def phonon_flow(workdir, manager, scf_input, ph_inputs):
"""
Build an `AbinitFlow` for phonon calculations.
Args:
workdir:
Working directory.
manager:
`TaskManager` used to submit the jobs
scf_input:
Input for the GS SCF run.
ph_inputs:
List of Inputs for the phonon runs.
Returns:
`AbinitFlow`
"""
natom = len(scf_input.structure)
# Create the container that will manage the different workflows.
flow = AbinitFlow(workdir, manager)
# Register the first workflow (GS calculation)
scf_task = flow.register_task(scf_input, task_class=ScfTask)
# Build a temporary workflow with a shell manager just to run
# ABINIT to get the list of irreducible pertubations for this q-point.
shell_manager = manager.to_shell_manager(mpi_ncpus=1)
if not isinstance(ph_inputs, (list, tuple)):
ph_inputs = [ph_inputs]
for i, ph_input in enumerate(ph_inputs):
fake_input = ph_input.deepcopy()
# Run abinit on the front-end to get the list of irreducible pertubations.
tmp_dir = os.path.join(workdir, "__ph_run" + str(i) + "__")
w = Workflow(workdir=tmp_dir, manager=shell_manager)
fake_task = w.register(fake_input)
# Use the magic value paral_rf = -1
# to get the list of irreducible perturbations for this q-point.
vars = dict(paral_rf=-1,
rfatpol=[1, natom], # Set of atoms to displace.
rfdir=[1, 1, 1], # Along this set of reduced coordinate axis.
)
fake_task.strategy.add_extra_abivars(vars)
w.start(wait=True)
# Parse the file to get the perturbations.
irred_perts = yaml_read_irred_perts(fake_task.log_file.path)
print(irred_perts)
w.rmtree()
# Now we can build the final list of workflows:
# One workflow per q-point, each workflow computes all
# the irreducible perturbations for a singe q-point.
work_qpt = PhononWorkflow()
for irred_pert in irred_perts:
print(irred_pert)
new_input = ph_input.deepcopy()
#rfatpol 1 1 # Only the first atom is displaced
#rfdir 1 0 0 # Along the first reduced coordinate axis
qpt = irred_pert["qpt"]
idir = irred_pert["idir"]
ipert = irred_pert["ipert"]
# TODO this will work for phonons, but not for the other types of perturbations.
rfdir = 3 * [0]
rfdir[idir -1] = 1
rfatpol = [ipert, ipert]
new_input.set_variables(
#rfpert=1,
qpt=qpt,
rfdir=rfdir,
rfatpol=rfatpol,
)
work_qpt.register(new_input, deps={scf_task: "WFK"}, task_class=PhononTask)
flow.register_work(work_qpt)
return flow.allocate()
def phonon_flow(workdir, manager, scf_input, ph_inputs):
"""
Build an `AbinitFlow` for phonon calculations.
Args:
workdir:
Working directory.
manager:
`TaskManager` used to submit the jobs
scf_input:
Input for the GS SCF run.
ph_inputs:
List of Inputs for the phonon runs.
Returns:
`AbinitFlow`
"""
natom = len(scf_input.structure)
# Create the container that will manage the different workflows.
flow = AbinitFlow(workdir, manager)
# Register the first workflow (GS calculation)
scf_task = flow.register_task(scf_input, task_class=ScfTask)
# Build a temporary workflow with a shell manager just to run
# ABINIT to get the list of irreducible pertubations for this q-point.
shell_manager = manager.to_shell_manager(mpi_ncpus=1)
if not isinstance(ph_inputs, (list, tuple)):
ph_inputs = [ph_inputs]
for i, ph_input in enumerate(ph_inputs):
fake_input = ph_input.deepcopy()
# Run abinit on the front-end to get the list of irreducible pertubations.
tmp_dir = os.path.join(workdir, "__ph_run" + str(i) + "__")
w = Workflow(workdir=tmp_dir, manager=shell_manager)
fake_task = w.register(fake_input)
# Use the magic value paral_rf = -1 to get the list of irreducible perturbations for this q-point.
vars = dict(
paral_rf=-1,
rfatpol=[1, natom], # Set of atoms to displace.
rfdir=[1, 1, 1], # Along this set of reduced coordinate axis.
)
fake_task.strategy.add_extra_abivars(vars)
w.allocate()
w.start(wait=True)
# Parse the file to get the perturbations.
irred_perts = yaml_read_irred_perts(fake_task.log_file.path)
print(irred_perts)
w.rmtree()
# Now we can build the final list of workflows:
# One workflow per q-point, each workflow computes all
# the irreducible perturbations for a singe q-point.
work_qpt = PhononWorkflow()
for irred_pert in irred_perts:
print(irred_pert)
new_input = ph_input.deepcopy()
#rfatpol 1 1 # Only the first atom is displaced
#rfdir 1 0 0 # Along the first reduced coordinate axis
qpt = irred_pert["qpt"]
idir = irred_pert["idir"]
ipert = irred_pert["ipert"]
# TODO this will work for phonons, but not for the other types of perturbations.
rfdir = 3 * [0]
rfdir[idir - 1] = 1
rfatpol = [ipert, ipert]
new_input.set_variables(
#rfpert=1,
qpt=qpt,
rfdir=rfdir,
rfatpol=rfatpol,
)
work_qpt.register(new_input,
deps={scf_task: "WFK"},
task_class=PhononTask)
flow.register_work(work_qpt)
return flow.allocate()
