def check_restart_task_type(self, lp, fworker, tmpdir, fw_id, task_tag):
# resume the task for tag
wf = lp.get_wf_by_fw_id(fw_id)
fw = get_fw_by_task_index(wf, task_tag, index=1)
assert fw is not None
assert fw.state == "PAUSED"
lp.resume_fw(fw.fw_id)
# run the FW
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=1)
# the job should have a detour for the restart
wf = lp.get_wf_by_fw_id(fw_id)
fw = get_fw_by_task_index(wf, task_tag, index=2)
assert fw is not None
assert fw.state == "READY"
# run all the following and check that the last is correctly completed (if convergence is not achieved
# the final state should be FIZZLED)
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(fw_id)
fw = get_fw_by_task_index(wf, task_tag, index=-1)
assert fw.state == "COMPLETED"
def check_restart_task_type(lp, fworker, tmpdir, fw_id, task_tag):
# resume the task for tag
wf = lp.get_wf_by_fw_id(fw_id)
fw = get_fw_by_task_index(wf, task_tag, index=1)
assert fw is not None
assert fw.state == "PAUSED"
lp.resume_fw(fw.fw_id)
# run the FW
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=1)
# the job should have a detour for the restart
wf = lp.get_wf_by_fw_id(fw_id)
fw = get_fw_by_task_index(wf, task_tag, index=2)
assert fw is not None
assert fw.state == "READY"
# run all the following and check that the last is correctly completed (if convergence is not achieved
# the final state should be FIZZLED)
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(fw_id)
fw = get_fw_by_task_index(wf, task_tag, index=-1)
assert fw.state == "COMPLETED"
def itest_dte_skip_permutations(self, lp, fworker, tmpdir,
input_scf_phonon_gan_low):
"""
Simple test of DteFWWorkflow without phonons.
"""
# dte calculations only work with selected values of ixc
input_scf_phonon_gan_low['ixc'] = 7
dte_inputs = dte_from_gsinput(input_scf_phonon_gan_low,
use_phonons=False,
skip_dte_permutations=False,
ph_tol={"tolvrs": 1.0e-7},
ddk_tol={"tolwfr": 1.0e-16},
dde_tol={"tolvrs": 1.0e-7})
wf = DteFWWorkflow(input_scf_phonon_gan_low,
ddk_inp=dte_inputs.filter_by_tags(DDK),
dde_inp=dte_inputs.filter_by_tags(DDE),
dte_inp=dte_inputs.filter_by_tags(DTE),
ph_inp=dte_inputs.filter_by_tags(PH_Q_PERT),
autoparal=False)
wf.add_anaddb_dte_fw(input_scf_phonon_gan_low.structure,
dieflag=2,
nlflag=3,
ramansr=0,
alphon=0,
prtmbm=0)
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
if self.check_numerical_values:
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
with scf_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-680.402255069, rel=0.005)
ana_task = load_abitask(
get_fw_by_task_index(wf, "anaddb", index=None))
with ana_task.open_anaddbnc() as ananc:
assert float(ananc.dchide[0, 0,
2]) == pytest.approx(-1.69328765210,
rel=0.15)
def itest_not_converged(self, lp, fworker, tmpdir,
input_scf_phonon_si_low):
"""
Tests the missed convergence and restart for all the different kinds of tasks
"""
# set a point not belonging to the grid so to trigger the calculation of WFQ and gamma for the DDE and DDK
ph_inp = phonons_from_gsinput(input_scf_phonon_si_low,
qpoints=[[0, 0, 0],
[0.11111, 0.22222, 0.33333]],
ph_tol={"tolvrs": 1.0e-7},
ddk_tol={"tolwfr": 1.0e-16},
dde_tol={"tolvrs": 1.0e-7},
wfq_tol={"tolwfr": 1.0e-16})
ph_inp.set_vars(nstep=3)
wf_full = PhononFullFWWorkflow(input_scf_phonon_si_low,
ph_inp,
autoparal=False)
scf_id = wf_full.scf_fw.fw_id
old_new = wf_full.add_to_db(lpad=lp)
scf_id = old_new[scf_id]
# run the scf
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=1)
# pause all the remaining workflow and reignite the task types one by one to check the restart
lp.pause_wf(scf_id)
# DDK
check_restart_task_type(lp, fworker, tmpdir, scf_id, "ddk_0")
# reignite and run the other DDK to get to the DDE
wf = lp.get_wf_by_fw_id(scf_id)
lp.resume_fw(get_fw_by_task_index(wf, "ddk_1", index=1).fw_id)
lp.resume_fw(get_fw_by_task_index(wf, "ddk_2", index=1).fw_id)
rapidfire(lp, fworker, m_dir=str(tmpdir))
# DDE
check_restart_task_type(lp, fworker, tmpdir, scf_id, "dde_0")
# NSCF
check_restart_task_type(lp, fworker, tmpdir, scf_id, "nscf_wfq_0")
# phonon
check_restart_task_type(lp, fworker, tmpdir, scf_id, "phonon_0")
# don't run the wf until the end to save time. Other tests covered that.
wf = lp.get_wf_by_fw_id(scf_id)
assert wf.state == "PAUSED"
def itest_scf_wf(self, lp, fworker, tmpdir, input_scf_si_low, use_autoparal):
"""
Tests a simple scf run with the ScfFWWorkflow
"""
wf = ScfFWWorkflow(input_scf_si_low, autoparal=use_autoparal)
wf.add_final_cleanup(["WFK"])
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
fw = lp.get_fw_by_id(scf_fw_id)
assert fw.state == "COMPLETED"
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
# check the effect of the final cleanup
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_DEN"))) == 1
assert len(glob.glob(os.path.join(scf_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(scf_task.indir.path, "*"))) == 0
if self.check_numerical_values:
with scf_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-241.239839134, rel=0.05)
def itest_scf_wf(self, lp, fworker, tmpdir, input_scf_si_low,
use_autoparal):
"""
Tests a simple scf run with the ScfFWWorkflow
"""
wf = ScfFWWorkflow(input_scf_si_low, autoparal=use_autoparal)
wf.add_final_cleanup(["WFK"])
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
fw = lp.get_fw_by_id(scf_fw_id)
assert fw.state == "COMPLETED"
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
# check the effect of the final cleanup
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_DEN"))) == 1
assert len(glob.glob(os.path.join(scf_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(scf_task.indir.path, "*"))) == 0
if self.check_numerical_values:
with scf_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-241.239839134, rel=0.05)
def itest_dilatmx_error(self, lp, fworker, tmpdir, inputs_relax_si_low, db_data):
"""
Test the workflow when a dilatmx error shows up.
Also tests the skip_ion option of RelaxFWWorkflow
"""
# set the dilatmx to a small value, so that the dilatmx error will show up
initial_dilatmx = 1.001
inputs_relax_si_low[1]['dilatmx'] = initial_dilatmx
# also test the skip_ion
wf = RelaxFWWorkflow(*inputs_relax_si_low, autoparal=False, skip_ion=True)
wf.add_mongoengine_db_insertion(db_data)
initial_ion_structure = inputs_relax_si_low[0].structure
ioncell_fw_id = wf.ioncell_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
ioncell_fw_id = old_new[ioncell_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=1)
ioncell_fw = lp.get_fw_by_id(ioncell_fw_id)
assert ioncell_fw.state == "COMPLETED"
launch = ioncell_fw.launches[-1]
assert any(event.yaml_tag == DilatmxError.yaml_tag for event in launch.action.stored_data['report'])
links_ioncell = lp.get_wf_by_fw_id(ioncell_fw_id).links[ioncell_fw_id]
# there should be an additional child (the detour)
assert len(links_ioncell) == 2
# run the detour restarting froom previous structure
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=1)
wf = lp.get_wf_by_fw_id(ioncell_fw_id)
fw_detour = get_fw_by_task_index(wf, "ioncell", index=2)
assert fw_detour.state == "COMPLETED"
detour_abiinput = fw_detour.spec['_tasks'][0].abiinput
assert detour_abiinput['dilatmx'] == initial_dilatmx
restart_structure = detour_abiinput.structure
# check that the structure has been updated when restarting
assert initial_ion_structure != restart_structure
# complete the wf. Just check that the saving without the ion tasks completes without error
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(ioncell_fw_id)
assert wf.state == "COMPLETED"
def itest_uncoverged(self, lp, fworker, tmpdir, inputs_relax_si_low):
"""
Testing restart when the ionic convercence is not reached
"""
inputs_relax_si_low[0]['ntime']=3
wf = RelaxFWWorkflow(*inputs_relax_si_low, autoparal=False)
initial_ion_structure = inputs_relax_si_low[0].structure
ion_fw_id = wf.ion_fw.fw_id
ioncell_fw_id = wf.ioncell_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
ion_fw_id = old_new[ion_fw_id]
ioncell_fw_id = old_new[ioncell_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=1)
ion_fw = lp.get_fw_by_id(ion_fw_id)
ioncell_fw = lp.get_fw_by_id(ioncell_fw_id)
assert ion_fw.state == "COMPLETED"
assert ioncell_fw.state == "WAITING"
launch = ion_fw.launches[-1]
assert any(event.yaml_tag == RelaxFWTask.CRITICAL_EVENTS[0].yaml_tag for event in launch.action.stored_data['report'])
links_ion = lp.get_wf_by_fw_id(ion_fw_id).links[ion_fw_id]
# there should be an additional child (the detour)
assert len(links_ion) == 2
links_ion.remove(ioncell_fw_id)
fw_detour_id = links_ion[0]
# run the detour
rapidfire(lp, fworker, m_dir=str(tmpdir))
fw_detour = lp.get_fw_by_id(fw_detour_id)
assert fw_detour.state == "COMPLETED"
restart_structure = fw_detour.spec['_tasks'][0].abiinput.structure
wf = lp.get_wf_by_fw_id(ion_fw_id)
assert wf.state == "COMPLETED"
# check that the structure has been updated when restarting
assert initial_ion_structure != restart_structure
if self.check_numerical_values:
last_ioncell_task = load_abitask(get_fw_by_task_index(wf, "ioncell", index=-1))
with last_ioncell_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-240.28203726305696, rel=0.01)
assert gsr.structure.lattice.abc == pytest.approx(
np.array((3.8101428225862084, 3.810143911539674, 3.8101432797789698)), rel=0.05)
def itest_not_converged(self, lp, fworker, tmpdir, input_ebands_si_low):
"""
Tests the running of the NscfFWWorkflow with non convergence and restart
"""
input_ebands_si_low[1].set_vars(nstep=5)
wf = NscfFWWorkflow(*input_ebands_si_low, autoparal=False)
scf_fw_id = wf.scf_fw.fw_id
nscf_fw_id = wf.nscf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
nscf_fw_id = old_new[nscf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=2)
nscf_fw = lp.get_fw_by_id(nscf_fw_id)
assert nscf_fw.state == "COMPLETED"
launch = nscf_fw.launches[-1]
assert any(event.yaml_tag == NscfFWTask.CRITICAL_EVENTS[0].yaml_tag
for event in launch.action.stored_data['report'])
links = lp.get_wf_by_fw_id(scf_fw_id).links
assert nscf_fw_id in links and len(links[nscf_fw_id]) == 1
fw_child_id = links[nscf_fw_id][0]
fw_child = lp.get_fw_by_id(fw_child_id)
assert fw_child.state == "READY"
rapidfire(lp, fworker, m_dir=str(tmpdir))
fw_child = lp.get_fw_by_id(fw_child_id)
assert fw_child.state == "COMPLETED"
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
if self.check_numerical_values:
scf_task = load_abitask(lp.get_fw_by_id(scf_fw_id))
with scf_task.open_gsr() as scf_gsr:
assert scf_gsr.energy == pytest.approx(-241.239839134,
rel=0.01)
last_nscf_task = load_abitask(
get_fw_by_task_index(wf, "nscf", index=-1))
with last_nscf_task.open_gsr() as nscf_gsr:
assert np.allclose((-6.2581504, 5.5974646, 5.5974646),
nscf_gsr.ebands.eigens[0, 0, :3],
rtol=0.1)
def itest_not_converged(self, lp, fworker, tmpdir, input_scf_phonon_si_low):
"""
Tests the missed convergence and restart for all the different kinds of tasks
"""
# set a point not belonging to the grid so to trigger the calculation of WFQ and gamma for the DDE and DDK
ph_inp = phonons_from_gsinput(input_scf_phonon_si_low, qpoints=[[0, 0, 0], [0.11111, 0.22222, 0.33333]],
ph_tol = {"tolvrs": 1.0e-7}, ddk_tol = {"tolwfr": 1.0e-16},
dde_tol = {"tolvrs": 1.0e-7}, wfq_tol = {"tolwfr": 1.0e-16})
ph_inp.set_vars(nstep=3)
wf_full = PhononFullFWWorkflow(input_scf_phonon_si_low, ph_inp, autoparal=False)
scf_id = wf_full.scf_fw.fw_id
old_new = wf_full.add_to_db(lpad=lp)
scf_id = old_new[scf_id]
# run the scf
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=1)
# pause all the remaining workflow and reignite the task types one by one to check the restart
lp.pause_wf(scf_id)
# DDK
self.check_restart_task_type(lp, fworker, tmpdir, scf_id, "ddk_0")
# reignite and run the other DDK to get to the DDE
wf = lp.get_wf_by_fw_id(scf_id)
lp.resume_fw(get_fw_by_task_index(wf, "ddk_1", index=1).fw_id)
lp.resume_fw(get_fw_by_task_index(wf, "ddk_2", index=1).fw_id)
rapidfire(lp, fworker, m_dir=str(tmpdir))
# DDE
self.check_restart_task_type(lp, fworker, tmpdir, scf_id, "dde_0")
# NSCF
self.check_restart_task_type(lp, fworker, tmpdir, scf_id, "nscf_wfq_0")
# phonon
self.check_restart_task_type(lp, fworker, tmpdir, scf_id, "phonon_0")
# don't run the wf until the end to save time. Other tests covered that.
wf = lp.get_wf_by_fw_id(scf_id)
assert wf.state == "PAUSED"
def itest_dfpt_full(self, lp, fworker, tmpdir, input_scf_phonon_gan_low,
use_autoparal, db_data):
"""
Simple test of DteFWWorkflow with autoparal True and False.
Doesn't run anaddb since anaddb does not support a DDB with third order perturbations along with
other perturbations.
Skips dte permutations.
"""
# dte calculations only work with selected values of ixc
input_scf_phonon_gan_low['ixc'] = 7
dfpt_inputs = dfpt_from_gsinput(input_scf_phonon_gan_low,
ph_ngqpt=[2, 2, 2],
do_ddk=True,
do_dde=True,
do_strain=True,
do_dte=True,
skip_dte_permutations=True,
ddk_tol={"tolwfr": 1.0e-16},
dde_tol={"tolvrs": 1.0e-7},
strain_tol={"tolvrs": 1.0e-7},
ph_tol={"tolvrs": 1.0e-7})
wf = DfptFWWorkflow(input_scf_phonon_gan_low,
ddk_inp=dfpt_inputs.filter_by_tags(DDK),
dde_inp=dfpt_inputs.filter_by_tags(DDE),
strain_inp=dfpt_inputs.filter_by_tags(STRAIN),
ph_inp=dfpt_inputs.filter_by_tags(PH_Q_PERT),
dte_inp=dfpt_inputs.filter_by_tags(DTE),
nscf_inp=dfpt_inputs.filter_by_tags(NSCF),
initialization_info={"kppa": 100},
autoparal=use_autoparal)
wf.add_mongoengine_db_insertion(db_data)
wf.add_final_cleanup(["WFK"])
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
# check the effect of the final cleanup
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_DEN"))) == 1
assert len(glob.glob(os.path.join(scf_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(scf_task.indir.path, "*"))) == 0
def itest_dfpt_anaddb_dte(self, lp, fworker, tmpdir,
input_scf_phonon_gan_low, db_data):
"""
Simple test of DteFWWorkflow with dte.
Does not run anaddb due to problems when dealing with DDB file containing 3rd order derivatives and
other terms.
"""
# dte calculations only work with selected values of ixc
input_scf_phonon_gan_low['ixc'] = 7
dfpt_inputs = dfpt_from_gsinput(input_scf_phonon_gan_low,
ph_ngqpt=[1, 1, 1],
do_ddk=True,
do_dde=True,
do_strain=False,
do_dte=True,
skip_dte_permutations=True,
ddk_tol={"tolwfr": 1.0e-16},
dde_tol={"tolvrs": 1.0e-7},
strain_tol={"tolvrs": 1.0e-7},
ph_tol={"tolvrs": 1.0e-7})
wf = DfptFWWorkflow(input_scf_phonon_gan_low,
ddk_inp=dfpt_inputs.filter_by_tags(DDK),
dde_inp=dfpt_inputs.filter_by_tags(DDE),
strain_inp=dfpt_inputs.filter_by_tags(STRAIN),
ph_inp=dfpt_inputs.filter_by_tags(PH_Q_PERT),
dte_inp=dfpt_inputs.filter_by_tags(DTE),
nscf_inp=dfpt_inputs.filter_by_tags(NSCF),
initialization_info={"kppa": 100},
autoparal=False)
wf.add_anaddb_dfpt_fw(input_scf_phonon_gan_low.structure)
wf.add_mongoengine_db_insertion(db_data)
wf.add_final_cleanup(additional_spec={"test_spec": 1})
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
if self.check_numerical_values:
ana_task = load_abitask(
get_fw_by_task_index(wf, "anaddb", index=None))
with ana_task.open_anaddbnc() as ananc:
assert float(ananc.dchide[0, 0,
2]) == pytest.approx(-1.69328765210,
rel=0.15)
def itest_dte_skip_permutations(self, lp, fworker, tmpdir, input_scf_phonon_gan_low):
"""
Simple test of DteFWWorkflow without phonons.
"""
# dte calculations only work with selected values of ixc
input_scf_phonon_gan_low['ixc'] = 7
dte_inputs = dte_from_gsinput(input_scf_phonon_gan_low, use_phonons=False, skip_dte_permutations=False,
ph_tol={"tolvrs": 1.0e-7}, ddk_tol = {"tolwfr": 1.0e-16},
dde_tol = {"tolvrs": 1.0e-7}, dte_tol = {"tolwfr": 1.0e-16})
wf = DteFWWorkflow(input_scf_phonon_gan_low, ddk_inp = dte_inputs.filter_by_tags(DDK),
dde_inp = dte_inputs.filter_by_tags(DDE), dte_inp = dte_inputs.filter_by_tags(DTE),
ph_inp = dte_inputs.filter_by_tags(PH_Q_PERT), autoparal=False)
wf.add_anaddb_dte_fw(input_scf_phonon_gan_low.structure, dieflag=2, nlflag=3, ramansr=0, alphon=0, prtmbm=0)
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
if self.check_numerical_values:
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
with scf_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-680.402255069, rel=0.005)
ana_task = load_abitask(get_fw_by_task_index(wf, "anaddb", index=None))
with ana_task.open_anaddbnc() as ananc:
assert float(ananc.dchide[0,0,2]) == pytest.approx(-1.69328765210, rel=0.15)
def itest_dfpt_full(self, lp, fworker, tmpdir, input_scf_phonon_gan_low, use_autoparal, db_data):
"""
Simple test of DteFWWorkflow with autoparal True and False.
Doesn't run anaddb since anaddb does not support a DDB with third order perturbations along with
other perturbations.
Skips dte permutations.
"""
# dte calculations only work with selected values of ixc
input_scf_phonon_gan_low['ixc'] = 7
dfpt_inputs = dfpt_from_gsinput(input_scf_phonon_gan_low, ph_ngqpt=[2, 2, 2], do_ddk=True, do_dde=True,
do_strain=True, do_dte=True, skip_dte_permutations=True,
ddk_tol = {"tolwfr": 1.0e-16}, dde_tol = {"tolvrs": 1.0e-7},
strain_tol={"tolvrs": 1.0e-7}, ph_tol={"tolvrs": 1.0e-7})
wf = DfptFWWorkflow(input_scf_phonon_gan_low, ddk_inp = dfpt_inputs.filter_by_tags(DDK),
dde_inp = dfpt_inputs.filter_by_tags(DDE), strain_inp=dfpt_inputs.filter_by_tags(STRAIN),
ph_inp = dfpt_inputs.filter_by_tags(PH_Q_PERT), dte_inp = dfpt_inputs.filter_by_tags(DTE),
nscf_inp=dfpt_inputs.filter_by_tags(NSCF),initialization_info={"kppa": 100},
autoparal=use_autoparal)
wf.add_mongoengine_db_insertion(db_data)
wf.add_final_cleanup(["WFK"])
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
# check the effect of the final cleanup
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_DEN"))) == 1
assert len(glob.glob(os.path.join(scf_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(scf_task.indir.path, "*"))) == 0
def itest_nscf_wf(self, lp, fworker, tmpdir, input_ebands_si_low,
use_autoparal):
"""
Simple test of NscfFWWorkflow with autoparal True and False.
"""
wf = NscfFWWorkflow(*input_ebands_si_low, autoparal=False)
wf.add_final_cleanup(["WFK"])
scf_fw_id = wf.scf_fw.fw_id
nscf_fw_id = wf.nscf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
nscf_fw_id = old_new[nscf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
# check the effect of the final cleanup
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_DEN"))) == 1
assert len(glob.glob(os.path.join(scf_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(scf_task.indir.path, "*"))) == 0
if self.check_numerical_values:
scf_task = load_abitask(lp.get_fw_by_id(scf_fw_id))
with scf_task.open_gsr() as scf_gsr:
assert scf_gsr.energy == pytest.approx(-241.239839134,
rel=0.01)
nscf_task = load_abitask(lp.get_fw_by_id(nscf_fw_id))
with nscf_task.open_gsr() as nscf_gsr:
assert np.allclose((-6.2581504, 5.5974646, 5.5974646),
nscf_gsr.ebands.eigens[0, 0, :3],
rtol=0.1)
def itest_dfpt_anaddb_dte(self, lp, fworker, tmpdir, input_scf_phonon_gan_low, db_data):
"""
Simple test of DteFWWorkflow with dte.
Does not run anaddb due to problems when dealing with DDB file containing 3rd order derivatives and
other terms.
"""
# dte calculations only work with selected values of ixc
input_scf_phonon_gan_low['ixc'] = 7
dfpt_inputs = dfpt_from_gsinput(input_scf_phonon_gan_low, ph_ngqpt=[1,1,1], do_ddk=True, do_dde=True,
do_strain=False, do_dte=True, skip_dte_permutations=True,
ddk_tol = {"tolwfr": 1.0e-16}, dde_tol = {"tolvrs": 1.0e-7},
strain_tol={"tolvrs": 1.0e-7}, ph_tol={"tolvrs": 1.0e-7})
wf = DfptFWWorkflow(input_scf_phonon_gan_low, ddk_inp = dfpt_inputs.filter_by_tags(DDK),
dde_inp = dfpt_inputs.filter_by_tags(DDE), strain_inp=dfpt_inputs.filter_by_tags(STRAIN),
ph_inp = dfpt_inputs.filter_by_tags(PH_Q_PERT), dte_inp = dfpt_inputs.filter_by_tags(DTE),
nscf_inp=dfpt_inputs.filter_by_tags(NSCF),initialization_info={"kppa": 100},
autoparal=False)
wf.add_anaddb_dfpt_fw(input_scf_phonon_gan_low.structure)
wf.add_mongoengine_db_insertion(db_data)
wf.add_final_cleanup(additional_spec={"test_spec":1})
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
if self.check_numerical_values:
ana_task = load_abitask(get_fw_by_task_index(wf, "anaddb", index=None))
with ana_task.open_anaddbnc() as ananc:
assert float(ananc.dchide[0,0,2]) == pytest.approx(-1.69328765210, rel=0.15)
def itest_relax_wf(self, lp, fworker, tmpdir, inputs_relax_si_low,
use_autoparal, db_data):
"""
Tests the basic functionality of a RelaxFWWorkflow with autoparal True and False.
"""
wf = RelaxFWWorkflow(*inputs_relax_si_low,
autoparal=use_autoparal,
initialization_info={"kppa": 100})
wf.add_mongoengine_db_insertion(db_data)
wf.add_final_cleanup(["WFK"])
initial_ion_structure = inputs_relax_si_low[0].structure
ion_fw_id = wf.ion_fw.fw_id
ioncell_fw_id = wf.ioncell_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
ion_fw_id = old_new[ion_fw_id]
ioncell_fw_id = old_new[ioncell_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(ion_fw_id)
assert wf.state == "COMPLETED"
ioncell_fw = get_fw_by_task_index(wf, "ioncell", index=-1)
ioncell_task = load_abitask(ioncell_fw)
ioncell_hist_path = ioncell_task.outdir.has_abiext("HIST")
with HistFile(ioncell_hist_path) as hist:
initial_ioncell_structure = hist.structures[0]
assert initial_ion_structure != initial_ioncell_structure
# check the effect of the final cleanup
assert len(glob.glob(os.path.join(ioncell_task.outdir.path,
"*_WFK"))) == 0
assert len(glob.glob(os.path.join(ioncell_task.outdir.path,
"*_DEN"))) > 0
assert len(glob.glob(os.path.join(ioncell_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(ioncell_task.indir.path, "*"))) == 0
# check the result in the DB
from abiflows.database.mongoengine.abinit_results import RelaxResult
with db_data.switch_collection(RelaxResult) as RelaxResult:
results = RelaxResult.objects()
assert len(results) == 1
r = results[0]
# test input structure
assert r.abinit_input.structure.to_mgobj() == initial_ion_structure
# test output structure
# remove site properties, otherwise the "cartesian_forces" won't match due to the presence of a
# list instead of an array in the deserialization
db_structure = r.abinit_output.structure.to_mgobj()
for s in db_structure:
s.properties = {}
hist_structure = hist.structures[-1]
for s in hist_structure:
s.properties = {}
assert db_structure == hist_structure
assert r.abinit_input.ecut == inputs_relax_si_low[0]['ecut']
assert r.abinit_input.kppa == 100
nptu.assert_array_equal(
r.abinit_input.last_input.to_mgobj()['ngkpt'],
inputs_relax_si_low[0]['ngkpt'])
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.gsr.read())
db_file.seek(0)
assert filecmp.cmp(ioncell_task.gsr_path, db_file.name)
if self.check_numerical_values:
with ioncell_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-240.28203726305696,
rel=0.01)
assert np.allclose((3.8101419256822333, 3.8101444012342616,
3.8101434297177068),
gsr.structure.lattice.abc,
rtol=0.05)
def itest_dilatmx(self, lp, fworker, tmpdir, inputs_relax_si_low):
"""
Test the workflow with a target dilatmx
"""
# set the dilatmx to 1.05 to keep the change independt on the generation of the input
inputs_relax_si_low[1]['dilatmx'] = 1.05
wf = RelaxFWWorkflow(*inputs_relax_si_low,
autoparal=False,
target_dilatmx=1.03)
initial_ion_structure = inputs_relax_si_low[0].structure
ion_fw_id = wf.ion_fw.fw_id
ioncell_fw_id = wf.ioncell_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
ion_fw_id = old_new[ion_fw_id]
ioncell_fw_id = old_new[ioncell_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir), nlaunches=2)
ion_fw = lp.get_fw_by_id(ion_fw_id)
ioncell_fw = lp.get_fw_by_id(ioncell_fw_id)
assert ion_fw.state == "COMPLETED"
assert ioncell_fw.state == "COMPLETED"
launch = ioncell_fw.launches[-1]
links_ioncell = lp.get_wf_by_fw_id(ioncell_fw_id).links[ioncell_fw_id]
# there should be an additional child (the detour)
assert len(links_ioncell) == 1
fw_detour_id = links_ioncell[0]
# run the detour with lowered dilatmx
rapidfire(lp, fworker, m_dir=str(tmpdir))
fw_detour = lp.get_fw_by_id(fw_detour_id)
assert fw_detour.state == "COMPLETED"
detour_abiinput = fw_detour.spec['_tasks'][0].abiinput
assert detour_abiinput['dilatmx'] == 1.03
restart_structure = detour_abiinput.structure
# check that the structure has been updated when restarting
assert initial_ion_structure != restart_structure
wf = lp.get_wf_by_fw_id(ion_fw_id)
assert wf.state == "COMPLETED"
# check that the structure has been updated when restarting
assert initial_ion_structure != restart_structure
if self.check_numerical_values:
last_ioncell_task = load_abitask(
get_fw_by_task_index(wf, "ioncell", index=-1))
with last_ioncell_task.open_gsr() as gsr:
assert gsr.structure.lattice.abc == pytest.approx(np.array(
(3.8101419255677951, 3.8101444011173897,
3.8101434296150889)),
rel=0.05)
def itest_dte_with_phonons(self, lp, fworker, tmpdir, input_scf_phonon_gan_low, use_autoparal, db_data):
"""
Simple test of DteFWWorkflow with autoparal True and False.
Skips dte permutations.
"""
# dte calculations only work with selected values of ixc
input_scf_phonon_gan_low['ixc'] = 7
dte_inputs = dte_from_gsinput(input_scf_phonon_gan_low, use_phonons=True, skip_dte_permutations=True,
ph_tol={"tolvrs": 1.0e-7}, ddk_tol = {"tolwfr": 1.0e-16},
dde_tol = {"tolvrs": 1.0e-7}, dte_tol = {"tolwfr": 1.0e-15})
wf = DteFWWorkflow(input_scf_phonon_gan_low, ddk_inp = dte_inputs.filter_by_tags(DDK),
dde_inp = dte_inputs.filter_by_tags(DDE), dte_inp = dte_inputs.filter_by_tags(DTE),
ph_inp = dte_inputs.filter_by_tags(PH_Q_PERT), autoparal=False,
initialization_info={"kppa": 100})
wf.add_anaddb_dte_fw(input_scf_phonon_gan_low.structure, dieflag=1, nlflag=1)
wf.add_mongoengine_db_insertion(db_data)
wf.add_final_cleanup(["WFK"])
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
# check the effect of the final cleanup
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_DEN"))) == 1
assert len(glob.glob(os.path.join(scf_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(scf_task.indir.path, "*"))) == 0
# check the save in the DB
from abiflows.database.mongoengine.abinit_results import DteResult
with db_data.switch_collection(DteResult) as DteResult:
results = DteResult.objects()
assert len(results) == 1
r = results[0]
assert r.abinit_input.structure.to_mgobj() == input_scf_phonon_gan_low.structure
assert r.abinit_output.structure.to_mgobj() == input_scf_phonon_gan_low.structure
assert r.abinit_input.ecut == input_scf_phonon_gan_low['ecut']
assert r.abinit_input.kppa == 100
nptu.assert_array_equal(r.abinit_input.gs_input.to_mgobj()['ngkpt'], input_scf_phonon_gan_low['ngkpt'])
ana_task = load_abitask(get_fw_by_task_index(wf, "anaddb", index=None))
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.anaddb_nc.read())
db_file.seek(0)
assert filecmp.cmp(ana_task.anaddb_nc_path, db_file.name)
mrgddb_task = load_abitask(get_fw_by_task_index(wf, "mrgddb", index=None))
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.ddb.read())
db_file.seek(0)
assert filecmp.cmp(mrgddb_task.merged_ddb_path, db_file.name)
if self.check_numerical_values:
with scf_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-680.402255069, rel=0.005)
ana_task = load_abitask(get_fw_by_task_index(wf, "anaddb", index=None))
with ana_task.open_anaddbnc() as ananc:
assert float(ananc.dchide[0,0,2]) == pytest.approx(-1.69328765210, rel=0.15)
def itest_phonon_wf(self, lp, fworker, tmpdir, input_scf_phonon_si_low,
use_autoparal, db_data):
"""
Tests the complete running of PhononFullFWWorkflow and PhononFWWorkflow
"""
# test at gamma.
ph_fac = PhononsFromGsFactory(qpoints=[[0, 0, 0]],
ph_tol={"tolvrs": 1.0e-7},
ddk_tol={"tolwfr": 1.0e-16},
dde_tol={"tolvrs": 1.0e-7},
wfq_tol={"tolwfr": 1.0e-16})
# first run the phonon workflow with generation task
wf_gen = PhononFWWorkflow(input_scf_phonon_si_low,
ph_fac,
autoparal=use_autoparal,
initialization_info={
"ngqpt": [1, 1, 1],
"kppa": 100
})
wf_gen.add_anaddb_ph_bs_fw(input_scf_phonon_si_low.structure,
ph_ngqpt=[1, 1, 1],
ndivsm=2,
nqsmall=2)
wf_gen.add_mongoengine_db_insertion(db_data)
wf_gen.add_final_cleanup(["WFK"])
scf_id = wf_gen.scf_fw.fw_id
ph_generation_fw_id = wf_gen.ph_generation_fw.fw_id
old_new = wf_gen.add_to_db(lpad=lp)
scf_id = old_new[scf_id]
ph_generation_fw_id = old_new[ph_generation_fw_id]
# run all the workflow
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf_gen = lp.get_wf_by_fw_id(scf_id)
assert wf_gen.state == "COMPLETED"
ph_task = load_abitask(
get_fw_by_task_index(wf_gen, "phonon_0", index=-1))
# check the effect of the final cleanup
assert len(glob.glob(os.path.join(ph_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(ph_task.outdir.path, "*_DEN1"))) > 0
assert len(glob.glob(os.path.join(ph_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(ph_task.indir.path, "*"))) == 0
# check the save in the DB
from abiflows.database.mongoengine.abinit_results import PhononResult
with db_data.switch_collection(PhononResult) as PhononResult:
results = PhononResult.objects()
assert len(results) == 1
r = results[0]
assert r.abinit_input.structure.to_mgobj(
) == input_scf_phonon_si_low.structure
assert r.abinit_output.structure.to_mgobj(
) == input_scf_phonon_si_low.structure
assert r.abinit_input.ecut == input_scf_phonon_si_low['ecut']
assert r.abinit_input.kppa == 100
nptu.assert_array_equal(
r.abinit_input.gs_input.to_mgobj()['ngkpt'],
input_scf_phonon_si_low['ngkpt'])
nptu.assert_array_equal(r.abinit_input.ngqpt, [1, 1, 1])
ana_task = load_abitask(
get_fw_by_task_index(wf_gen, "anaddb", index=None))
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.phonon_bs.read())
db_file.seek(0)
assert filecmp.cmp(ana_task.phbst_path, db_file.name)
mrgddb_task = load_abitask(
get_fw_by_task_index(wf_gen, "mrgddb", index=None))
# read/write in binary for py3k compatibility with mongoengine
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.ddb.read())
db_file.seek(0)
assert filecmp.cmp(mrgddb_task.merged_ddb_path, db_file.name)
# then rerun a similar workflow, but completely generated at its creation
wf_full = PhononFullFWWorkflow(input_scf_phonon_si_low,
ph_fac,
autoparal=use_autoparal)
wf_full.add_anaddb_ph_bs_fw(input_scf_phonon_si_low.structure,
ph_ngqpt=[1, 1, 1],
ndivsm=2,
nqsmall=2)
wf_full.add_mongoengine_db_insertion(db_data)
scf_id = wf_full.scf_fw.fw_id
old_new = wf_full.add_to_db(lpad=lp)
scf_id = old_new[scf_id]
# run all the workflow
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf_full = lp.get_wf_by_fw_id(scf_id)
assert wf_full.state == "COMPLETED"
# the full workflow doesn't contain the generation FW and the cleanup tasks, but should have the same
# amount of perturbations.
if use_autoparal:
diff = 1
else:
diff = 2
assert len(wf_full.id_fw) + diff == len(wf_gen.id_fw)
if self.check_numerical_values:
gen_scf_task = load_abitask(
get_fw_by_task_index(wf_gen, "scf", index=-1))
with gen_scf_task.open_gsr() as gen_gsr:
gen_energy = gen_gsr.energy
assert gen_energy == pytest.approx(-240.264972012, rel=0.01)
gen_ana_task = load_abitask(
get_fw_by_task_index(wf_gen, "anaddb", index=None))
with gen_ana_task.open_phbst() as gen_phbst:
gen_phfreq = gen_phbst.phbands.phfreqs[0, 3]
assert gen_phfreq == pytest.approx(0.06029885, rel=0.1)
full_scf_task = load_abitask(
get_fw_by_task_index(wf_gen, "scf", index=-1))
with full_scf_task.open_gsr() as full_gsr:
full_energy = full_gsr.energy
assert full_energy == pytest.approx(-240.264972012, rel=0.01)
full_ana_task = load_abitask(
get_fw_by_task_index(wf_gen, "anaddb", index=None))
with full_ana_task.open_phbst() as full_phbst:
full_phfreqs = full_phbst.phbands.phfreqs[0, 3]
assert full_phfreqs == pytest.approx(0.06029885, rel=0.1)
assert gen_energy == pytest.approx(full_energy, rel=1e-6)
assert gen_phfreq == pytest.approx(full_phfreqs, rel=1e-6)
def itest_dfpt_anaddb_ph(self, lp, fworker, tmpdir, input_scf_phonon_gan_low, db_data):
"""
Simple test of DteFWWorkflow with autoparal True and False.
Skips dte permutations.
"""
dfpt_inputs = dfpt_from_gsinput(input_scf_phonon_gan_low, ph_ngqpt=[2, 2, 2], do_ddk=True, do_dde=True,
do_strain=True, do_dte=False,
ddk_tol = {"tolwfr": 1.0e-16}, dde_tol = {"tolvrs": 1.0e-7},
strain_tol={"tolvrs": 1.0e-7}, ph_tol={"tolvrs": 1.0e-7})
wf = DfptFWWorkflow(input_scf_phonon_gan_low, ddk_inp = dfpt_inputs.filter_by_tags(DDK),
dde_inp = dfpt_inputs.filter_by_tags(DDE), strain_inp=dfpt_inputs.filter_by_tags(STRAIN),
ph_inp = dfpt_inputs.filter_by_tags(PH_Q_PERT), dte_inp = dfpt_inputs.filter_by_tags(DTE),
nscf_inp=dfpt_inputs.filter_by_tags(NSCF),initialization_info={"kppa": 100},
autoparal=False)
wf.add_anaddb_dfpt_fw(input_scf_phonon_gan_low.structure, ph_ngqpt=[2, 2, 2], nqsmall=2, ndivsm=3)
wf.add_mongoengine_db_insertion(db_data)
wf.add_final_cleanup(["WFK"])
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
# check the save in the DB
from abiflows.database.mongoengine.abinit_results import DfptResult
with db_data.switch_collection(DfptResult) as DteResult:
results = DteResult.objects()
assert len(results) == 1
r = results[0]
assert r.abinit_input.structure.to_mgobj() == input_scf_phonon_gan_low.structure
assert r.abinit_output.structure.to_mgobj() == input_scf_phonon_gan_low.structure
assert r.abinit_input.ecut == input_scf_phonon_gan_low['ecut']
assert r.abinit_input.kppa == 100
nptu.assert_array_equal(r.abinit_input.gs_input.to_mgobj()['ngkpt'], input_scf_phonon_gan_low['ngkpt'])
ana_task = load_abitask(get_fw_by_task_index(wf, "anaddb", index=None))
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.anaddb_nc.read())
db_file.seek(0)
assert filecmp.cmp(ana_task.anaddb_nc_path, db_file.name)
mrgddb_task = load_abitask(get_fw_by_task_index(wf, "mrgddb", index=None))
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.ddb.read())
db_file.seek(0)
assert filecmp.cmp(mrgddb_task.merged_ddb_path, db_file.name)
if self.check_numerical_values:
with scf_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-680.402255069, rel=0.005)
ana_task = load_abitask(get_fw_by_task_index(wf, "anaddb", index=None))
with ana_task.open_anaddbnc() as ananc:
assert float(ananc.eps0[0,0]) == pytest.approx(64.8276774889143, rel=0.15)
e = ananc.elastic_data
if has_abinit("8.9.3"):
assert float(e.elastic_relaxed[0,0,0,0]) == pytest.approx(41.230540749230556, rel=0.15)
def itest_phonon_wf(self, lp, fworker, tmpdir, input_scf_phonon_si_low, use_autoparal, db_data):
"""
Tests the complete running of PhononFullFWWorkflow and PhononFWWorkflow
"""
# test at gamma. Pass a custom manager, to check proper serialization
manager_path = os.path.join(abidata.dirpath, 'managers', "travis_manager.yml")
ph_fac = PhononsFromGsFactory(qpoints=[[0,0,0]], ph_tol = {"tolvrs": 1.0e-7}, ddk_tol = {"tolwfr": 1.0e-16},
dde_tol = {"tolvrs": 1.0e-7}, wfq_tol = {"tolwfr": 1.0e-16},
manager=TaskManager.from_file(manager_path))
# first run the phonon workflow with generation task
wf_gen = PhononFWWorkflow(input_scf_phonon_si_low, ph_fac, autoparal=use_autoparal,
initialization_info={"ngqpt": [1,1,1], "kppa": 100})
wf_gen.add_anaddb_ph_bs_fw(input_scf_phonon_si_low.structure, ph_ngqpt=[1,1,1], ndivsm=2, nqsmall=2)
wf_gen.add_mongoengine_db_insertion(db_data)
wf_gen.add_final_cleanup(["WFK"])
scf_id = wf_gen.scf_fw.fw_id
ph_generation_fw_id = wf_gen.ph_generation_fw.fw_id
old_new = wf_gen.add_to_db(lpad=lp)
scf_id = old_new[scf_id]
ph_generation_fw_id = old_new[ph_generation_fw_id]
# run all the workflow
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf_gen = lp.get_wf_by_fw_id(scf_id)
assert wf_gen.state == "COMPLETED"
ph_task = load_abitask(get_fw_by_task_index(wf_gen, "phonon_0", index=-1))
# check the effect of the final cleanup
assert len(glob.glob(os.path.join(ph_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(ph_task.outdir.path, "*_DEN1"))) > 0
assert len(glob.glob(os.path.join(ph_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(ph_task.indir.path, "*"))) == 0
# check the save in the DB
from abiflows.database.mongoengine.abinit_results import PhononResult
with db_data.switch_collection(PhononResult) as PhononResult:
results = PhononResult.objects()
assert len(results) == 1
r = results[0]
assert r.abinit_input.structure.to_mgobj() == input_scf_phonon_si_low.structure
assert r.abinit_output.structure.to_mgobj() == input_scf_phonon_si_low.structure
assert r.abinit_input.ecut == input_scf_phonon_si_low['ecut']
assert r.abinit_input.kppa == 100
nptu.assert_array_equal(r.abinit_input.gs_input.to_mgobj()['ngkpt'], input_scf_phonon_si_low['ngkpt'])
nptu.assert_array_equal(r.abinit_input.ngqpt, [1,1,1])
ana_task = load_abitask(get_fw_by_task_index(wf_gen, "anaddb", index=None))
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.phonon_bs.read())
db_file.seek(0)
assert filecmp.cmp(ana_task.phbst_path, db_file.name)
mrgddb_task = load_abitask(get_fw_by_task_index(wf_gen, "mrgddb", index=None))
# read/write in binary for py3k compatibility with mongoengine
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.ddb.read())
db_file.seek(0)
assert filecmp.cmp(mrgddb_task.merged_ddb_path, db_file.name)
# then rerun a similar workflow, but completely generated at its creation
wf_full = PhononFullFWWorkflow(input_scf_phonon_si_low, ph_fac, autoparal=use_autoparal)
wf_full.add_anaddb_ph_bs_fw(input_scf_phonon_si_low.structure, ph_ngqpt=[1,1,1], ndivsm=2, nqsmall=2)
wf_full.add_mongoengine_db_insertion(db_data)
scf_id = wf_full.scf_fw.fw_id
old_new = wf_full.add_to_db(lpad=lp)
scf_id = old_new[scf_id]
# run all the workflow
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf_full = lp.get_wf_by_fw_id(scf_id)
assert wf_full.state == "COMPLETED"
# the full workflow doesn't contain the generation FW and the cleanup tasks, but should have the same
# amount of perturbations.
if use_autoparal:
diff = 1
else:
diff = 2
assert len(wf_full.id_fw) + diff == len(wf_gen.id_fw)
if self.check_numerical_values:
gen_scf_task = load_abitask(get_fw_by_task_index(wf_gen, "scf", index=-1))
with gen_scf_task.open_gsr() as gen_gsr:
gen_energy = gen_gsr.energy
assert gen_energy == pytest.approx(-240.264972012, rel=0.01)
gen_ana_task = load_abitask(get_fw_by_task_index(wf_gen, "anaddb", index=None))
with gen_ana_task.open_phbst() as gen_phbst:
gen_phfreq = gen_phbst.phbands.phfreqs[0, 3]
assert gen_phfreq == pytest.approx(0.06029885, rel=0.1)
full_scf_task = load_abitask(get_fw_by_task_index(wf_gen, "scf", index=-1))
with full_scf_task.open_gsr() as full_gsr:
full_energy = full_gsr.energy
assert full_energy == pytest.approx(-240.264972012, rel=0.01)
full_ana_task = load_abitask(get_fw_by_task_index(wf_gen, "anaddb", index=None))
with full_ana_task.open_phbst() as full_phbst:
full_phfreqs = full_phbst.phbands.phfreqs[0, 3]
assert full_phfreqs == pytest.approx(0.06029885, rel=0.1)
assert gen_energy == pytest.approx(full_energy, rel=1e-6)
assert gen_phfreq == pytest.approx(full_phfreqs, rel=1e-6)
def itest_dte_with_phonons(self, lp, fworker, tmpdir,
input_scf_phonon_gan_low, use_autoparal,
db_data):
"""
Simple test of DteFWWorkflow with autoparal True and False.
Skips dte permutations.
"""
# dte calculations only work with selected values of ixc
input_scf_phonon_gan_low['ixc'] = 7
dte_inputs = dte_from_gsinput(input_scf_phonon_gan_low,
use_phonons=True,
skip_dte_permutations=True,
ph_tol={"tolvrs": 1.0e-7},
ddk_tol={"tolwfr": 1.0e-16},
dde_tol={"tolvrs": 1.0e-7})
wf = DteFWWorkflow(input_scf_phonon_gan_low,
ddk_inp=dte_inputs.filter_by_tags(DDK),
dde_inp=dte_inputs.filter_by_tags(DDE),
dte_inp=dte_inputs.filter_by_tags(DTE),
ph_inp=dte_inputs.filter_by_tags(PH_Q_PERT),
autoparal=use_autoparal,
initialization_info={"kppa": 100})
wf.add_anaddb_dte_fw(input_scf_phonon_gan_low.structure,
dieflag=1,
nlflag=1)
wf.add_mongoengine_db_insertion(db_data)
wf.add_final_cleanup(["WFK"])
scf_fw_id = wf.scf_fw.fw_id
old_new = wf.add_to_db(lpad=lp)
scf_fw_id = old_new[scf_fw_id]
rapidfire(lp, fworker, m_dir=str(tmpdir))
wf = lp.get_wf_by_fw_id(scf_fw_id)
assert wf.state == "COMPLETED"
# check the effect of the final cleanup
scf_task = load_abitask(get_fw_by_task_index(wf, "scf", index=1))
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_WFK"))) == 0
assert len(glob.glob(os.path.join(scf_task.outdir.path, "*_DEN"))) == 1
assert len(glob.glob(os.path.join(scf_task.tmpdir.path, "*"))) == 0
assert len(glob.glob(os.path.join(scf_task.indir.path, "*"))) == 0
# check the save in the DB
from abiflows.database.mongoengine.abinit_results import DteResult
with db_data.switch_collection(DteResult) as DteResult:
results = DteResult.objects()
assert len(results) == 1
r = results[0]
assert r.abinit_input.structure.to_mgobj(
) == input_scf_phonon_gan_low.structure
assert r.abinit_output.structure.to_mgobj(
) == input_scf_phonon_gan_low.structure
assert r.abinit_input.ecut == input_scf_phonon_gan_low['ecut']
assert r.abinit_input.kppa == 100
nptu.assert_array_equal(
r.abinit_input.gs_input.to_mgobj()['ngkpt'],
input_scf_phonon_gan_low['ngkpt'])
ana_task = load_abitask(
get_fw_by_task_index(wf, "anaddb", index=None))
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.anaddb_nc.read())
db_file.seek(0)
assert filecmp.cmp(ana_task.anaddb_nc_path, db_file.name)
mrgddb_task = load_abitask(
get_fw_by_task_index(wf, "mrgddb", index=None))
with tempfile.NamedTemporaryFile(mode="wb") as db_file:
db_file.write(r.abinit_output.ddb.read())
db_file.seek(0)
assert filecmp.cmp(mrgddb_task.merged_ddb_path, db_file.name)
if self.check_numerical_values:
with scf_task.open_gsr() as gsr:
assert gsr.energy == pytest.approx(-680.402255069, rel=0.005)
ana_task = load_abitask(
get_fw_by_task_index(wf, "anaddb", index=None))
with ana_task.open_anaddbnc() as ananc:
assert float(ananc.dchide[0, 0,
2]) == pytest.approx(-1.69328765210,
rel=0.15)
