def test_dte_from_gsinput(self):
"""Testing for dte_from_gsinput"""
#self.skip_if_not_abinit(version='8.3.2')
from abipy.abio.factories import dte_from_gsinput
pseudos = [self.ga_pseudo.pseudo_with_symbol('Ga'), self.n_pseudo.pseudo_with_symbol('N')]
gs_inp = gs_input(self.gan_structure, pseudos, kppa=None, ecut=2,
spin_mode="unpolarized", smearing=None)
# dte calculations only work with selected values of ixc
gs_inp['ixc'] = 7
multi = dte_from_gsinput(gs_inp, use_phonons=False, skip_dte_permutations=False)
self.abivalidate_multi(multi)
multi = dte_from_gsinput(gs_inp, use_phonons=True, skip_dte_permutations=True)
self.abivalidate_multi(multi)
inp1 = multi[0]
inp2 = multi[5]
if False:
with open('dte_from_gsinput_1.json', mode='w') as fp:
json.dump(inp1.as_dict(), fp, indent=2)
with open('dte_from_gsinput_2.json', mode='w') as fp:
json.dump(inp2.as_dict(), fp, indent=2)
self.assert_input_equality('dte_from_gsinput_1.json', inp1)
self.assert_input_equality('dte_from_gsinput_2.json', inp2)
def test_dte_from_gsinput(self):
"""Testing for dte_from_gsinput"""
#self.skip_if_not_abinit(version='8.3.2')
from abipy.abio.factories import dte_from_gsinput
pseudos = [self.ga_pseudo.pseudo_with_symbol('Ga'), self.n_pseudo.pseudo_with_symbol('N')]
gs_inp = gs_input(self.gan_structure, pseudos, kppa=None, ecut=2,
spin_mode="unpolarized", smearing=None)
# dte calculations only work with selected values of ixc
gs_inp['ixc'] = 7
multi = dte_from_gsinput(gs_inp, use_phonons=False, skip_dte_permutations=False)
self.abivalidate_multi(multi)
multi = dte_from_gsinput(gs_inp, use_phonons=True, skip_dte_permutations=True)
self.abivalidate_multi(multi)
inp1 = multi[0]
inp2 = multi[5]
if False:
print("Updating json reference files.")
#with open('dte_from_gsinput_1.json', mode='w') as fp:
# json.dump(inp1.as_dict(), fp, indent=2)
#with open('dte_from_gsinput_2.json', mode='w') as fp:
# json.dump(inp2.as_dict(), fp, indent=2)
self.assert_input_equality('dte_from_gsinput_1.json', inp1)
self.assert_input_equality('dte_from_gsinput_2.json', inp2)
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_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_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)
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)