def get_irred_perts(qpt, inp, manager=None, workdir="."):
fake_vars = dict(
rfphon=1,
nqpt=1,
qpt=qpt,
paral_rf=-1,
rfatpol=[1, len(inp.structure)],
rfdir=[1, 1, 1],
)
w = _setup_faketask('ph', manager=manager, workdir=workdir)
fake_input = inp.deepcopy()
fake_input.set_variables(**fake_vars)
fake_task = w.register(fake_input)
w.allocate()
w.start(wait=True)
irred_perts = yaml_read_irred_perts(fake_task.log_file.path)
mem = 0
for line in fake_task.log_file.readlines():
if "P This job should need less than" in line:
mem = float(line.split()[7])
break
w.rmtree()
return irred_perts, mem
def get_irred_perts(self,
ngkpt=None,
shiftk=None,
kptopt=None,
qpoint=None,
workdir=None,
manager=None):
"""
This function, computes the list of irreducible perturbations for DFPT.
It should be called with an input file that contains all the mandatory variables required by ABINIT.
Args:
ngkpt: Number of divisions for the k-mesh (default None i.e. use ngkpt from self)
shiftk: Shiftks (default None i.e. use shiftk from self)
qpoint: qpoint in reduced coordinates. Used to shift the k-mesh (default None i.e no shift)
workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
manager: :class:`TaskManager` of the task. If None, the manager is initialized from the config file.
Returns:
List of dictionaries with the Abinit variables defining the irreducible perturbation
Example:
[{'idir': 1, 'ipert': 1, 'qpt': [0.25, 0.0, 0.0]},
{'idir': 2, 'ipert': 1, 'qpt': [0.25, 0.0, 0.0]}]
.. warning::
Multiple datasets are ignored. Only the list of k-points for dataset 1 are returned.
"""
if self.ndtset != 1:
raise RuntimeError(
"get_irred_perts cannot be used if the input contains more than one dataset"
)
warnings.warn("get_irred_perts is still under development.")
# Avoid modifications in self.
inp = self.split_datasets()[0].deepcopy()
# Use the magic value paral_rf = -1 to get the list of irreducible perturbations for this q-point.
d = dict(
paral_rf=-1,
rfatpol=[1, len(inp.structure)], # Set of atoms to displace.
rfdir=[1, 1, 1], # Along this set of reduced coordinate axis.
)
inp.set_vars(d)
# Build a Task to run Abinit in a shell subprocess
task = AbinitTask.temp_shell_task(inp,
workdir=workdir,
manager=manager)
task.start_and_wait(autoparal=False)
# Parse the file to get the perturbations.
try:
return yaml_read_irred_perts(task.log_file.path)
except Exception as exc:
# Try to understand if it's a problem with the Abinit input.
report = task.get_event_report()
if report.errors: raise self.Error(str(report))
raise exc
def get_irred_perts(self, ngkpt=None, shiftk=None, kptopt=None, qpoint=None, workdir=None, manager=None):
"""
This function, computes the list of irreducible perturbations for DFPT.
It should be called with an input file that contains all the mandatory variables required by ABINIT.
Args:
ngkpt: Number of divisions for the k-mesh (default None i.e. use ngkpt from self)
shiftk: Shiftks (default None i.e. use shiftk from self)
qpoint: qpoint in reduced coordinates. Used to shift the k-mesh (default None i.e no shift)
workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
manager: :class:`TaskManager` of the task. If None, the manager is initialized from the config file.
Returns:
List of dictionaries with the Abinit variables defining the irreducible perturbation
Example:
[{'idir': 1, 'ipert': 1, 'qpt': [0.25, 0.0, 0.0]},
{'idir': 2, 'ipert': 1, 'qpt': [0.25, 0.0, 0.0]}]
.. warning::
Multiple datasets are ignored. Only the list of k-points for dataset 1 are returned.
"""
if self.ndtset != 1:
raise RuntimeError("get_irred_perts cannot be used if the input contains more than one dataset")
warnings.warn("get_irred_perts is still under development.")
# Avoid modifications in self.
inp = self.split_datasets()[0].deepcopy()
# Use the magic value paral_rf = -1 to get the list of irreducible perturbations for this q-point.
d = dict(
paral_rf=-1,
rfatpol=[1, len(inp.structure)], # Set of atoms to displace.
rfdir=[1, 1, 1], # Along this set of reduced coordinate axis.
)
inp.set_vars(d)
# Build a Task to run Abinit in a shell subprocess
task = AbinitTask.temp_shell_task(inp, workdir=workdir, manager=manager)
task.start_and_wait(autoparal=False)
# Parse the file to get the perturbations.
try:
return yaml_read_irred_perts(task.log_file.path)
except Exception as exc:
# Try to understand if it's a problem with the Abinit input.
report = task.get_event_report()
if report.errors: raise self.Error(str(report))
raise exc
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()
