def itest_not_converged(self, lp, fworker, tmpdir, input_scf_phonon_si_low):
"""
Tests the missed convergence and restart for the Strain task. Other restarts are checked in
the PhononWorkflow tests.
"""
# only strain perturbations included
dfpt_inputs = dfpt_from_gsinput(input_scf_phonon_si_low, do_ddk=False, do_dde=False,
do_strain=True, do_dte=False, skip_dte_permutations=True,
strain_tol={"tolvrs": 1.0e-7} )
dfpt_inputs.set_vars(nstep=3)
wf = DfptFWWorkflow(input_scf_phonon_si_low, ddk_inp=None, dde_inp=None, ph_inp=None,
strain_inp=dfpt_inputs.filter_by_tags(STRAIN), dte_inp=None,
nscf_inp=None, initialization_info=None, autoparal=False)
scf_id = wf.scf_fw.fw_id
old_new = wf.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)
# strain
check_restart_task_type(lp, fworker, tmpdir, scf_id, "strain_pert_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_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_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_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)
relax_input = relaxed.abinit_input.last_input.to_mgobj()
# We use the same k and q point grid
qppa = kppa
extra_abivars = dict(chkprim=1, nstep=100, chksymbreak=1)
# as for the relax workflow, information stored in the database for the calculation. In particular information
# about the source structure.
initialization_info = dict(kppa=kppa, mp_id=mp_id,
relax_db=source_db.as_dict_no_credentials(), relax_id=relaxed.id,
relax_tol_val=1e-6, qppa=qppa)
# In this case the base is the input file of the of the relax workflow.
# Use the DfptFWWorkflow that allow to calculate the different kind of Dfpt perturbations
# with abinit in a single workflow. In this case only the phonons.
gen = DfptFWWorkflow.from_gs_input(structure=structure, gs_input=relax_input, extra_abivars=extra_abivars, autoparal=True,
initialization_info=initialization_info, do_ddk=True, do_dde=True, ph_ngqpt=[1,1,1],
do_strain=False)
# add to the workflow a step that automatically adds the results to the database in the collection specified above.
gen.add_mongoengine_db_insertion(db)
# add a step to the workflow that cleans up files with this extensions once the other calculations are completed.
# The list of extensions is customizable and these are usually file that won't be needed again.
# Here we do not delete the DDB files.
gen.add_final_cleanup(["WFK", "1WF", "WFQ", "1POT", "1DEN"])
# This will specify that all the steps will be forced to be executed on the same worker
# and will set the worker to the one chosen before for the existing fireworks. This step is not mandatory.
gen.fix_fworker(fworker_name)
# adds the workflow to the fireworks database. It will use the fireworks LaunchPad that has been set by default.