def build_flow(options):
# 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_")
# Initialize structure and pseudos.
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudos = abidata.pseudos("14si.pspnc")
# Initialize the flow.
flow = flowtk.Flow(workdir=workdir,
manager=options.manager,
remove=options.remove)
# Use ebands_input factory function to build inputs.
multi = abilab.ebands_input(structure,
pseudos,
kppa=40,
nscf_nband=6,
ndivsm=10,
ecut=6)
work = flowtk.BandStructureWork(scf_input=multi[0], nscf_input=multi[1])
flow.register_work(work)
return flow
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
if os.getenv("READTHEDOCS", False):
__file__ = os.path.join(os.getcwd(), "run_ht_si_ebands.py")
options.workdir = os.path.basename(__file__).replace(
".py", "").replace("run_", "flow_")
# Initialize structure and pseudos.
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudos = abidata.pseudos("14si.pspnc")
# Initialize the flow.
flow = flowtk.Flow(workdir=options.workdir, manager=options.manager)
# Use the ebands_input factory function to build a MultiDataset.
# keyword args are optional (default values are given or computed automatically, see docs).
multi = abilab.ebands_input(structure,
pseudos,
kppa=40,
dos_kppa=80,
nscf_nband=6,
ndivsm=10,
ecut=6,
spin_mode="unpolarized")
work = flowtk.BandStructureWork(scf_input=multi[0],
nscf_input=multi[1],
dos_inputs=multi[2])
flow.register_work(work)
return flow
def itest_htc_bandstructure(fwp, tvars):
"""Test band-structure calculations done with the HTC interface."""
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudos = abidata.pseudos("14si.pspnc")
# Initialize the flow.
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
# Use ebands_input factory function to build inputs.
multi = abilab.ebands_input(structure,
pseudos,
kppa=20,
nscf_nband=6,
ndivsm=5,
ecut=2,
dos_kppa=40,
spin_mode="unpolarized")
work = flowtk.BandStructureWork(scf_input=multi[0],
nscf_input=multi[1],
dos_inputs=multi[2:])
multi.set_vars(paral_kgb=tvars.paral_kgb)
flow.register_work(work)
flow.allocate()
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 3
flow.show_status()
if not flow.all_ok:
flow.debug()
raise RuntimeError()
assert all(work.finalized for work in flow)
# Test if GSR files are produced and are readable.
for i, task in enumerate(work):
with task.open_gsr() as gsr:
assert gsr.nsppol == 1
#assert gsr.structure == structure
if i == 0:
gsr.to_string(verbose=2)
if i == 1:
# Bandstructure case
assert gsr.ebands.has_bzpath
assert not gsr.ebands.has_bzmesh
with pytest.raises(ValueError):
gsr.ebands.get_edos()
if i == 2:
# DOS case
assert gsr.ebands.has_bzmesh
assert not gsr.ebands.has_bzpath
gsr.ebands.get_edos()
def itest_htc_bandstructure(fwp, tvars):
"""Test band-structure calculations done with the HTC interface."""
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudos = abidata.pseudos("14si.pspnc")
# TODO: Add this options because I don't like the kppa approach
# I had to use it because it was the approach used in VaspIO
#dos_ngkpt = [4,4,4]
#dos_shiftk = [0.1, 0.2, 0.3]
# Initialize the flow.
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
# Use ebands_input factory function to build inputs.
multi = abilab.ebands_input(structure, pseudos, kppa=20, nscf_nband=6, ndivsm=5,
ecut=2, dos_kppa=40, spin_mode="unpolarized")
work = abilab.BandStructureWork(scf_input=multi[0], nscf_input=multi[1], dos_inputs=multi[2:])
multi.set_vars(paral_kgb=tvars.paral_kgb)
flow.register_work(work)
flow.allocate()
flow.build_and_pickle_dump()
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 3
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# Test if GSR files are produced and are readable.
for i, task in enumerate(work):
with task.open_gsr() as gsr:
print(gsr)
assert gsr.nsppol == 1
#assert gsr.structure == structure
ebands = gsr.ebands
# TODO: This does not work yet because GSR files do not contain
# enough info to understand if we have a path or a mesh.
#if i == 2:
# Bandstructure case
#assert ebands.has_bzpath
#with pytest.raises(ebands.Error):
# ebands.get_edos()
if i == 3:
# DOS case
assert ebands.has_bzmesh
gsr.bands.get_edos()
def itest_htc_bandstructure(fwp, tvars):
"""Test band-structure calculations done with the HTC interface."""
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudos = abidata.pseudos("14si.pspnc")
# Initialize the flow.
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
# Use ebands_input factory function to build inputs.
multi = abilab.ebands_input(structure, pseudos, kppa=20, nscf_nband=6, ndivsm=5,
ecut=2, dos_kppa=40, spin_mode="unpolarized")
work = flowtk.BandStructureWork(scf_input=multi[0], nscf_input=multi[1], dos_inputs=multi[2:])
multi.set_vars(paral_kgb=tvars.paral_kgb)
flow.register_work(work)
flow.allocate()
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 3
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# Test if GSR files are produced and are readable.
for i, task in enumerate(work):
with task.open_gsr() as gsr:
assert gsr.nsppol == 1
#assert gsr.structure == structure
if i == 0:
gsr.to_string(verbose=2)
if i == 1:
# Bandstructure case
assert gsr.ebands.has_bzpath
assert not gsr.ebands.has_bzmesh
with pytest.raises(ValueError):
gsr.ebands.get_edos()
if i == 2:
# DOS case
assert gsr.ebands.has_bzmesh
assert not gsr.ebands.has_bzpath
gsr.ebands.get_edos()
def build_flow(options):
# 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_")
# Initialize structure and pseudos.
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudos = abidata.pseudos("14si.pspnc")
# Initialize the flow.
flow = abilab.Flow(workdir=workdir, manager=options.manager, remove=options.remove)
# Use ebands_input factory function to build inputs.
multi = abilab.ebands_input(structure, pseudos, kppa=40, nscf_nband=6, ndivsm=10, ecut=6)
work = abilab.BandStructureWork(scf_input=multi[0], nscf_input=multi[1])
flow.register_work(work)
return flow
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
# Initialize structure and pseudos.
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudos = abidata.pseudos("14si.pspnc")
# Initialize the flow.
flow = flowtk.Flow(workdir=options.workdir, manager=options.manager)
# Use the ebands_input factory function to build a MultiDataset.
# keyword args are optional (default values are given or computed automatically, see docs).
multi = abilab.ebands_input(structure, pseudos, kppa=40, dos_kppa=80,
nscf_nband=6, ndivsm=10, ecut=6, spin_mode="unpolarized")
work = flowtk.BandStructureWork(scf_input=multi[0], nscf_input=multi[1], dos_inputs=multi[2])
flow.register_work(work)
return flow
def itest_htc_bandstructure(fwp, tvars):
"""Test band-structure calculations done with the HTC interface."""
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudos = abidata.pseudos("14si.pspnc")
# TODO: Add this options because I don't like the kppa approach
# I had to use it because it was the approach used in VaspIO
#dos_ngkpt = [4,4,4]
#dos_shiftk = [0.1, 0.2, 0.3]
# Initialize the flow.
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
# Use ebands_input factory function to build inputs.
multi = abilab.ebands_input(structure,
pseudos,
kppa=20,
nscf_nband=6,
ndivsm=5,
ecut=2,
dos_kppa=40,
spin_mode="unpolarized")
work = flowtk.BandStructureWork(scf_input=multi[0],
nscf_input=multi[1],
dos_inputs=multi[2:])
multi.set_vars(paral_kgb=tvars.paral_kgb)
flow.register_work(work)
flow.allocate()
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 3
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# Test if GSR files are produced and are readable.
for i, task in enumerate(work):
with task.open_gsr() as gsr:
print(gsr)
assert gsr.nsppol == 1
#assert gsr.structure == structure
ebands = gsr.ebands
# TODO: This does not work yet because GSR files do not contain
# enough info to understand if we have a path or a mesh.
#if i == 2:
# Bandstructure case
#assert ebands.has_bzpath
#with pytest.raises(ebands.Error):
# ebands.get_edos()
if i == 3:
# DOS case
assert ebands.has_bzmesh
gsr.bands.get_edos()
