def itest_atomic_relaxation(fwp, tvars):
"""Test atomic relaxation with automatic restart."""
# Build the flow
flow = flowtk.Flow(fwp.workdir, manager=fwp.manager)
ion_input = ion_relaxation(tvars, ntime=2)
ion_input["chksymtnons"] = 0
work = flow.register_task(ion_input, task_class=flowtk.RelaxTask)
flow.allocate()
flow.build_and_pickle_dump(abivalidate=True)
# Run t0, and check status
t0 = work[0]
t0.start_and_wait()
assert t0.returncode == 0
t0.check_status()
assert t0.status == t0.S_UNCONVERGED
assert t0.initial_structure == ion_input.structure
unconverged_structure = t0.get_final_structure()
assert unconverged_structure != t0.initial_structure
# Use the default value ntime=50 and we can converge the calculation.
t0.input.set_vars(ntime=50)
t0.build()
assert t0.restart()
t0.wait()
assert t0.num_restarts == 1
# At this point, we should have reached S_OK.
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
final_structure = t0.get_final_structure()
assert final_structure != unconverged_structure
flow.show_status()
assert all(work.finalized for work in flow)
if not flow.all_ok:
flow.debug()
raise RuntimeError()
# post-processing tools
if has_matplotlib():
assert t0.inspect(show=False) is not None
with t0.open_hist() as hist:
hist.to_string(verbose=2)
# from_file accepts HIST files as well.
assert np.all(hist.structures[-1].frac_coords ==
abilab.Structure.from_file(hist.filepath).frac_coords)
with t0.open_gsr() as gsr:
gsr.to_string(verbose=2)
gsr.pressure == 1.8280
t0.get_results()
def itest_atomic_relaxation(fwp, tvars):
"""Test atomic relaxation with automatic restart."""
# Build the flow
flow = flowtk.Flow(fwp.workdir, manager=fwp.manager)
ion_input = ion_relaxation(tvars, ntime=2)
work = flow.register_task(ion_input, task_class=flowtk.RelaxTask)
flow.allocate()
flow.build_and_pickle_dump(abivalidate=True)
# Run t0, and check status
t0 = work[0]
t0.start_and_wait()
assert t0.returncode == 0
t0.check_status()
assert t0.status == t0.S_UNCONVERGED
assert t0.initial_structure == ion_input.structure
unconverged_structure = t0.get_final_structure()
assert unconverged_structure != t0.initial_structure
# Use the default value ntime=50 and we can converge the calculation.
t0.input.set_vars(ntime=50)
t0.build()
assert t0.restart()
t0.wait()
assert t0.num_restarts == 1
# At this point, we should have reached S_OK.
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
final_structure = t0.get_final_structure()
assert final_structure != unconverged_structure
flow.show_status()
assert all(work.finalized for work in flow)
assert flow.all_ok
# post-processing tools
if has_matplotlib():
assert t0.inspect(show=False) is not None
with t0.open_hist() as hist:
hist.to_string(verbose=2)
# from_file accepts HIST files as well.
assert np.all(hist.structures[-1].frac_coords == abilab.Structure.from_file(hist.filepath).frac_coords)
with t0.open_gsr() as gsr:
gsr.to_string(verbose=2)
gsr.pressure == 1.8280
t0.get_results()
def test_psps_nc_silicon(self):
"""Very preliminary test for PSPS.nc file with Ga.oncvpsp"""
pseudo = abidata.pseudo("Ga.oncvpsp")
with pseudo.open_pspsfile(ecut=10) as psps:
print(psps)
r = psps.reader
assert r.usepaw == 0 and r.ntypat == 1
if has_matplotlib():
psps.plot(what="all", show=False)
psps.compare(psps, show=False)
def test_psps_nc_silicon(self):
"""Test PSPS.nc file with Ga.oncvpsp"""
pseudo = abidata.pseudo("Ga.oncvpsp")
with pseudo.open_pspsfile(ecut=10) as psps:
print(psps)
r = psps.reader
assert r.usepaw == 0 and r.ntypat == 1
if has_matplotlib():
psps.plot(what="all", show=False)
psps.compare(psps, show=False)
def itest_phonon_flow(fwp, tvars):
"""
Create an `Abinit` for phonon calculations:
1) One work for the GS run.
2) nqpt works for phonon calculations. Each work contains
nirred tasks where nirred is the number of irreducible phonon perturbations
for that particular q-point.
"""
if tvars.paral_kgb == 1:
pytest.xfail("Phonon flow with paral_kgb==1 is expected to fail (implementation problem)")
all_inps = scf_ph_inputs(tvars)
scf_input, ph_inputs = all_inps[0], all_inps[1:]
flow = abilab.phonon_flow(fwp.workdir, scf_input, ph_inputs, manager=fwp.manager)
flow.build_and_pickle_dump()
t0 = flow[0][0]
t0.start_and_wait()
assert t0.uses_paral_kgb(tvars.paral_kgb)
flow.check_status()
assert t0.status == t0.S_OK
flow.show_status()
for work in flow[1:]:
for task in work:
task.start_and_wait()
assert task.status == t0.S_DONE
flow.check_status(show=True)
# We should have a DDB files with IFC(q) in work.outdir
ddb_files = []
for work in flow[1:]:
ddbs = work.outdir.list_filepaths(wildcard="*DDB")
assert len(ddbs) == 1
ddb_files.append(ddbs[0])
assert all(work.finalized for work in flow)
assert flow.all_ok
# Merge the DDB files
out_ddb = flow.outdir.path_in("flow_DDB")
ddb_path = abilab.Mrgddb().merge(flow.outdir.path, ddb_files, out_ddb=out_ddb,
description="DDB generated by %s" % __file__)
assert ddb_path == out_ddb
# Test PhononTask inspect method
ph_task = flow[1][0]
# paral_kgb does not make sense for DFPT!
assert not ph_task.uses_paral_kgb(tvars.paral_kgb)
if has_matplotlib():
ph_task.inspect(show=False)
# Test get_results
ph_task.get_results()
# Build new work with Anaddb tasks.
# Construct a manager with mpi_procs==1 since anaddb do not support mpi_procs > 1 (except in elphon)
shell_manager = fwp.manager.to_shell_manager(mpi_procs=1)
awork = abilab.Work(manager=shell_manager)
# Phonons bands and DOS with gaussian method
anaddb_input = abilab.AnaddbInput.phbands_and_dos(
scf_input.structure, ngqpt=(4, 4, 4), ndivsm=5, nqsmall=10, dos_method="gaussian: 0.001 eV")
atask = abilab.AnaddbTask(anaddb_input, ddb_node=ddb_path, manager=shell_manager)
awork.register(atask)
# Phonons bands and DOS with tetrahedron method
anaddb_input = abilab.AnaddbInput.phbands_and_dos(
scf_input.structure, ngqpt=(4, 4, 4), ndivsm=5, nqsmall=10, dos_method="tetra")
atask = abilab.AnaddbTask(anaddb_input, ddb_node=ddb_path, manager=shell_manager)
awork.register(atask)
flow.register_work(awork)
flow.allocate()
flow.build()
for i, atask in enumerate(awork):
atask.history.info("about to run anaddb task: %d", i)
atask.start_and_wait()
assert atask.status == atask.S_DONE
atask.check_status()
assert atask.status == atask.S_OK
def itest_phonon_flow(fwp, tvars):
"""
Create a flow for phonon calculations:
1) One work for the GS run.
2) nqpt works for phonon calculations. Each work contains
nirred tasks where nirred is the number of irreducible phonon perturbations
for that particular q-point.
"""
all_inps = scf_ph_inputs(tvars)
scf_input, ph_inputs = all_inps[0], all_inps[1:]
ph_ngqpt = (2, 2, 2)
flow = flowtk.PhononFlow.from_scf_input(fwp.workdir,
scf_input,
ph_ngqpt=ph_ngqpt,
with_becs=False)
scheduler = flow.make_scheduler()
assert scheduler.start() == 0
flow.check_status(show=True)
assert all(work.finalized for work in flow)
if not flow.all_ok:
flow.debug()
raise RuntimeError()
with flow.open_final_ddb() as ddb:
ddb_path = ddb.filepath
ddb.to_string(verbose=2)
assert len(ddb.structure) == 2
#assert ddb.qpoints.frac_coords
# Test PhononTask inspect method
ph_task = flow[1][0]
if has_matplotlib():
assert ph_task.inspect(show=False)
# Test get_results
#ph_task.get_results()
# Build new work with Anaddb tasks.
# Construct a manager with mpi_procs==1 since anaddb do not support mpi_procs > 1 (except in elphon)
shell_manager = fwp.manager.to_shell_manager(mpi_procs=1)
awork = flowtk.Work(manager=shell_manager)
# Phonons bands and DOS with gaussian method
anaddb_input = abilab.AnaddbInput.phbands_and_dos(
scf_input.structure,
ngqpt=ph_ngqpt,
ndivsm=5,
nqsmall=10,
dos_method="gaussian: 0.001 eV")
atask = flowtk.AnaddbTask(anaddb_input,
ddb_node=ddb_path,
manager=shell_manager)
awork.register(atask)
# Phonons bands and DOS with tetrahedron method
anaddb_input = abilab.AnaddbInput.phbands_and_dos(scf_input.structure,
ngqpt=ph_ngqpt,
ndivsm=5,
nqsmall=10,
dos_method="tetra")
atask = flowtk.AnaddbTask(anaddb_input,
ddb_node=ddb_path,
manager=shell_manager)
awork.register(atask)
flow.register_work(awork)
flow.allocate()
flow.build()
for i, atask in enumerate(awork):
atask.history.info("About to run anaddb task: %d", i)
atask.start_and_wait()
assert atask.status == atask.S_DONE
atask.check_status()
assert atask.status == atask.S_OK
# These output files should be produced in the task workdir.
# Actually they should be in outdir but anaddb uses different conventions.
assert len(atask.wdir.list_filepaths(wildcard="*PHBST.nc")) == 1
assert len(atask.wdir.list_filepaths(wildcard="*PHDOS.nc")) == 1
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 = abilab.bandstructure_flow(fwp.workdir, scf_input, nscf_input, manager=fwp.manager)
flow.allocate()
# Use smart-io
flow.use_smartio()
flow.build_and_pickle_dump()
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
dt = t0.datetimes
assert (dt.submission, dt.start, dt.end) == (None, None, None)
t0.start_and_wait()
t0.reset_from_scratch()
# Datetime counters shouls be set to None
dt = t0.datetimes
assert (dt.submission, dt.start, dt.end) == (None, None, None)
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()
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_phonon_flow(fwp, tvars):
"""
Create a flow for phonon calculations:
1) One work for the GS run.
2) nqpt works for phonon calculations. Each work contains
nirred tasks where nirred is the number of irreducible phonon perturbations
for that particular q-point.
"""
all_inps = scf_ph_inputs(tvars)
scf_input, ph_inputs = all_inps[0], all_inps[1:]
ph_ngqpt = (2, 2, 2)
flow = flowtk.PhononFlow.from_scf_input(fwp.workdir, scf_input, ph_ngqpt=ph_ngqpt, with_becs=False)
scheduler = flow.make_scheduler()
assert scheduler.start() == 0
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
with flow.open_final_ddb() as ddb:
ddb_path = ddb.filepath
ddb.to_string(verbose=2)
assert len(ddb.structure) == 2
#assert ddb.qpoints.frac_coords
# Test PhononTask inspect method
ph_task = flow[1][0]
if has_matplotlib():
assert ph_task.inspect(show=False)
# Test get_results
#ph_task.get_results()
# Build new work with Anaddb tasks.
# Construct a manager with mpi_procs==1 since anaddb do not support mpi_procs > 1 (except in elphon)
shell_manager = fwp.manager.to_shell_manager(mpi_procs=1)
awork = flowtk.Work(manager=shell_manager)
# Phonons bands and DOS with gaussian method
anaddb_input = abilab.AnaddbInput.phbands_and_dos(
scf_input.structure, ngqpt=ph_ngqpt, ndivsm=5, nqsmall=10, dos_method="gaussian: 0.001 eV")
atask = flowtk.AnaddbTask(anaddb_input, ddb_node=ddb_path, manager=shell_manager)
awork.register(atask)
# Phonons bands and DOS with tetrahedron method
anaddb_input = abilab.AnaddbInput.phbands_and_dos(
scf_input.structure, ngqpt=ph_ngqpt, ndivsm=5, nqsmall=10, dos_method="tetra")
atask = flowtk.AnaddbTask(anaddb_input, ddb_node=ddb_path, manager=shell_manager)
awork.register(atask)
flow.register_work(awork)
flow.allocate()
flow.build()
for i, atask in enumerate(awork):
atask.history.info("About to run anaddb task: %d", i)
atask.start_and_wait()
assert atask.status == atask.S_DONE
atask.check_status()
assert atask.status == atask.S_OK
# These output files should be produced in the task workdir.
# Actually they should be in outdir but anaddb uses different conventions.
assert len(atask.wdir.list_filepaths(wildcard="*PHBST.nc")) == 1
assert len(atask.wdir.list_filepaths(wildcard="*PHDOS.nc")) == 1
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)
