME: This does not work because new works that have been created.
#for task in flow.iflat_tasks():
# assert not task.outdir.has_abiext("WFK")
for work in flow[1:]:
out_filenames = set(
[os.path.basename(f) for f in work.outdir.list_filepaths()])
nmiss = 0
for f in [
"POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf",
"band-dos.conf", "README.md"
]:
if f not in out_filenames:
nmiss += 1
print("Cannot find %s in work.outdir" % f)
assert nmiss == 0