def test_dojoreport_plots(self):
"""Testing dojoreport plotting methods"""
if not self.has_matplotlib():
raise unittest.SkipTest("Skipping matplotlib tests")
oxygen = pdj_data.pseudo("O.psp8")
report = oxygen.dojo_report
assert report.plot_deltafactor_convergence(xc=oxygen.xc, show=False)
assert report.plot_deltafactor_convergence(xc=oxygen.xc,
code="VASP",
with_soc=False,
show=False)
assert report.plot_deltafactor_convergence(
xc=oxygen.xc, with_soc=True, show=False) is None
assert report.plot_deltafactor_eos(show=False)
assert report.plot_deltafactor_eos(with_soc=True, show=False) is None
assert report.plot_etotal_vs_ecut(show=False)
assert report.plot_etotal_vs_ecut(inv_ecut=True, show=False)
assert report.plot_etotal_vs_ecut(with_soc=True, show=False) is None
assert report.plot_gbrv_convergence(show=False)
assert report.plot_gbrv_convergence(with_soc=True, show=False) is None
assert report.plot_gbrv_eos('bcc', show=False)
assert report.plot_gbrv_eos('fcc', show=False)
assert report.plot_gbrv_eos('fcc', with_soc=True, show=False) is None
assert report.plot_phonon_convergence(show=False)
assert report.plot_phonon_convergence(with_soc=True,
show=False) is None
assert report.plot_ebands(show=False)
assert report.plot_ebands(with_soc=True, show=False) is None
def itest_ghosts_gga_pawxml_flow(fwp, tvars):
"""Testing the ghosts flow for PAW-XML"""
pseudo = pdj_data.pseudo("Si.GGA_PBE-JTH-paw.xml").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
print(pseudo)
assert pseudo.has_dojo_report
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
factory = GhostsFactory(xc=pseudo.xc)
ecut = 10
pawecutdg = 2 * ecut if pseudo.ispaw else None
# maxene 200 will make the task restart.
work = factory.work_for_pseudo(pseudo, kppa=20, maxene=200, ecut=ecut, pawecutdg=pawecutdg,
spin_mode="unpolarized")
assert work.dojo_trial == "ghosts"
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
assert not pseudo.dojo_report.exceptions
assert pseudo.dojo_report.has_trial("ghosts", ecut=ecut)
key = "%.1f" % ecut
data = pseudo.dojo_report["ghosts"][key]
assert data["dojo_status"] == 0
assert data["ecut"] == ecut
ebands = abilab.ElectronBands.from_dict(data["ebands"])
def itest_gbrv_gga_pawxml_flow(fwp, tvars):
"""Testing the GBRV flow with GGA and PAW-XML (relaxation + EOS)"""
pseudo = pdj_data.pseudo("Si.GGA_PBE-JTH-paw.xml").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
assert pseudo.has_dojo_report
assert not pseudo.dojo_report.exceptions
factory = GbrvFactory(pseudo.xc)
ecut = 4
pawecutdg = 2 * ecut if pseudo.ispaw else None
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
struct_types = ["fcc",] # "bcc"]
assert not pseudo.dojo_report.has_trial("gbrv_fcc", ecut=ecut)
for struct_type in struct_types:
work = factory.relax_and_eos_work(pseudo, struct_type, ecut, pawecutdg=pawecutdg, paral_kgb=tvars.paral_kgb)
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
print(pseudo.dojo_report)
assert pseudo.dojo_report.has_trial("gbrv_fcc", ecut=ecut)
assert not pseudo.dojo_report.exceptions
def itest_lantanides_gga_flow(fwp, tvars):
"""Testing the ghosts flow for NC+SOC pseudos."""
pseudo = pdj_data.pseudo("Lu-sp.psp8").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
print(pseudo)
assert pseudo.has_dojo_report
assert not pseudo.supports_soc
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
factory = RocksaltRelaxationFactory(xc=pseudo.xc)
ecut_list = [33]
ngkpt = [1, 1, 1]
#pawecutdg = 2 * ecut if pseudo.ispaw else None
work = factory.work_for_pseudo(pseudo,
ecut_list,
pawecutdg=None,
ngkpt=ngkpt,
include_soc=False)
assert work.dojo_trial == "raren_relax"
flow.register_work(work)
#flow.build_and_pickle_dump(abivalidate=True)
assert flow.make_scheduler().start() == 0
flow.check_status(show=True, verbose=1)
assert all(work.finalized for work in flow)
assert flow.all_ok
def test_oncvpsp_dojo_report(self):
"""Testing pseudopotentials with dojo report"""
h_wdr = pdj_data.pseudo("H-wdr.psp8")
# Test DOJO REPORT and md5
assert h_wdr.symbol == "H"
assert h_wdr.xc == "PBE"
ref_md5 = "8db4531eb441143fdda8032d237d0769"
assert h_wdr.compute_md5() == ref_md5
assert h_wdr.md5 == ref_md5
assert "md5" in h_wdr.dojo_report and h_wdr.dojo_report[
"md5"] == ref_md5
repr(h_wdr)
str(h_wdr)
assert isinstance(h_wdr.as_dict(), dict)
# Test DojoReport
#report = h_wdr.read_dojo_report()
#report = h_wdr.read_dojo_report()
assert h_wdr.has_dojo_report
report = h_wdr.dojo_report
#print(report)
assert report.symbol == "H"
assert report.element.symbol == "H"
assert report["pseudo_type"] == "NC"
assert report["version"] == "1.0"
assert not report.has_hints
# Basic consistency tests.
missings = report.find_missing_entries()
assert "ghosts" in missings
assert not report.has_trial("foo")
for trial in report.trials:
assert report.has_trial(trial)
assert report.has_trial("deltafactor", ecut=32)
# Test deltafactor entry.
self.assert_almost_equal(report["deltafactor"][32]["etotals"][1],
-63.503524424394556)
self.assert_almost_equal(report["deltafactor"][32]["volumes"][1],
66.80439150995784)
assert not report.has_trial("deltafactor", ecut=-1)
assert not report.has_trial("deafactor", ecut="32.00")
# Test GBRV entries
self.assert_almost_equal(report["gbrv_bcc"][32]["a0"],
1.8069170394120007)
self.assert_almost_equal(report["gbrv_fcc"][34]["a0_rel_err"],
0.044806085362549146)
# Test Phonon entry
self.assert_almost_equal(report["phgamma"][36][-1], 528.9531110978663)
# Test API to add ecuts and find missing entries.
assert np.all(
report.ecuts == [32.0, 34.0, 36.0, 38.0, 40.0, 42.0, 52.0])
def itest_ghosts_gga_pawxml_flow(fwp, tvars):
"""Testing the ghosts flow for PAW-XML"""
pseudo = pdj_data.pseudo("Si.GGA_PBE-JTH-paw.xml").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
print(pseudo)
assert pseudo.has_dojo_report
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
factory = GhostsFactory(xc=pseudo.xc)
ecut = 10
pawecutdg = 2 * ecut if pseudo.ispaw else None
# maxene 200 will make the task restart.
work = factory.work_for_pseudo(pseudo, kppa=20, maxene=200, ecut=ecut, pawecutdg=pawecutdg,
spin_mode="unpolarized")
assert work.dojo_trial == "ghosts"
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
assert not pseudo.dojo_report.exceptions
assert pseudo.dojo_report.has_trial("ghosts", ecut=ecut)
key = "%.1f" % ecut
data = pseudo.dojo_report["ghosts"][key]
assert data["dojo_status"] == 0
assert data["ecut"] == ecut
ebands = abilab.ElectronBands.from_dict(data["ebands"])
def itest_lantanides_gga_flow(fwp, tvars):
"""Testing the ghosts flow for NC+SOC pseudos."""
pseudo = pdj_data.pseudo("Lu-sp.psp8").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
print(pseudo)
assert pseudo.has_dojo_report
assert not pseudo.supports_soc
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
factory = RocksaltRelaxationFactory(xc=pseudo.xc)
ecut_list = [33]
ngkpt = [1, 1, 1]
#pawecutdg = 2 * ecut if pseudo.ispaw else None
work = factory.work_for_pseudo(pseudo, ecut_list, pawecutdg=None, ngkpt=ngkpt, include_soc=False)
assert work.dojo_trial == "raren_relax"
flow.register_work(work)
#flow.build_and_pickle_dump(abivalidate=True)
assert flow.make_scheduler().start() == 0
flow.check_status(show=True, verbose=1)
assert all(work.finalized for work in flow)
assert flow.all_ok
def itest_nc_phonons_gamma(fwp, tvars):
"""Testing the calculation of phonons at Gamma with/without the Asr (NC pseudos)."""
#pseudo = pdj_data.pseudo("Si.GGA_PBE-JTH-paw.xml").as_tmpfile(fwp.workdir)
pseudo = pdj_data.pseudo("Si.psp8").as_tmpfile(fwp.workdir)
assert pseudo is not None
assert pseudo.has_dojo_report
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
ecut = 8
pawecutdg = 2 * ecut if pseudo.ispaw else None
# This one requires deltafactor!
factory = GammaPhononFactory(xc=pseudo.xc)
work = factory.work_for_pseudo(pseudo, kppa=20, ecut=ecut, pawecutdg=pawecutdg)
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
#return
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
assert not pseudo.dojo_report.exceptions
assert pseudo.dojo_report.has_trial("phgamma", ecut=ecut)
def test_dojoreport_plots(self):
"""Testing dojoreport plotting methods"""
h_wdr = pdj_data.pseudo("H-wdr.psp8")
report = h_wdr.dojo_report
assert isinstance(report.plot_deltafactor_convergence(xc=h_wdr.xc, show=False), Fig)
assert report.plot_deltafactor_convergence(xc=h_wdr.xc, with_soc=True, show=False) is None
assert isinstance(report.plot_deltafactor_eos(show=False), Fig)
assert isinstance(report.plot_etotal_vs_ecut(show=False), Fig)
assert isinstance(report.plot_gbrv_convergence(show=False), Fig)
assert isinstance(report.plot_gbrv_eos('bcc', show=False), Fig)
assert isinstance(report.plot_gbrv_eos('fcc', show=False), Fig)
assert isinstance(report.plot_phonon_convergence(show=False), Fig)
def test_oncvpsp_dojo_report(self):
"""Testing pseudopotentials with dojo report"""
h_wdr = pdj_data.pseudo("H-wdr.psp8")
# Test DOJO REPORT and md5
assert h_wdr.symbol == "H"
assert h_wdr.xc == "PBE"
ref_md5 = "8db4531eb441143fdda8032d237d0769"
assert h_wdr.compute_md5() == ref_md5
assert h_wdr.md5 == ref_md5
assert "md5" in h_wdr.dojo_report and h_wdr.dojo_report["md5"] == ref_md5
repr(h_wdr); str(h_wdr)
assert isinstance(h_wdr.as_dict(), dict)
# Test DojoReport
#report = h_wdr.read_dojo_report()
#report = h_wdr.read_dojo_report()
assert h_wdr.has_dojo_report
report = h_wdr.dojo_report
#print(report)
assert report.symbol == "H"
assert report.element.symbol == "H"
assert report["pseudo_type"] == "NC"
assert report["version"] == "1.0"
assert not report.has_hints
# Basic consistency tests.
missings = report.find_missing_entries()
assert "ghosts" in missings
assert not report.has_trial("foo")
for trial in report.trials:
assert report.has_trial(trial)
assert report.has_trial("deltafactor", ecut=32)
# Test deltafactor entry.
self.assert_almost_equal(report["deltafactor"][32]["etotals"][1], -63.503524424394556)
self.assert_almost_equal(report["deltafactor"][32]["volumes"][1], 66.80439150995784)
assert not report.has_trial("deltafactor", ecut=-1)
assert not report.has_trial("deafactor", ecut="32.00")
# Test GBRV entries
self.assert_almost_equal(report["gbrv_bcc"][32]["a0"], 1.8069170394120007)
self.assert_almost_equal(report["gbrv_fcc"][34]["a0_rel_err"], 0.044806085362549146)
# Test Phonon entry
self.assert_almost_equal(report["phgamma"][36][-1], 528.9531110978663)
# Test API to add ecuts and find missing entries.
assert np.all(report.ecuts == [32.0, 34.0, 36.0, 38.0, 40.0, 42.0, 52.0])
def test_nc_silicon_gammaphonon_factory(self):
"""Testing GammaPhononFactory for NC silicon."""
pseudo = pdj_data.pseudo("Si.psp8")
phgamma_factory = GammaPhononFactory(xc=pseudo.xc)
flow = abilab.Flow.temporary_flow()
work = phgamma_factory.work_for_pseudo(pseudo, ecut=3, pawecutdg=None)
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
flow.check_status(show=True)
flow.rmtree()
def test_dojo_report_base_api(self):
"""Testing dojo report low-level API."""
#report = DojoReport.from_hints(10, "Si")
pseudo = pdj_data.pseudo("Si.psp8")
ppgen_hints = {
"low": {
"ecut": 8.0,
"pawecutdg": 8.0
},
"normal": {
"ecut": 10.0,
"pawecutdg": 10.0
},
"high": {
"ecut": 16.0,
"pawecutdg": 16.0
},
}
report = DojoReport.empty_from_pseudo(pseudo, ppgen_hints, devel=False)
repr(repr)
str(report)
assert report.symbol == "Si"
assert report.element.symbol == "Si"
assert report.ecuts
assert not report.trials
for trial in report.ALL_TRIALS:
assert not report.has_trial(trial)
assert not report.has_hints
assert report.check()
#prev_ecuts = copy(report.ecuts)
#report.add_ecuts(10000)
#assert np.all(report.ecuts == prev_ecuts + [10000])
report.add_hints([10, 20, 30])
assert report.has_hints
assert report["hints"]["low"]["ecut"] == 10
assert report["hints"]["high"]["ecut"] == 30
assert not report.isvalidated
#assert not report.md5
# Test add_entry
with self.assertRaises(ValueError):
report.add_entry("foobar", ecut=10, entry={})
assert not report.has_trial("deltafactor", ecut=10)
report.add_entry("deltafactor", ecut=10, entry={})
repr(report)
str(report)
assert report.has_trial("deltafactor", ecut=10)
def test_nc_silicon_gbrv_factory(self):
"""Testing GBRV work for NC silicon."""
pseudo = pdj_data.pseudo("Si.psp8")
gbrv_factory = GbrvFactory(xc=pseudo.xc)
flow = abilab.Flow.temporary_flow()
for struct_type in ("fcc", "bcc"):
work = gbrv_factory.relax_and_eos_work(pseudo, struct_type, ecut=3, pawecutdg=None)
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
flow.check_status(show=True)
assert len(flow[0]) == 1
flow.rmtree()
def itest_deltafactor_gga_pawxml(fwp, tvars):
"""
Testing the flow used for the computation of the deltafactor with PAW and GGA XC.
"""
# Path of the pseudopotential to test.
pseudo = pdj_data.pseudo("Si.GGA_PBE-JTH-paw.xml").as_tmpfile(
tmpdir=fwp.workdir)
assert pseudo is not None
assert pseudo.has_dojo_report
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
# Build the workflow for the computation of the deltafactor.
# The workflow will produce a pdf file with the equation of state
# and a file deltafactor.txt with the final results in the
# outdir directory DELTAFACTOR/work_0/outdir.
kppa = 20 # this value is for testing purpose (6570 is the correct one)
ecut = 2
pawecutdg = ecut * 2 if pseudo.ispaw else None
assert not pseudo.dojo_report.has_trial("deltafactor", ecut=ecut)
work = DeltaFactory(pseudo.xc).work_for_pseudo(pseudo,
kppa=kppa,
ecut=ecut,
pawecutdg=pawecutdg,
include_soc=False,
paral_kgb=tvars.paral_kgb)
# Register the workflow.
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
for task in flow[0]:
task.start_and_wait()
flow.check_status(show=True)
assert flow.all_ok
assert all(work.finalized for work in flow)
results = flow[0].get_results()
#20.453 ang^3 88.545 GPa 4.31 20.8658081501 336.680999051 GPa -35.681897152
#delta Equation of State: deltafactor_polyfit
#Minimum volume = 20.87 Ang^3
#modulus = 2.10 eV/Ang^3 = 336.68 GPa, b1 = -35.68
#Deltafactor = 15.681 meV
assert pseudo.dojo_report.has_trial("deltafactor", ecut=ecut)
assert not pseudo.dojo_report.exceptions
def itest_deltafactor_gga_ncsoc(fwp, tvars):
"""
Testing the flow used for the computation of the deltafactor with GGA and NC+SOC.
"""
# return
# Path of the pseudopotential to test.
pseudo = pdj_data.pseudo("Pb-d-3_r.psp8").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo.has_dojo_report
assert pseudo.supports_soc
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
# Build the workflow for the computation of the deltafactor.
# The workflow will produce a pdf file with the equation of state
# and a file deltafactor.txt with the final results in the
# outdir directory DELTAFACTOR/work_0/outdir.
kppa = 40 # this value is for testing purpose (6570 is the correct one)
ecut = 8
pawecutdg = ecut * 2 if pseudo.ispaw else None
assert pseudo.dojo_report.has_trial("deltafactor", ecut=12)
assert not pseudo.dojo_report.has_trial("deltafactor_soc", ecut=ecut)
work = DeltaFactory(pseudo.xc).work_for_pseudo(pseudo,
kppa=kppa,
ecut=ecut,
pawecutdg=pawecutdg,
include_soc=True,
paral_kgb=tvars.paral_kgb)
# Register the workflow.
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
for task in flow[0]:
task.start_and_wait()
flow.check_status(show=True)
assert flow.all_ok
assert all(work.finalized for work in flow)
results = flow[0].get_results()
assert pseudo.dojo_report.has_trial("deltafactor_soc", ecut=ecut)
assert not pseudo.dojo_report.exceptions
def itest_deltafactor_gga_pawxml(fwp, tvars):
"""
Testing the flow used for the computation of the deltafactor with PAW and GGA XC.
"""
# Path of the pseudopotential to test.
pseudo = pdj_data.pseudo("Si.GGA_PBE-JTH-paw.xml").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
assert pseudo.has_dojo_report
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
# Build the workflow for the computation of the deltafactor.
# The workflow will produce a pdf file with the equation of state
# and a file deltafactor.txt with the final results in the
# outdir directory DELTAFACTOR/work_0/outdir.
kppa = 20 # this value is for testing purpose (6570 is the correct one)
ecut = 2
pawecutdg = ecut * 2 if pseudo.ispaw else None
assert not pseudo.dojo_report.has_trial("deltafactor", ecut=ecut)
work = DeltaFactory(pseudo.xc).work_for_pseudo(pseudo,
kppa=kppa, ecut=ecut, pawecutdg=pawecutdg,
include_soc=False,
paral_kgb=tvars.paral_kgb)
# Register the workflow.
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
for task in flow[0]:
task.start_and_wait()
flow.check_status(show=True)
assert flow.all_ok
assert all(work.finalized for work in flow)
results = flow[0].get_results()
#20.453 ang^3 88.545 GPa 4.31 20.8658081501 336.680999051 GPa -35.681897152
#delta Equation of State: deltafactor_polyfit
#Minimum volume = 20.87 Ang^3
#modulus = 2.10 eV/Ang^3 = 336.68 GPa, b1 = -35.68
#Deltafactor = 15.681 meV
assert pseudo.dojo_report.has_trial("deltafactor", ecut=ecut)
assert not pseudo.dojo_report.exceptions
def test_nc_silicon_df(self):
"""Testing df factory for NC silicon."""
pseudo = pdj_data.pseudo("Si.psp8")
df_factory = DeltaFactory(xc=pseudo.xc)
extra_abivars = {
"mem_test": 0,
"fband": 2,
"nstep": 100,
"paral_kgb": 0,
}
flow = abilab.Flow.temporary_flow()
work = df_factory.work_for_pseudo(pseudo, kppa=1, ecut=2, pawecutdg=None, **extra_abivars)
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
flow.check_status(show=True)
flow.rmtree()
def itest_gbrv_gga_ncsoc_flow(fwp, tvars):
"""Testing the GBRV flow with GGA and ONCVPSP+SO (relaxation + EOS)"""
#return
pseudo = pdj_data.pseudo("Pb-d-3_r.psp8").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
assert pseudo.supports_soc
assert not pseudo.dojo_report.exceptions
factory = GbrvFactory(pseudo.xc)
ecut = 2
#ecut = 6
pawecutdg = 2 * ecut if pseudo.ispaw else None
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
struct_types = [
"fcc",
] # "bcc"]
assert pseudo.dojo_report.has_trial("gbrv_fcc", ecut=4)
assert not pseudo.dojo_report.has_trial("gbrv_fcc", ecut=ecut)
for struct_type in struct_types:
work = factory.relax_and_eos_work(pseudo,
struct_type,
ecut,
pawecutdg=pawecutdg,
include_soc=True,
paral_kgb=tvars.paral_kgb)
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
print(pseudo.dojo_report)
assert pseudo.dojo_report.has_trial("gbrv_fcc_soc", ecut=ecut)
assert not pseudo.dojo_report.exceptions
def itest_ghosts_gga_ncsoc_flow(fwp, tvars):
"""Testing the ghosts flow for NC+SOC pseudos."""
pseudo = pdj_data.pseudo("Pb-d-3_r.psp8").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
print(pseudo)
assert pseudo.has_dojo_report
assert pseudo.supports_soc
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
factory = GhostsFactory(xc=pseudo.xc)
ecut = 4
pawecutdg = 2 * ecut if pseudo.ispaw else None
kppa = 20 # this value is for testing purpose
work = factory.work_for_pseudo(pseudo,
kppa=kppa,
maxene=2,
ecut=ecut,
pawecutdg=pawecutdg,
spin_mode="spinor",
include_soc=True)
assert work.dojo_trial == "ghosts_soc"
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
# Reconstruct ElectronBands from JSON.
assert not pseudo.dojo_report.exceptions
print(list(pseudo.dojo_report.keys()))
assert pseudo.dojo_report.has_trial("ghosts_soc", ecut=ecut)
key = "%.1f" % ecut
data = pseudo.dojo_report["ghosts_soc"][key]
assert data["dojo_status"] == 0
assert data["ecut"] == ecut
ebands = abilab.ElectronBands.from_dict(data["ebands"])
def itest_deltafactor_gga_ncsoc(fwp, tvars):
"""
Testing the flow used for the computation of the deltafactor with GGA and NC+SOC.
"""
# return
# Path of the pseudopotential to test.
pseudo = pdj_data.pseudo("Pb-d-3_r.psp8").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo.has_dojo_report
assert pseudo.supports_soc
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
# Build the workflow for the computation of the deltafactor.
# The workflow will produce a pdf file with the equation of state
# and a file deltafactor.txt with the final results in the
# outdir directory DELTAFACTOR/work_0/outdir.
kppa = 40 # this value is for testing purpose (6570 is the correct one)
ecut = 8
pawecutdg = ecut * 2 if pseudo.ispaw else None
assert pseudo.dojo_report.has_trial("deltafactor", ecut=12)
assert not pseudo.dojo_report.has_trial("deltafactor_soc", ecut=ecut)
work = DeltaFactory(pseudo.xc).work_for_pseudo(pseudo,
kppa=kppa, ecut=ecut, pawecutdg=pawecutdg,
include_soc=True,
paral_kgb=tvars.paral_kgb)
# Register the workflow.
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
for task in flow[0]:
task.start_and_wait()
flow.check_status(show=True)
assert flow.all_ok
assert all(work.finalized for work in flow)
results = flow[0].get_results()
assert pseudo.dojo_report.has_trial("deltafactor_soc", ecut=ecut)
assert not pseudo.dojo_report.exceptions
def itest_gbrv_gga_pawxml_flow(fwp, tvars):
"""Testing the GBRV flow with GGA and PAW-XML (relaxation + EOS)"""
pseudo = pdj_data.pseudo("Si.GGA_PBE-JTH-paw.xml").as_tmpfile(
tmpdir=fwp.workdir)
assert pseudo is not None
assert pseudo.has_dojo_report
assert not pseudo.dojo_report.exceptions
factory = GbrvFactory(pseudo.xc)
ecut = 4
pawecutdg = 2 * ecut if pseudo.ispaw else None
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
struct_types = [
"fcc",
] # "bcc"]
assert not pseudo.dojo_report.has_trial("gbrv_fcc", ecut=ecut)
for struct_type in struct_types:
work = factory.relax_and_eos_work(pseudo,
struct_type,
ecut,
pawecutdg=pawecutdg,
paral_kgb=tvars.paral_kgb)
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
print(pseudo.dojo_report)
assert pseudo.dojo_report.has_trial("gbrv_fcc", ecut=ecut)
assert not pseudo.dojo_report.exceptions
def test_dojo_report_base_api(self):
"""Testing dojo report low-level API."""
#report = DojoReport.from_hints(10, "Si")
pseudo = pdj_data.pseudo("Si.psp8")
ppgen_hints = {
"low": {"ecut": 8.0, "pawecutdg": 8.0},
"normal": {"ecut": 10.0, "pawecutdg": 10.0},
"high": { "ecut": 16.0, "pawecutdg": 16.0},
}
report = DojoReport.empty_from_pseudo(pseudo, ppgen_hints, devel=False)
repr(repr); str(report)
assert report.symbol == "Si"
assert report.element.symbol == "Si"
assert report.ecuts
assert not report.trials
for trial in report.ALL_TRIALS:
assert not report.has_trial(trial)
assert not report.has_hints
assert report.check()
#prev_ecuts = copy(report.ecuts)
#report.add_ecuts(10000)
#assert np.all(report.ecuts == prev_ecuts + [10000])
report.add_hints([10, 20, 30])
assert report.has_hints
assert report["hints"]["low"]["ecut"] == 10
assert report["hints"]["high"]["ecut"] == 30
assert not report.isvalidated
#assert not report.md5
# Test add_entry
with self.assertRaises(ValueError):
report.add_entry("foobar", ecut=10, entry={})
assert not report.has_trial("deltafactor", ecut=10)
report.add_entry("deltafactor", ecut=10, entry={})
repr(report); str(report)
assert report.has_trial("deltafactor", ecut=10)
def itest_ghosts_gga_ncsoc_flow(fwp, tvars):
"""Testing the ghosts flow for NC+SOC pseudos."""
pseudo = pdj_data.pseudo("Pb-d-3_r.psp8").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
print(pseudo)
assert pseudo.has_dojo_report
assert pseudo.supports_soc
assert not pseudo.dojo_report.exceptions
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
factory = GhostsFactory(xc=pseudo.xc)
ecut = 4
pawecutdg = 2 * ecut if pseudo.ispaw else None
kppa = 20 # this value is for testing purpose
work = factory.work_for_pseudo(pseudo, kppa=kppa, maxene=2, ecut=ecut, pawecutdg=pawecutdg,
spin_mode="spinor", include_soc=True)
assert work.dojo_trial == "ghosts_soc"
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
# Reconstruct ElectronBands from JSON.
assert not pseudo.dojo_report.exceptions
print(list(pseudo.dojo_report.keys()))
assert pseudo.dojo_report.has_trial("ghosts_soc", ecut=ecut)
key = "%.1f" % ecut
data = pseudo.dojo_report["ghosts_soc"][key]
assert data["dojo_status"] == 0
assert data["ecut"] == ecut
ebands = abilab.ElectronBands.from_dict(data["ebands"])
def itest_gbrv_gga_ncsoc_flow(fwp, tvars):
"""Testing the GBRV flow with GGA and ONCVPSP+SO (relaxation + EOS)"""
#return
pseudo = pdj_data.pseudo("Pb-d-3_r.psp8").as_tmpfile(tmpdir=fwp.workdir)
assert pseudo is not None
assert pseudo.supports_soc
assert not pseudo.dojo_report.exceptions
factory = GbrvFactory(pseudo.xc)
ecut = 2
#ecut = 6
pawecutdg = 2 * ecut if pseudo.ispaw else None
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager)
struct_types = ["fcc",] # "bcc"]
assert pseudo.dojo_report.has_trial("gbrv_fcc", ecut=4)
assert not pseudo.dojo_report.has_trial("gbrv_fcc", ecut=ecut)
for struct_type in struct_types:
work = factory.relax_and_eos_work(pseudo, struct_type, ecut, pawecutdg=pawecutdg,
include_soc=True, paral_kgb=tvars.paral_kgb)
flow.register_work(work)
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
flow.check_status(show=True)
assert all(work.finalized for work in flow)
assert flow.all_ok
print(pseudo.dojo_report)
assert pseudo.dojo_report.has_trial("gbrv_fcc_soc", ecut=ecut)
assert not pseudo.dojo_report.exceptions
def test_dojoreport_plots(self):
"""Testing dojoreport plotting methods"""
if not self.has_matplotlib():
raise unittest.SkipTest("Skipping matplotlib tests")
oxygen = pdj_data.pseudo("O.psp8")
report = oxygen.dojo_report
assert report.plot_deltafactor_convergence(xc=oxygen.xc, show=False)
assert report.plot_deltafactor_convergence(xc=oxygen.xc, code="VASP", with_soc=False, show=False)
assert report.plot_deltafactor_convergence(xc=oxygen.xc, with_soc=True, show=False) is None
assert report.plot_deltafactor_eos(show=False)
assert report.plot_deltafactor_eos(with_soc=True, show=False) is None
assert report.plot_etotal_vs_ecut(show=False)
assert report.plot_etotal_vs_ecut(inv_ecut=True, show=False)
assert report.plot_etotal_vs_ecut(with_soc=True, show=False) is None
assert report.plot_gbrv_convergence(show=False)
assert report.plot_gbrv_convergence(with_soc=True, show=False) is None
assert report.plot_gbrv_eos('bcc', show=False)
assert report.plot_gbrv_eos('fcc', show=False)
assert report.plot_gbrv_eos('fcc', with_soc=True, show=False) is None
assert report.plot_phonon_convergence(show=False)
assert report.plot_phonon_convergence(with_soc=True, show=False) is None
assert report.plot_ebands(show=False)
assert report.plot_ebands(with_soc=True, show=False) is None
