def make_electronic_structure_flow(ngkpts_for_dos=((2, 2, 2), (4, 4, 4),
(6, 6, 6), (8, 8, 8))):
"""Band structure calculation."""
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
pseudos=abidata.pseudos("14si.pspnc"),
ndtset=2 + len(ngkpts_for_dos))
# Global variables
multi.set_vars(ecut=10)
# Dataset 1
multi[0].set_vars(tolvrs=1e-9)
multi[0].set_kmesh(ngkpt=[4, 4, 4], shiftk=[0, 0, 0])
# Dataset 2
multi[1].set_vars(tolwfr=1e-15)
multi[1].set_kpath(ndivsm=5)
# Dataset 3
for i, ngkpt in enumerate(ngkpts_for_dos):
multi[2 + i].set_vars(tolwfr=1e-15)
multi[2 + i].set_kmesh(ngkpt=ngkpt, shiftk=[0, 0, 0])
inputs = multi.split_datasets()
scf_input, nscf_input, dos_input = inputs[0], inputs[1], inputs[2:]
return flowtk.bandstructure_flow(workdir="flow_dos_bands",
scf_input=scf_input,
nscf_input=nscf_input,
dos_inputs=dos_input)
def build_ebands_flow(options):
"""
Band structure calculation.
First, a SCF density computation, then a non-SCF band structure calculation.
Similar to tbase3_5.in
"""
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
pseudos=abidata.pseudos("14si.pspnc"),
ndtset=2)
# Global variables
shiftk = [
float(s)
for s in "0.5 0.5 0.5 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5".split()
]
multi.set_vars(ecut=8, diemac=12, iomode=3)
# Dataset 1
multi[0].set_vars(tolvrs=1e-9)
multi[0].set_kmesh(ngkpt=[4, 4, 4], shiftk=shiftk)
# Dataset 2
multi[1].set_vars(tolwfr=1e-15)
multi[1].set_kpath(ndivsm=5)
scf_input, nscf_input = multi.split_datasets()
workdir = options.workdir if (options
and options.workdir) else "flow_base3_ebands"
return flowtk.bandstructure_flow(workdir,
scf_input=scf_input,
nscf_input=nscf_input)
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
if os.getenv("READTHEDOCS", False):
__file__ = os.path.join(os.getcwd(), "run_mgb2_edoses.py")
options.workdir = os.path.basename(__file__).replace(
".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
nval = structure.num_valence_electrons(pseudos)
#print(nval)
inputs = make_scf_nscf_inputs(structure, pseudos)
scf_input, nscf_input, dos_inputs = inputs[0], inputs[1], inputs[2:]
return flowtk.bandstructure_flow(options.workdir,
scf_input,
nscf_input,
dos_inputs=dos_inputs,
manager=options.manager)
def run_flow(options):
"""Run test flow, return exit code."""
import tempfile
workdir = tempfile.mkdtemp(dir=options.flow_dir)
cprint("Running small flow in workdir: %s" % workdir, "yellow")
print()
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
# Build the flow.
flow = flowtk.bandstructure_flow(workdir,
scf_input,
nscf_input,
manager=None)
flow.build_and_pickle_dump()
scheduler = flow.make_scheduler()
retcode = scheduler.start()
if retcode != 0:
cprint("Scheduler returned retcode %s" % retcode, "red")
return retcode
flow.show_status()
if not flow.all_ok:
cprint("Not all tasks in flow reached all_ok", "red")
retcode = 1
return retcode
def itest_bandstructure_schedflow(fwp, tvars):
"""
Testing bandstructure flow with the scheduler.
"""
#print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(
tvars, pp_paths="Si.GGA_PBE-JTH-paw.xml")
# Build the flow and create the database.
flow = flowtk.bandstructure_flow(fwp.workdir,
scf_input,
nscf_input,
manager=fwp.manager)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
#print(fwp.scheduler)
# scheduler cannot handle more than one flow.
with pytest.raises(fwp.scheduler.Error):
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 2
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
for task in flow[0]:
assert not task.outdir.has_abiext("WFK")
# Test if GSR files are produced and are readable.
for i, task in enumerate(flow[0]):
with task.open_gsr() as gsr:
assert gsr.nsppol == 1
assert gsr.to_string(verbose=2)
#assert gsr.structure == structure
# TODO: This does not work yet because GSR files do not contain
# enough info to understand if we have a path or a mesh.
if i == 0:
# DOS case
assert gsr.ebands.has_bzmesh
assert not gsr.ebands.has_bzpath
edos = gsr.ebands.get_edos()
assert abs(edos.tot_idos.values[-1] - edos.nelect) < 1e-3
if i == 1:
# Bandstructure case
assert gsr.ebands.has_bzpath
assert not gsr.ebands.has_bzmesh
with pytest.raises(ValueError):
gsr.ebands.get_edos()
def itest_bandstructure_schedflow(fwp, tvars):
"""
Testing bandstructure flow with the scheduler.
"""
#print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="Si.GGA_PBE-JTH-paw.xml")
# Build the flow and create the database.
flow = flowtk.bandstructure_flow(fwp.workdir, scf_input, nscf_input, manager=fwp.manager)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
#print(fwp.scheduler)
# scheduler cannot handle more than one flow.
with pytest.raises(fwp.scheduler.Error):
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 2
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
for task in flow[0]:
assert not task.outdir.has_abiext("WFK")
# Test if GSR files are produced and are readable.
for i, task in enumerate(flow[0]):
with task.open_gsr() as gsr:
assert gsr.nsppol == 1
assert gsr.to_string(verbose=2)
#assert gsr.structure == structure
# TODO: This does not work yet because GSR files do not contain
# enough info to understand if we have a path or a mesh.
if i == 0:
# DOS case
assert gsr.ebands.has_bzmesh
assert not gsr.ebands.has_bzpath
edos = gsr.ebands.get_edos()
assert abs(edos.tot_idos.values[-1] - edos.nelect) < 1e-3
if i == 1:
# Bandstructure case
assert gsr.ebands.has_bzpath
assert not gsr.ebands.has_bzmesh
with pytest.raises(ValueError):
gsr.ebands.get_edos()
def build_flow(options):
# Set working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
# Build the flow.
return flowtk.bandstructure_flow(options.workdir, scf_input, nscf_input, manager=options.manager)
def build_flow(options):
# Set working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
# Build the flow.
return flowtk.bandstructure_flow(options.workdir, scf_input, nscf_input, manager=options.manager)
def test_with_flow(self):
"""Testing abirun.py commands with flow (no execution)"""
env = self.get_env(check_help_version=False)
no_logo_colors = ["--no-logo", "--no-colors"]
# Build a flow.
flowdir = env.base_path
scf_input, nscf_input = make_scf_nscf_inputs()
flow = flowtk.bandstructure_flow(flowdir,
scf_input,
nscf_input,
manager=None)
flow.build_and_pickle_dump()
# Test abirun commands requiring a flow (no submission)
for command in [
"status",
"debug",
"debug_reset",
"deps",
"inputs",
"corrections",
"events",
"history",
"handlers",
"cancel",
"tail",
"inspect",
"structures",
"ebands",
"hist",
"cycles",
"dims",
"tricky",
]:
r = env.run(self.script,
flowdir,
command,
self.loglevel,
self.verbose,
*no_logo_colors,
expect_stderr=self.expect_stderr)
assert r.returncode == 0
r = env.run(self.script,
flowdir,
"abivars",
"-vn",
"ecut,nband",
self.loglevel,
self.verbose,
*no_logo_colors,
expect_stderr=self.expect_stderr)
assert r.returncode == 0
def build_flow(options):
# Set working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
if os.getenv("READTHEDOCS", False):
__file__ = os.path.join(os.getcwd(), "run_si_ebands.py")
options.workdir = os.path.basename(__file__).replace(
".py", "").replace("run_", "flow_")
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
# Build the flow.
return flowtk.bandstructure_flow(options.workdir,
scf_input,
nscf_input,
manager=options.manager)
def itest_bandstructure_schedflow(fwp, tvars):
"""
Testing bandstructure flow with the scheduler.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(
tvars, pp_paths="Si.GGA_PBE-JTH-paw.xml")
# Build the flow and create the database.
flow = flowtk.bandstructure_flow(fwp.workdir,
scf_input,
nscf_input,
manager=fwp.manager)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
print(fwp.scheduler)
# scheduler cannot handle more than one flow.
with pytest.raises(fwp.scheduler.Error):
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 2
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
for task in flow[0]:
assert not task.outdir.has_abiext("WFK")
# Test if GSR files are produced and are readable.
for i, task in enumerate(flow[0]):
with task.open_gsr() as gsr:
print(gsr)
assert gsr.nsppol == 1
#assert gsr.structure == structure
ebands = gsr.ebands
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
nval = structure.num_valence_electrons(pseudos)
#print(nval)
inputs = make_scf_nscf_inputs(structure, pseudos)
scf_input, nscf_input, dos_inputs = inputs[0], inputs[1], inputs[2:]
return flowtk.bandstructure_flow(options.workdir, scf_input, nscf_input,
dos_inputs=dos_inputs, manager=options.manager)
def make_ebands_flow():
"""Band structure calculation."""
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
pseudos=abidata.pseudos("14si.pspnc"),
ndtset=2)
# Global variables
multi.set_vars(ecut=10)
# Dataset 1
multi[0].set_vars(tolvrs=1e-9)
multi[0].set_kmesh(ngkpt=[4, 4, 4], shiftk=[0, 0, 0])
# Dataset 2
multi[1].set_vars(tolwfr=1e-15)
multi[1].set_kpath(ndivsm=5)
scf_input, nscf_input = multi.split_datasets()
return flowtk.bandstructure_flow(workdir="flow_base3_ebands",
scf_input=scf_input,
nscf_input=nscf_input)
def test_with_flow(self):
"""Testing abirun.py commands with flow (no execution)"""
env = self.get_env(check_help_version=False)
no_logo_colors = ["--no-logo", "--no-colors"]
# Build a flow.
flowdir = env.base_path
scf_input, nscf_input = make_scf_nscf_inputs()
flow = flowtk.bandstructure_flow(flowdir, scf_input, nscf_input, manager=None)
flow.build_and_pickle_dump()
# Test abirun commands requiring a flow (no submission)
for command in ["status", "debug", "debug_reset", "deps", "inputs", "corrections", "events",
"history", "handlers", "cancel", "tail", "inspect", "structures", "ebands", "hist",
"cycles", "dims", "tricky",]:
r = env.run(self.script, flowdir, command, self.loglevel, self.verbose, *no_logo_colors,
expect_stderr=self.expect_stderr)
assert r.returncode == 0
r = env.run(self.script, flowdir, "abivars", "-vn", "ecut,nband", self.loglevel, self.verbose, *no_logo_colors,
expect_stderr=self.expect_stderr)
assert r.returncode == 0
def itest_bandstructure_flow(fwp, tvars):
"""
Testing band-structure flow with one dependency: SCF -> NSCF.
"""
#print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc")
# Build the flow and create the database.
flow = flowtk.bandstructure_flow(fwp.workdir, scf_input, nscf_input, manager=fwp.manager)
flow.build_and_pickle_dump(abivalidate=True)
t0 = flow[0][0]
t1 = flow[0][1]
# Test initialization status, task properties and links (t1 requires t0)
assert t0.status == t0.S_INIT
assert t1.status == t1.S_INIT
assert t0.can_run
assert not t1.can_run
assert t1.depends_on(t0)
assert not t1.depends_on(t1)
assert t0.isnc
assert not t0.ispaw
# Flow properties and methods
assert flow.num_tasks == 2
assert not flow.all_ok
assert flow.ncores_reserved == 0
assert flow.ncores_allocated == 0
assert flow.ncores_used == 0
flow.check_dependencies()
flow.show_status()
flow.show_receivers()
# Run t0, and check status
assert t0.returncode == 0
t0.start_and_wait()
assert t0.returncode == 0
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert t1.can_run
# Cannot start t0 twice...
with pytest.raises(t0.Error):
t0.start()
# But we can restart it.
fired = t0.restart()
assert fired
t0.wait()
assert t0.num_restarts == 1
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert not t0.can_run
# Now we can run t1.
t1.start_and_wait()
assert t1.status == t0.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
assert not t1.can_run
# FIXME This one does not work yet
#fired = t1.restart()
#atrue(fired)
#t1.wait()
#aequal(t1.num_restarts, 1)
#aequal(t1.status, t1.S_DONE)
#t1.check_status()
#aequal(t1.status, t1.S_OK)
#afalse(t1.can_run)
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
for task in flow.iflat_tasks():
assert len(task.outdir.list_filepaths(wildcard="*GSR.nc")) == 1
# Test GSR robot
with abilab.Robot.from_flow(flow, ext="GSR") as robot:
table = robot.get_dataframe()
assert table is not None
#print(table)
# Test AbinitTimer.
timer = t0.parse_timing()
assert str(timer)
if has_matplotlib():
assert timer.plot_pie(show=False)
assert timer.plot_stacked_hist(show=False)
assert timer.plot_efficiency(show=False)
# Test CUT3D API provided by DensityFortranFile.
den_path = t0.outdir.has_abiext("DEN")
assert den_path
if not den_path.endswith(".nc"):
denfile = abilab.DensityFortranFile(den_path)
str(denfile)
workdir = flow.outdir.path
denfile.get_cube("den.cube", workdir=workdir)
denfile.get_xsf("den.xsf", workdir=workdir)
denfile.get_tecplot("den.tecplot", workdir=workdir)
denfile.get_molekel("den.molekel", workdir=workdir)
denfile.get_3d_indexed("den.data_indexed", workdir=workdir)
denfile.get_3d_formatted("den.data_formatted", workdir=workdir)
ae_path = os.path.join(abidata.pseudo_dir, "0.14-Si.8.density.AE")
hc = denfile.get_hirshfeld(scf_input.structure, all_el_dens_paths=[ae_path] * 2)
assert np.abs(hc.net_charges[0]) < 0.1
# This feature requires Abinit 8.5.2
if flow.manager.abinit_build.version_ge("8.5.2"):
den = denfile.get_density(workdir=workdir)
assert den.structure is not None and hasattr(den, "datar")
def itest_unconverged_scf(fwp, tvars):
"""Testing the treatment of unconverged GS calculations."""
#print("tvars:\n %s" % str(tvars))
# Build the SCF and the NSCF input (note nstep to have an unconverged run)
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc", nstep=1)
# Build the flow and create the database.
flow = flowtk.bandstructure_flow(fwp.workdir, scf_input, nscf_input, manager=fwp.manager)
flow.allocate()
# Use smart-io
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
t0 = flow[0][0]
t1 = flow[0][1]
assert t0.uses_paral_kgb(tvars.paral_kgb)
assert t1.uses_paral_kgb(tvars.paral_kgb)
# This run should not converge.
t0.start_and_wait()
t0.check_status()
assert t0.status == t0.S_UNCONVERGED
# Unconverged with smart-io --> WFK must be there
assert t0.outdir.has_abiext("WFK")
# Remove nstep from the input so that we use the default value.
# Then restart the GS task and test that GS is OK.
assert not t1.can_run
t0.input.pop("nstep")
assert t0.num_restarts == 0
t0.restart()
t0.wait()
assert t0.num_restarts == 1
t0.check_status()
assert t0.status == t1.S_OK
# Converged with smart-io --> WFK is not written
assert not t0.outdir.has_abiext("WFK")
# Now we can start the NSCF step
assert t1.can_run
t1.start_and_wait()
t1.check_status()
assert t1.status == t0.S_UNCONVERGED
assert not flow.all_ok
# Restart (same trick as the one used for the GS run)
t1.input.pop("nstep")
assert t1.num_restarts == 0
assert t1.restart()
t1.wait()
assert t1.num_restarts == 1
assert t1.status == t1.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
flow.show_status()
assert flow.all_ok
# Test inspect methods
if has_matplotlib():
assert t0.inspect(show=False)
# Test get_results
t0.get_results()
t1.get_results()
# Build tarball file.
tarfile = flow.make_tarfile()
# Test reset_from_scratch
t0.reset_from_scratch()
assert t0.status == t0.S_READY
# Datetime counters shouls be set to None
# FIXME: This does not work
#dt = t0.datetimes
#assert (dt.submission, dt.start, dt.end) == (None, None, None)
t0.start_and_wait()
t0.reset_from_scratch()
def itest_unconverged_scf(fwp, tvars):
"""Testing the treatment of unconverged GS calculations."""
print("tvars:\n %s" % str(tvars))
# Build the SCF and the NSCF input (note nstep to have an unconverged run)
scf_input, nscf_input = make_scf_nscf_inputs(tvars,
pp_paths="14si.pspnc",
nstep=1)
# Build the flow and create the database.
flow = flowtk.bandstructure_flow(fwp.workdir,
scf_input,
nscf_input,
manager=fwp.manager)
flow.allocate()
# Use smart-io
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
t0 = flow[0][0]
t1 = flow[0][1]
assert t0.uses_paral_kgb(tvars.paral_kgb)
assert t1.uses_paral_kgb(tvars.paral_kgb)
# This run should not converge.
t0.start_and_wait()
t0.check_status()
assert t0.status == t0.S_UNCONVERGED
# Unconverged with smart-io --> WFK must be there
assert t0.outdir.has_abiext("WFK")
#assert 0
# Remove nstep from the input so that we use the default value.
# Then restart the GS task and test that GS is OK.
assert not t1.can_run
t0.input.pop("nstep")
assert t0.num_restarts == 0
t0.restart()
t0.wait()
assert t0.num_restarts == 1
t0.check_status()
assert t0.status == t1.S_OK
# Converged with smart-io --> WFK is not written
assert not t0.outdir.has_abiext("WFK")
# Now we can start the NSCF step
assert t1.can_run
t1.start_and_wait()
t1.check_status()
assert t1.status == t0.S_UNCONVERGED
assert not flow.all_ok
# Restart (same trick as the one used for the GS run)
t1.input.pop("nstep")
assert t1.num_restarts == 0
assert t1.restart()
t1.wait()
assert t1.num_restarts == 1
assert t1.status == t1.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
flow.show_status()
assert flow.all_ok
# Test inspect methods
if has_matplotlib():
t0.inspect(show=False)
# Test get_results
t0.get_results()
t1.get_results()
# Build tarball file.
tarfile = flow.make_tarfile()
#assert flow.validate_json_schema()
# Test reset_from_scratch
t0.reset_from_scratch()
assert t0.status == t0.S_READY
# Datetime counters shouls be set to None
# FIXME: This does not work
#dt = t0.datetimes
#assert (dt.submission, dt.start, dt.end) == (None, None, None)
t0.start_and_wait()
t0.reset_from_scratch()
def itest_bandstructure_flow(fwp, tvars):
"""
Testing band-structure flow with one dependency: SCF -> NSCF.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc")
# Build the flow and create the database.
flow = flowtk.bandstructure_flow(fwp.workdir,
scf_input,
nscf_input,
manager=fwp.manager)
flow.build_and_pickle_dump(abivalidate=True)
t0 = flow[0][0]
t1 = flow[0][1]
# Test initialization status, task properties and links (t1 requires t0)
assert t0.status == t0.S_INIT
assert t1.status == t1.S_INIT
assert t0.can_run
assert not t1.can_run
assert t1.depends_on(t0)
assert not t1.depends_on(t1)
assert t0.isnc
assert not t0.ispaw
# Flow properties and methods
assert flow.num_tasks == 2
assert not flow.all_ok
assert flow.ncores_reserved == 0
assert flow.ncores_allocated == 0
assert flow.ncores_used == 0
flow.check_dependencies()
flow.show_status()
flow.show_receivers()
# Run t0, and check status
assert t0.returncode == 0
t0.start_and_wait()
assert t0.returncode == 0
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert t1.can_run
# Cannot start t0 twice...
with pytest.raises(t0.Error):
t0.start()
# But we can restart it.
fired = t0.restart()
assert fired
t0.wait()
assert t0.num_restarts == 1
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert not t0.can_run
# Now we can run t1.
t1.start_and_wait()
assert t1.status == t0.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
assert not t1.can_run
# This one does not work yet
#fired = t1.restart()
#atrue(fired)
#t1.wait()
#aequal(t1.num_restarts, 1)
#aequal(t1.status, t1.S_DONE)
#t1.check_status()
#aequal(t1.status, t1.S_OK)
#afalse(t1.can_run)
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
for task in flow.iflat_tasks():
assert len(task.outdir.list_filepaths(wildcard="*GSR.nc")) == 1
# Test GSR robot
with abilab.abirobot(flow, "GSR") as robot:
table = robot.get_dataframe()
assert table is not None
print(table)
# Test AbinitTimer.
timer = t0.parse_timing()
print(timer)
if has_matplotlib():
timer.plot_pie(show=False)
timer.plot_stacked_hist(show=False)
timer.plot_efficiency(show=False)
# Test CUT3D API provided by DensityFortranFile.
den_path = t0.outdir.has_abiext("DEN")
assert den_path
if not den_path.endswith(".nc"):
denfile = abilab.DensityFortranFile(den_path)
workdir = flow.outdir.path
denfile.get_cube("den.cube", workdir=workdir)
denfile.get_xsf("den.xsf", workdir=workdir)
denfile.get_tecplot("den.tecplot", workdir=workdir)
denfile.get_molekel("den.molekel", workdir=workdir)
denfile.get_3d_indexed("den.data_indexed", workdir=workdir)
denfile.get_3d_formatted("den.data_formatted", workdir=workdir)
def itest_bandstructure_flow(fwp, tvars):
"""
Testing band-structure flow with one dependency: SCF -> NSCF.
"""
#print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc")
# Build the flow and create the database.
flow = flowtk.bandstructure_flow(fwp.workdir,
scf_input,
nscf_input,
manager=fwp.manager)
flow.build_and_pickle_dump(abivalidate=True)
t0 = flow[0][0]
t1 = flow[0][1]
# Test initialization status, task properties and links (t1 requires t0)
assert t0.status == t0.S_INIT
assert t1.status == t1.S_INIT
assert t0.can_run
assert not t1.can_run
assert t1.depends_on(t0)
assert not t1.depends_on(t1)
assert t0.isnc
assert not t0.ispaw
# Flow properties and methods
assert flow.num_tasks == 2
assert not flow.all_ok
assert flow.ncores_reserved == 0
assert flow.ncores_allocated == 0
assert flow.ncores_used == 0
flow.check_dependencies()
flow.show_status()
flow.show_receivers()
# Run t0, and check status
assert t0.returncode == 0
t0.start_and_wait()
assert t0.returncode == 0
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert t1.can_run
# Cannot start t0 twice...
with pytest.raises(t0.Error):
t0.start()
# But we can restart it.
fired = t0.restart()
assert fired
t0.wait()
assert t0.num_restarts == 1
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert not t0.can_run
# Now we can run t1.
t1.start_and_wait()
assert t1.status == t0.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
assert not t1.can_run
# FIXME This one does not work yet
#fired = t1.restart()
#atrue(fired)
#t1.wait()
#aequal(t1.num_restarts, 1)
#aequal(t1.status, t1.S_DONE)
#t1.check_status()
#aequal(t1.status, t1.S_OK)
#afalse(t1.can_run)
flow.show_status()
if not flow.all_ok:
flow.debug()
raise RuntimeError()
assert all(work.finalized for work in flow)
for task in flow.iflat_tasks():
assert len(task.outdir.list_filepaths(wildcard="*GSR.nc")) == 1
# Test GSR robot
with abilab.Robot.from_flow(flow, ext="GSR") as robot:
table = robot.get_dataframe()
assert table is not None
#print(table)
# Test AbinitTimer.
timer = t0.parse_timing()
assert str(timer)
if has_matplotlib():
assert timer.plot_pie(show=False)
assert timer.plot_stacked_hist(show=False)
assert timer.plot_efficiency(show=False)
df, ebands_plotter = flow.compare_ebands(verbose=2,
with_spglib=False,
printout=True,
with_colors=True)
# Test CUT3D API provided by DensityFortranFile.
den_path = t0.outdir.has_abiext("DEN")
assert den_path
if not den_path.endswith(".nc"):
denfile = abilab.DensityFortranFile(den_path)
str(denfile)
workdir = flow.outdir.path
denfile.get_cube("den.cube", workdir=workdir)
denfile.get_xsf("den.xsf", workdir=workdir)
denfile.get_tecplot("den.tecplot", workdir=workdir)
denfile.get_molekel("den.molekel", workdir=workdir)
denfile.get_3d_indexed("den.data_indexed", workdir=workdir)
denfile.get_3d_formatted("den.data_formatted", workdir=workdir)
ae_path = os.path.join(abidata.pseudo_dir, "0.14-Si.8.density.AE")
hc = denfile.get_hirshfeld(scf_input.structure,
all_el_dens_paths=[ae_path] * 2)
assert np.abs(hc.net_charges[0]) < 0.1
# This feature requires Abinit 8.5.2
if flow.manager.abinit_build.version_ge("8.5.2"):
den = denfile.get_density(workdir=workdir)
assert den.structure is not None and hasattr(den, "datar")
df = flow.get_dims_dataframe(printout=False, with_colors=True)
assert "natom" in df
df = flow.compare_abivars(["ecut", "natom"],
printout=True,
with_colors=True)
assert np.all(df["natom"].values == 2)
