def optic_flow_from_files():
# Optic does not support MPI with ncpus > 1.
manager = abilab.TaskManager.from_user_config()
manager.set_mpi_procs(1)
flow = abilab.Flow(workdir="OPTIC_FROM_FILE", manager=manager)
ddk_nodes = [
"/Users/gmatteo/Coding/abipy/abipy/data/runs/OPTIC/work_1/task_0/outdata/out_1WF",
"/Users/gmatteo/Coding/abipy/abipy/data/runs/OPTIC/work_1/task_1/outdata/out_1WF",
"/Users/gmatteo/Coding/abipy/abipy/data/runs/OPTIC/work_1/task_2/outdata/out_1WF",
]
nscf_node = "/Users/gmatteo/Coding/abipy/abipy/data/runs/OPTIC/work_0/task_1/outdata/out_WFK"
optic_task = abilab.OpticTask(optic_input, nscf_node=nscf_node, ddk_nodes=ddk_nodes)
flow.register_task(optic_task)
return flow
def build_flow(options):
flow = make_base_flow(options)
optic_input = abilab.OpticInput(
broadening=0.002,
domega=0.0003,
maxomega=0.3,
scissor=0.000,
tolerance=0.002,
num_lin_comp=1,
lin_comp=11,
num_nonlin_comp=2,
nonlin_comp=(123, 222),
)
mpi_list = options.mpi_list
if mpi_list is None:
mpi_list = [1, 2, 4, 8]
print("Using mpi_list:", mpi_list)
else:
print("Using mpi_list from cmd line:", mpi_list)
work = abilab.Work()
for mpi_procs, omp_threads in product(mpi_list, options.omp_list):
if not options.accept_mpi_omp(mpi_procs, omp_threads): continue
manager = options.manager.new_with_fixed_mpi_omp(
mpi_procs, omp_threads)
optic_task = abilab.OpticTask(optic_input,
manager=manager,
nscf_node=flow[0].nscf_task,
ddk_nodes=flow[1])
work.register_task(optic_task)
flow.register_work(work)
return flow.allocate()
def build_flow(options, paral_kgb=0):
# 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_")
multi = abilab.MultiDataset(structure=data.structure_from_ucell("GaAs"),
pseudos=data.pseudos("31ga.pspnc",
"33as.pspnc"),
ndtset=5)
# Global variables
kmesh = dict(ngkpt=[4, 4, 4],
nshiftk=4,
shiftk=[[0.5, 0.5, 0.5], [0.5, 0.0, 0.0], [0.0, 0.5, 0.0],
[0.0, 0.0, 0.5]])
global_vars = dict(ecut=2, paral_kgb=paral_kgb)
global_vars.update(kmesh)
multi.set_vars(global_vars)
# Dataset 1 (GS run)
multi[0].set_vars(
tolvrs=1e-6,
nband=4,
)
# NSCF run with large number of bands, and points in the the full BZ
multi[1].set_vars(
iscf=-2,
nband=20,
nstep=25,
kptopt=1,
tolwfr=1.e-9,
#kptopt=3,
)
# Fourth dataset : ddk response function along axis 1
# Fifth dataset : ddk response function along axis 2
# Sixth dataset : ddk response function along axis 3
for dir in range(3):
rfdir = 3 * [0]
rfdir[dir] = 1
multi[2 + dir].set_vars(
iscf=-3,
nband=20,
nstep=1,
nline=0,
prtwf=3,
kptopt=3,
nqpt=1,
qpt=[0.0, 0.0, 0.0],
rfdir=rfdir,
rfelfd=2,
tolwfr=1.e-9,
)
scf_inp, nscf_inp, ddk1, ddk2, ddk3 = multi.split_datasets()
# Initialize the flow.
flow = abilab.Flow(workdir, manager=options.manager, remove=options.remove)
bands_work = abilab.BandStructureWork(scf_inp, nscf_inp)
flow.register_work(bands_work)
ddk_work = abilab.Work()
for inp in [ddk1, ddk2, ddk3]:
ddk_work.register_ddk_task(inp, deps={bands_work.nscf_task: "WFK"})
flow.register_work(ddk_work)
# Optic does not support MPI with ncpus > 1.
optic_input = abilab.OpticInput(
broadening=0.002, # Value of the smearing factor, in Hartree
domega=0.0003, # Frequency mesh.
maxomega=0.3,
scissor=0.000, # Scissor shift if needed, in Hartree
tolerance=0.002, # Tolerance on closeness of singularities (in Hartree)
num_lin_comp=
1, # Number of components of linear optic tensor to be computed
lin_comp=11, # Linear coefficients to be computed (x=1, y=2, z=3)
num_nonlin_comp=
2, # Number of components of nonlinear optic tensor to be computed
nonlin_comp=(123, 222), # Non-linear coefficients to be computed
)
# TODO
# Check is the order of the 1WF files is relevant. Can we use DDK files ordered
# in an arbitrary way or do we have to pass (x,y,z)?
optic_task = abilab.OpticTask(optic_input,
nscf_node=bands_work.nscf_task,
ddk_nodes=ddk_work)
flow.register_task(optic_task)
return flow
def raman_work(structure, pseudos, ngkpt, shiftk, ddk_manager, shell_manager):
# Generate 3 different input files for computing optical properties with BSE.
multi = abilab.MultiDataset(structure, pseudos=pseudos, ndtset=5)
multi.set_vars(global_vars)
multi.set_kmesh(ngkpt=ngkpt, shiftk=shiftk)
# GS run
multi[0].set_vars(
tolvrs=1e+8,
nband=59,
)
# NSCF run
multi[1].set_vars(
iscf=-2,
nband=100,
kptopt=1,
tolwfr=1.e+12,
)
# DDK along 3 directions
# Third dataset : ddk response function along axis 1
# Fourth dataset : ddk response function along axis 2
# Fifth dataset : ddk response function along axis 3
for dir in range(3):
rfdir = 3 * [0]
rfdir[dir] = 1
multi[2 + dir].set_vars(
iscf=-3,
nband=100,
nstep=1,
nline=0,
prtwf=3,
kptopt=1,
nqpt=1,
qpt=[0.0, 0.0, 0.0],
rfdir=rfdir,
rfelfd=2,
tolwfr=1.e+12,
)
scf_inp, nscf_inp, ddk1, ddk2, ddk3 = multi.split_datasets()
ddk_inputs = [ddk1, ddk2, ddk3]
work = abilab.Work()
scf_t = work.register_scf_task(scf_inp)
nscf_t = work.register_nscf_task(nscf_inp, deps={scf_t: "DEN"})
ddk_nodes = []
for inp in ddk_inputs:
ddk_t = work.register_ddk_task(inp, deps={nscf_t: "WFK"})
ddk_t.set_manager(ddk_manager)
ddk_nodes.append(ddk_t)
optic_t = abilab.OpticTask(optic_input,
nscf_node=nscf_t,
ddk_nodes=ddk_nodes,
manager=shell_manager)
work.register(optic_t)
return work
def itest_optic_flow(fwp, tvars):
"""Test optic calculations."""
if tvars.paral_kgb == 1:
pytest.xfail(
"Optic flow with paral_kgb==1 is expected to fail (implementation problem)"
)
"""
0.002 ! Value of the smearing factor, in Hartree
0.0003 0.3 ! Difference between frequency values (in Hartree), and maximum frequency ( 1 Ha is about 27.211 eV)
0.000 ! Scissor shift if needed, in Hartree
0.002 ! Tolerance on closeness of singularities (in Hartree)
1 ! Number of components of linear optic tensor to be computed
11 ! Linear coefficients to be computed (x=1, y=2, z=3)
2 ! Number of components of nonlinear optic tensor to be computed
123 222 ! Non-linear coefficients to be computed
"""
optic_input = abilab.OpticInput(
broadening=0.002,
domega=0.0003,
maxomega=0.3,
scissor=0.000,
tolerance=0.002,
num_lin_comp=1,
lin_comp=11,
num_nonlin_comp=2,
nonlin_comp=(123, 222),
)
print(optic_input)
#raise ValueError()
scf_inp, nscf_inp, ddk1, ddk2, ddk3 = make_inputs(tvars)
flow = abilab.Flow(fwp.workdir, manager=fwp.manager)
bands_work = abilab.BandStructureWork(scf_inp, nscf_inp)
flow.register_work(bands_work)
# work with DDK tasks.
ddk_work = abilab.Work()
for inp in [ddk1, ddk2, ddk3]:
ddk_work.register_ddk_task(inp, deps={bands_work.nscf_task: "WFK"})
flow.register_work(ddk_work)
flow.allocate()
flow.build_and_pickle_dump(abivalidate=True)
# Run the tasks
for task in flow.iflat_tasks():
task.start_and_wait()
assert task.status == task.S_DONE
flow.check_status()
assert flow.all_ok
# Optic does not support MPI with ncores > 1 hence we have to construct a manager with mpi_procs==1
shell_manager = fwp.manager.to_shell_manager(mpi_procs=1)
# Build optic task and register it
optic_task1 = abilab.OpticTask(optic_input,
nscf_node=bands_work.nscf_task,
ddk_nodes=ddk_work,
manager=shell_manager)
flow.register_task(optic_task1)
flow.allocate()
flow.build_and_pickle_dump(abivalidate=True)
optic_task1.start_and_wait()
assert optic_task1.status == optic_task1.S_DONE
# Now we do a similar calculation but the dependencies are represented by
# strings with the path to the input files instead of task objects.
ddk_nodes = [task.outdir.has_abiext("1WF") for task in ddk_work]
#ddk_nodes = [task.outdir.has_abiext("DDK") for task in ddk_work]
print("ddk_nodes:", ddk_nodes)
assert all(ddk_nodes)
#nscf_node = bands_work.nscf_task
nscf_node = bands_work.nscf_task.outdir.has_abiext("WFK")
assert nscf_node
# This does not work yet
optic_task2 = abilab.OpticTask(optic_input,
nscf_node=nscf_node,
ddk_nodes=ddk_nodes)
flow.register_task(optic_task2)
flow.allocate()
flow.build_and_pickle_dump(abivalidate=True)
assert len(flow) == 4
optic_task2.start_and_wait()
assert optic_task2.status == optic_task2.S_DONE
flow.check_status()
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
#assert flow.validate_json_schema()
# Test get_results
optic_task2.get_results()