def register_task(self, input, deps=None, manager=None, task_class=None):
"""
Utility function that generates a `Workflow` made of a single task
Args:
input:
Abinit Input file or `Strategy` object of `Task` object.
deps:
List of `Dependency` objects specifying the dependency of this node.
An empy list of deps implies that this node has no dependencies.
manager:
The `TaskManager` responsible for the submission of the task.
If manager is None, we use the `TaskManager` specified during the creation of the workflow.
task_class:
Task subclass to instantiate. Default: `AbinitTask`
Returns:
The generated `Task`.
"""
work = Workflow(manager=manager)
task = work.register(input, deps=deps, task_class=task_class)
self.register_work(work)
return task
def register_task(self, input, deps=None, manager=None, task_class=None):
"""
Utility function that generates a `Workflow` made of a single task
Args:
input:
Abinit Input file or `Strategy` object of `Task` object.
deps:
List of `Dependency` objects specifying the dependency of this node.
An empy list of deps implies that this node has no dependencies.
manager:
The `TaskManager` responsible for the submission of the task.
If manager is None, we use the `TaskManager` specified during the creation of the workflow.
task_class:
Task subclass to instantiate. Default: `AbinitTask`
Returns:
The generated `Task`.
"""
work = Workflow(manager=manager)
task = work.register(input, deps=deps, task_class=task_class)
self.register_work(work)
return task
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()
kpt = numpy.array(kpts),
tolvrs = 0,
tolwfr = 1.e-15,
))
return inp
flow = AbinitFlow(manager = manager, workdir = workdir)
tasks = 9*[{}]
for i,(Z,phase) in enumerate(itertools.product(['N','P','Si'],['alpha','beta','gamma'])):
structure_opt = HalfHeusler(['Li','Mn',Z], phase, acell_opt[Z][phase])
structure_hm = HalfHeusler(['Li','Mn',Z], phase, acell_hm[Z][phase] )
inp_opt = get_input(structure_opt)
inp_hm = get_input(structure_hm)
work_Z = Workflow()
scf_opt_task = work_Z.register(inp_opt, manager = manager, task_class=ScfTask)
scf_hm_task = work_Z.register(inp_hm , manager = manager, task_class=ScfTask)
flow.register_work(work_Z)
tasks[i] = {
"opt": {
"input" : inp_opt,
"task": scf_opt_task,
},
"hm" : {
"input" : inp_hm,
"task": scf_hm_task,
}
}
for i,(Z,phase) in enumerate(itertools.product(['N','P','Si'],['alpha','beta','gamma'])):
istart = izero
iend = izero
while dos[1,istart] < 1e-5:
istart = istart - 1
while dos[1,iend] < 1e-5:
iend = iend + 1
if iend > istart:
gapdn = x[iend]-x[istart]
return (gapup,gapdn)
flow = AbinitFlow(manager = manager, workdir = workdir)
tasks = []
inpts = []
for Z,phase in itertools.product(['N','P','Si'],['alpha','beta','gamma']):
work = Workflow()
if acell_low[Z][phase] < 0.05:
continue
for acell in numpy.arange(acell_low[Z][phase],acell_hm[Z][phase]+0.05,0.05):
structure = HalfHeusler(['Li','Mn',Z], phase, acell)
inp = get_input(structure)
task = work.register(inp, manager = manager, task_class=ScfTask)
task._name = 'LiMn%s_%s_%f' % (Z,phase,acell)
print(task._name)
tasks.append(task)
inpts.append(inp)
flow.register_work(work)
work = Workflow()
for task,inp in zip(tasks,inpts):
work.register(dos_input(inp), deps={task:"DEN"},
manager=manager, task_class=NscfTask)
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()
