def build_flow(options):
gs_inp, ph_inp = make_inputs()
flow = BenchmarkFlow(workdir=options.get_workdir(__file__),
remove=options.remove)
gs_work = abilab.Work()
gs_work.register_scf_task(gs_inp)
flow.register_work(gs_work)
flow.exclude_from_benchmark(gs_work)
# Get the list of possible parallel configurations from abinit autoparal.
max_ncpus, min_eff = options.max_ncpus, options.min_eff
print("Getting all autoparal confs up to max_ncpus: ", max_ncpus,
" with efficiency >= ", min_eff)
pconfs = ph_inp.abiget_autoparal_pconfs(max_ncpus, autoparal=1)
print(pconfs)
work = abilab.Work()
for conf, omp_threads in product(pconfs, options.omp_list):
if not options.accept_conf(conf, omp_threads): continue
manager = options.manager.new_with_fixed_mpi_omp(
conf.mpi_procs, omp_threads)
inp = ph_inp.new_with_vars(conf.vars)
work.register_phonon_task(inp,
manager=manager,
deps={gs_work[0]: "WFK"})
print("Found %d configurations" % len(work))
flow.register_work(work)
return flow.allocate()
def build_flow(options):
gs_inp, nscf_inp, ddk_inp = make_inputs()
flow = BenchmarkFlow(workdir=options.get_workdir(__file__), remove=options.remove)
ebands_work = flowtk.BandStructureWork(gs_inp, nscf_inp)
flow.register_work(ebands_work)
flow.exclude_from_benchmark(ebands_work)
# Get the list of possible parallel configurations from abinit autoparal.
max_ncpus, min_eff = options.max_ncpus, options.min_eff
print("Getting all autoparal confs up to max_ncpus: ",max_ncpus," with efficiency >= ",min_eff)
pconfs = ddk_inp.abiget_autoparal_pconfs(max_ncpus, autoparal=1)
if options.verbose: print(pconfs)
work = flowtk.Work()
for conf, omp_threads in product(pconfs, options.omp_list):
mpi_procs = conf.mpi_ncpus
if not options.accept_conf(conf, omp_threads): continue
manager = options.manager.new_with_fixed_mpi_omp(mpi_procs, omp_threads)
inp = ddk_inp.new_with_vars(conf.vars)
work.register_ddk_task(inp, manager=manager, deps={ebands_work[1]: "WFK"})
print("Found %d configurations" % len(work))
flow.register_work(work)
return flow.allocate()
def build_flow(options):
"""
Build an `AbinitWorkflow` used for benchmarking ABINIT.
"""
gs_inp, bse_inp = make_inputs(paw=options.paw)
flow = BenchmarkFlow(workdir=options.get_workdir(__file__),
remove=options.remove)
gs_work = flowtk.Work()
gs_work.register_scf_task(gs_inp)
flow.register_work(gs_work)
flow.exclude_from_benchmark(gs_work)
mpi_list = options.mpi_list
if options.mpi_list is None:
nkpt = len(gs_inp.abiget_ibz().points)
ntrans = (2 * 2 * nkpt)**2
mpi_list = [p for p in range(1, 1 + ntrans) if ntrans % p == 0]
if options.verbose: print("Using mpi_list:", mpi_list)
bse_work = flowtk.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)
bse_work.register_bse_task(bse_inp,
manager=manager,
deps={gs_work[0]: "WFK"})
flow.register_work(bse_work)
return flow.allocate()
def build_flow(options):
"""
Build an `AbinitWorkflow` used for benchmarking ABINIT.
"""
gs_inp, nscf_inp, scr_inp = make_inputs(paw=options.paw)
flow = BenchmarkFlow(workdir=options.get_workdir(__file__), remove=options.remove)
bands = flowtk.BandStructureWork(gs_inp, nscf_inp)
flow.register_work(bands)
flow.exclude_from_benchmark(bands)
#for nband in [200, 400, 600]:
for nband in [600]:
scr_work = flowtk.Work()
inp = scr_inp.new_with_vars(nband=nband)
mpi_list = options.mpi_list
if mpi_list is None:
# Cannot call autoparal here because we need a WFK file.
print("Using hard coded values for mpi_list")
mpi_list = [np for np in range(1, nband+1) if abs((nband - 4) % np) < 1]
if options.verbose: print("Using nband %d and mpi_list: %s" % (nband, mpi_list))
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)
scr_work.register_scr_task(inp, manager=manager, deps={bands.nscf_task: "WFK"})
flow.register_work(scr_work)
return flow.allocate()
def build_flow(options):
"""
Build an `AbinitWorkflow` used for benchmarking ABINIT.
"""
gs_inp, nscf_inp, scr_inp = make_inputs(paw=options.paw)
flow = BenchmarkFlow(workdir=options.get_workdir(__file__), remove=options.remove)
bands = flowtk.BandStructureWork(gs_inp, nscf_inp)
flow.register_work(bands)
flow.exclude_from_benchmark(bands)
#for nband in [200, 400, 600]:
for nband in [600]:
scr_work = flowtk.Work()
inp = scr_inp.new_with_vars(nband=nband)
mpi_list = options.mpi_list
if mpi_list is None:
# Cannot call autoparal here because we need a WFK file.
print("Using hard coded values for mpi_list")
mpi_list = [np for np in range(1, nband+1) if abs((nband - 4) % np) < 1]
if options.verbose: print("Using nband %d and mpi_list: %s" % (nband, mpi_list))
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)
scr_work.register_scr_task(inp, manager=manager, deps={bands.nscf_task: "WFK"})
flow.register_work(scr_work)
return flow.allocate()
def build_flow(options):
"""
Build an `AbinitWorkflow` used for benchmarking ABINIT.
"""
gs_inp, bse_inp = make_inputs(paw=options.paw)
flow = BenchmarkFlow(workdir=options.get_workdir(__file__), remove=options.remove)
gs_work = flowtk.Work()
gs_work.register_scf_task(gs_inp)
flow.register_work(gs_work)
flow.exclude_from_benchmark(gs_work)
mpi_list = options.mpi_list
if options.mpi_list is None:
nkpt = len(gs_inp.abiget_ibz().points)
ntrans = (2*2*nkpt)**2
mpi_list = [p for p in range(1, 1 + ntrans) if ntrans % p == 0]
if options.verbose: print("Using mpi_list:", mpi_list)
bse_work = flowtk.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)
bse_work.register_bse_task(bse_inp, manager=manager, deps={gs_work[0]: "WFK"})
flow.register_work(bse_work)
return flow.allocate()
def build_flow(options):
gs_inp, ph_inp = make_inputs()
flow = BenchmarkFlow(workdir=options.get_workdir(__file__), remove=options.remove)
gs_work = flowtk.Work()
gs_work.register_scf_task(gs_inp)
flow.register_work(gs_work)
flow.exclude_from_benchmark(gs_work)
# Get the list of possible parallel configurations from abinit autoparal.
max_ncpus, min_eff = options.max_ncpus, options.min_eff
print("Getting all autoparal confs up to max_ncpus:", max_ncpus, "with efficiency >=", min_eff)
pconfs = ph_inp.abiget_autoparal_pconfs(max_ncpus, autoparal=1)
if options.verbose: print(pconfs)
omp_threads = 1
work = flowtk.Work()
for conf in pconfs:
mpi_procs = conf.mpi_ncpus
if not options.accept_mpi_omp(mpi_procs, omp_threads): continue
if min_eff is not None and conf.efficiency < min_eff: continue
if options.verbose: print(conf)
manager = options.manager.new_with_fixed_mpi_omp(mpi_procs, omp_threads)
inp = ph_inp.new_with_vars(conf.vars)
work.register_phonon_task(inp, manager=manager, deps={gs_work[0]: "WFK"})
print("Found %d configurations" % len(work))
flow.register_work(work)
return flow.allocate()
def make_base_flow(options):
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]])
paral_kgb = 1
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 = BenchmarkFlow(workdir=options.get_workdir(__file__),
remove=options.manager)
bands_work = flowtk.BandStructureWork(scf_inp, nscf_inp)
flow.register_work(bands_work)
flow.exclude_from_benchmark(bands_work)
ddk_work = flowtk.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.exclude_from_benchmark(ddk_work)
return flow
def make_base_flow(options):
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]]
)
paral_kgb = 1
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 = BenchmarkFlow(workdir=options.get_workdir(__file__), remove=options.manager)
bands_work = flowtk.BandStructureWork(scf_inp, nscf_inp)
flow.register_work(bands_work)
flow.exclude_from_benchmark(bands_work)
ddk_work = flowtk.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.exclude_from_benchmark(ddk_work)
return flow
def make_flow_ephinp(options):
# Preparatory run for E-PH calculations.
# The sequence of datasets makes the ground states and
# all of the independent perturbations of the single Al atom
# for the irreducible qpoints in a 4x4x4 grid.
# Note that the q-point grid must be a sub-grid of the k-point grid (here 8x8x8)
pseudos = abidata.pseudos("Al.oncvpsp") if not options.paw else \
abidata.pseudos("Al.GGA_PBE-JTH-paw.xml")
structure = abilab.Structure.from_abivars(
acell=3*[7.5],
rprim=[0.0, 0.5, 0.5,
0.5, 0.0, 0.5,
0.5, 0.5, 0.0],
typat=1,
xred=[0.0, 0.0, 0.0],
ntypat=1,
znucl=13,
)
gs_inp = abilab.AbinitInput(structure, pseudos)
gs_inp.set_vars(
nsppol=1,
prtpot=1,
istwfk="*1",
ecut=12.0,
nband=5,
occopt=7, # include metallic occupation function with a small smearing
tsmear=0.04,
tolvrs=1e-7,
timopt=-1,
)
# The kpoint grid is minimalistic to keep the calculation manageable.
gs_inp.set_kmesh(
ngkpt=[8, 8, 8],
kptopt=3,
shiftk=[0.0, 0.0, 0.0],
)
# Phonon calculation with 4x4x4
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,
2.50000000e-01, 2.50000000e-01, 0.00000000e+00,
5.00000000e-01, 2.50000000e-01, 0.00000000e+00,
-2.50000000e-01, 2.50000000e-01, 0.00000000e+00,
5.00000000e-01, 5.00000000e-01, 0.00000000e+00,
-2.50000000e-01, 5.00000000e-01, 2.50000000e-01,
], (-1,3))
flow = BenchmarkFlow(workdir=options.get_workdir(__file__), remove=options.remove)
work0 = flow.register_task(gs_inp, task_class=abilab.ScfTask)
flow.exclude_from_benchmark(work0)
ph_work = abilab.PhononWork.from_scf_task(work0[0], qpoints)
flow.register_work(ph_work)
flow.exclude_from_benchmark(ph_work)
# Build input file for E-PH run.
eph_inp = gs_inp.new_with_vars(
optdriver=7,
#ddb_ngqpt=[1, 1, 1], # q-mesh used to produce the DDB file (must be consisten with DDB data)
ddb_ngqpt=[4, 4, 4], # q-mesh used to produce the DDB file (must be consisten with DDB data)
eph_intmeth=2, # Tetra
eph_fsewin="0.8 eV", # Energy window around Ef
eph_mustar=0.12, # mustar parameter
# q-path for phonons and phonon linewidths.
ph_ndivsm=20,
ph_nqpath=3,
ph_qpath= [
0 , 0 , 0,
0.5, 0 , 0,
0.5, 0.5, 0,],
# phonon DOS obtained via Fourier interpolation
ph_intmeth=2, # Tetra for phonon DOS and A2F
ph_smear="0.001 eV",
ph_wstep="0.0001 eV",
ph_ngqpt=[16, 16, 16], # q-mesh for Fourier interpolatation of IFC and a2F(w)
ph_nqshift=1,
ph_qshift=[0, 0, 0],
)
return flow, eph_inp
