def build_flow(structure, workdir, options):
"""
Create a :class:`Flow` for phonon calculations:
1) One work 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-poin t.
"""
# Instantiate the TaskManager.
manager = abilab.TaskManager.from_user_config()
all_inps = scf_ph_inputs(structure, options)
scf_input, ph_inputs = all_inps[0], all_inps[1:]
if len(ph_inputs) == 1:
return abilab.phonon_flow(workdir,
manager,
scf_input,
ph_inputs,
with_nscf=False,
with_ddk=True,
with_dde=True)
else:
return abilab.phonon_flow(workdir,
manager,
scf_input,
ph_inputs,
with_nscf=True,
with_ddk=False,
with_dde=False)
def itest_phonon_restart(fwp):
"""Test the restart of phonon calculations with the scheduler."""
# Crystalline AlAs: computation of the second derivative of the total energy
structure = abidata.structure_from_ucell("AlAs")
# List of q-points for the phonon calculation (4,4,4) mesh.
qpoints = np.reshape([
0.00000000E+00, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 0.00000000E+00, 0.00000000E+00,
#5.00000000E-01, 0.00000000E+00, 0.00000000E+00, # XXX Uncomment this line to test restart from 1DEN
# Too long --> disabled
], (-1, 3))
# Global variables used both for the GS and the DFPT run.
global_vars = dict(nband=4,
ecut=3.0,
ngkpt=[4, 4, 4],
shiftk=[0, 0, 0],
tolvrs=1.0e-5,
)
multi = abilab.MultiDataset(structure=structure, pseudos=abidata.pseudos("13al.981214.fhi", "33as.pspnc"),
ndtset=1+len(qpoints))
multi.set_vars(global_vars)
for i, qpt in enumerate(qpoints):
# Response-function calculation for phonons.
multi[i+1].set_vars(
rfphon=1, # Will consider phonon-type perturbation.
nqpt=1, # One wavevector is to be considered.
qpt=qpt, # q-wavevector.
kptopt=3,
nstep=5, # This is to trigger the phonon restart.
)
#rfatpol 1 1 # Only the first atom is displaced
#rfdir 1 0 0 # Along the first reduced coordinate axis
#kptopt 2 # Automatic generation of k points, taking
# i == 0 --> restart from WFK
if i == 1: multi[i+1].set_vars(prtwf=-1, nstep=5) # Restart with WFK and smart- io.
if i == 2: multi[i+1].set_vars(prtwf=0, nstep=8) # Restart from 1DEN. Too long --> disabled.
all_inps = multi.split_datasets()
scf_input, ph_inputs = all_inps[0], all_inps[1:]
flow = abilab.phonon_flow(fwp.workdir, scf_input, ph_inputs, manager=fwp.manager)
flow.set_garbage_collector()
for task in flow.iflat_tasks():
task.manager.qadapter.max_num_launches = 20
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
assert sum(task.num_restarts for task in flow.iflat_tasks()) > 0
def build_flow(structure, workdir, options):
"""
Create a :class:`Flow` for phonon calculations:
1) One work 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-poin t.
"""
# Instantiate the TaskManager.
manager = abilab.TaskManager.from_user_config()
all_inps = scf_ph_inputs(structure, options)
scf_input, ph_inputs = all_inps[0], all_inps[1:]
if len(ph_inputs) == 1:
return abilab.phonon_flow(workdir, manager, scf_input, ph_inputs, with_nscf=False, with_ddk=True, with_dde=True)
else:
return abilab.phonon_flow(workdir, manager, scf_input, ph_inputs, with_nscf=True, with_ddk=False, with_dde=False)
def ph_flow(workdir="tmp_phonons"):
"""
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.
"""
manager = abilab.TaskManager.from_user_config()
all_inps = scf_ph_inputs()
scf_input, ph_inputs = all_inps[0], all_inps[1:]
flow = abilab.phonon_flow(workdir, manager, scf_input, ph_inputs)
return flow
def build_flow(options):
"""
Create a `Flow` for phonon calculations:
1) One workflow for the GS run.
2) nqpt works for phonon calculations. Each work 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:]
# scf_input, ph_inputs = all_inps[0], all_inps[1:3]
return abilab.phonon_flow(workdir, scf_input, ph_inputs, manager=options.manager)
def build_flow(options):
"""
Create a `Flow` for phonon calculations:
1) One workflow for the GS run.
2) nqpt works for phonon calculations. Each work 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:]
#scf_input, ph_inputs = all_inps[0], all_inps[1:3]
return abilab.phonon_flow(workdir,
scf_input,
ph_inputs,
manager=options.manager)
def itest_phonon_flow(fwp, tvars):
"""
Create an `Abinit` for phonon calculations:
1) One work for the GS run.
2) nqpt works for phonon calculations. Each work contains
nirred tasks where nirred is the number of irreducible phonon perturbations
for that particular q-point.
"""
if tvars.paral_kgb == 1:
pytest.xfail("Phonon flow with paral_kgb==1 is expected to fail (implementation problem)")
all_inps = scf_ph_inputs(tvars)
scf_input, ph_inputs = all_inps[0], all_inps[1:]
flow = abilab.phonon_flow(fwp.workdir, scf_input, ph_inputs, manager=fwp.manager)
flow.build_and_pickle_dump()
t0 = flow[0][0]
t0.start_and_wait()
assert t0.uses_paral_kgb(tvars.paral_kgb)
flow.check_status()
assert t0.status == t0.S_OK
flow.show_status()
for work in flow[1:]:
for task in work:
task.start_and_wait()
assert task.status == t0.S_DONE
flow.check_status(show=True)
# We should have a DDB files with IFC(q) in work.outdir
ddb_files = []
for work in flow[1:]:
ddbs = work.outdir.list_filepaths(wildcard="*DDB")
assert len(ddbs) == 1
ddb_files.append(ddbs[0])
assert all(work.finalized for work in flow)
assert flow.all_ok
# Merge the DDB files
out_ddb = flow.outdir.path_in("flow_DDB")
ddb_path = abilab.Mrgddb().merge(flow.outdir.path, ddb_files, out_ddb=out_ddb,
description="DDB generated by %s" % __file__)
assert ddb_path == out_ddb
# Test PhononTask inspect method
ph_task = flow[1][0]
# paral_kgb does not make sense for DFPT!
assert not ph_task.uses_paral_kgb(tvars.paral_kgb)
if has_matplotlib():
ph_task.inspect(show=False)
# Test get_results
ph_task.get_results()
# Build new work with Anaddb tasks.
# Construct a manager with mpi_procs==1 since anaddb do not support mpi_procs > 1 (except in elphon)
shell_manager = fwp.manager.to_shell_manager(mpi_procs=1)
awork = abilab.Work(manager=shell_manager)
# Phonons bands and DOS with gaussian method
anaddb_input = abilab.AnaddbInput.phbands_and_dos(
scf_input.structure, ngqpt=(4, 4, 4), ndivsm=5, nqsmall=10, dos_method="gaussian: 0.001 eV")
atask = abilab.AnaddbTask(anaddb_input, ddb_node=ddb_path, manager=shell_manager)
awork.register(atask)
# Phonons bands and DOS with tetrahedron method
anaddb_input = abilab.AnaddbInput.phbands_and_dos(
scf_input.structure, ngqpt=(4, 4, 4), ndivsm=5, nqsmall=10, dos_method="tetra")
atask = abilab.AnaddbTask(anaddb_input, ddb_node=ddb_path, manager=shell_manager)
awork.register(atask)
flow.register_work(awork)
flow.allocate()
flow.build()
for i, atask in enumerate(awork):
atask.history.info("about to run anaddb task: %d", i)
atask.start_and_wait()
assert atask.status == atask.S_DONE
atask.check_status()
assert atask.status == atask.S_OK
