def test_abipsps(self):
"""Testing abipsps.py"""
if not self.has_matplotlib(): return
si_pspnc = abidata.pseudo("14si.pspnc")
si_oncv = abidata.pseudo("Si.oncvpsp")
env = self.get_env()
env.run(self.script, si_pspnc.path, self.loglevel, self.verbose)
env.run(self.script, si_pspnc.path, si_oncv.path, self.loglevel, self.verbose,
expect_stderr=True)
def test_class(self):
pseudo = AbinitPseudoData()
pseudo.set_pseudos_from_abinit_input(self.scf_inp)
with tempfile.NamedTemporaryFile("wt") as files_file:
files_file.write("run.abi\nrun.abo\nin\n\out\ntmp\n")
files_file.writelines([
abidata.pseudo("C.oncvpsp").filepath,
abidata.pseudo("Ga.oncvpsp").filepath
])
pseudo.set_pseudos_from_files_file(files_file.name, 2)
def test_abipsps(self):
"""Testing abipsps.py"""
if not self.has_matplotlib(): return
si_pspnc = abidata.pseudo("14si.pspnc")
si_oncv = abidata.pseudo("Si.oncvpsp")
env = self.get_env()
env.run(self.script, si_pspnc.path, self.loglevel, self.verbose)
env.run(self.script,
si_pspnc.path,
si_oncv.path,
self.loglevel,
self.verbose,
expect_stderr=True)
def test_nc_silicon_gbrv_factory(self):
"""Testing GBRV work for NC silicon."""
flow = abilab.Flow(workdir=tempfile.mkdtemp())
gbrv_factory = GbrvFactory()
extra_abivars = {
"mem_test": 0,
"fband": 2,
"nstep": 100,
"paral_kgb": 0,
}
# Create a tmp pseudo because the flow will add the DOJO_REPORT
pseudo = abidata.pseudo("14si.pspnc").as_tmpfile()
for struct_type in ("fcc", "bcc"):
work = gbrv_factory.relax_and_eos_work(pseudo, struct_type, ecut=3, pawecutdg=None, **extra_abivars)
flow.register_work(work)
flow.build_and_pickle_dump()
isok, results = flow.abivalidate_inputs()
assert isok
flow.make_scheduler().start()
assert flow.all_ok
assert pseudo.has_dojo_report
flow.rmtree()
def test_nc_silicon_df(self):
"""Testing df factory for NC silicon."""
flow = abilab.Flow(workdir=tempfile.mkdtemp())
df_factory = DeltaFactory()
extra_abivars = {
"mem_test": 0,
"fband": 2,
"nstep": 100,
"paral_kgb": 0,
}
# Create a tmp pseudo because the flow will add the DOJO_REPORT
pseudo = abidata.pseudo("14si.pspnc").as_tmpfile()
work = df_factory.work_for_pseudo(pseudo, kppa=1, ecut=2, pawecutdg=None, **extra_abivars)
flow.register_work(work)
flow.build_and_pickle_dump()
print("Working in ", flow.workdir)
isok, results = flow.abivalidate_inputs()
if not isok:
print(results)
assert isok
if not DRY_RUN:
flow.make_scheduler().start()
assert flow.all_ok
assert all(work.finalized for work in flow)
assert pseudo.has_dojo_report
flow.rmtree()
def itest_deltafactor(fwp, tvars):
"""Testing the flow used for the computation of the deltafactor."""
# Path of the pseudopotential to test.
pseudo = abidata.pseudo("Si.GGA_PBE-JTH-paw.xml").as_tmpfile()
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
work = DeltaFactory().work_for_pseudo(pseudo, kppa=kppa, ecut=ecut, pawecutdg=pawecutdg, paral_kgb=tvars.paral_kgb)
# Register the workflow.
flow.register_work(work)
flow.allocate()
flow.build_and_pickle_dump()
for task in flow[0]:
task.start_and_wait()
flow.check_status()
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
results = flow[0].get_results()
def build_flow(options):
# Path of the pseudopotential to test.
#pseudo = data.pseudo("14si.pspnc")
pseudo = data.pseudo("Si.GGA_PBE-JTH-paw.xml")
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
# Initialize the flow.
flow = abilab.Flow(workdir=workdir, manager=options.manager, remove=options.remove)
# Build the workflow for the computation of the deltafactor.
# The calculation is done with the parameters and the cif files
# used in the original paper. We only have to specify
# the cutoff energy ecut (Ha) for the pseudopotential.
# 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.
factory = DeltaFactory()
kppa = 6750 # Use this to have the official k-point sampling
kppa = 50 # this value is for testing purpose.
ecut = 8
pawecutdg = ecut * 2 if pseudo.ispaw else None
work = factory.work_for_pseudo(pseudo, accuracy="normal", kppa=kppa,
ecut=ecut, pawecutdg=pawecutdg,
toldfe=1.e-8, smearing="fermi_dirac:0.0005")
# Register the workflow.
flow.register_work(work)
return flow
def test_lobsterinput(self):
"""Testing LobsterInput."""
lin = LobsterInput(atom_pairs=[(0, 1), (2, 3)], orbitalwise=True)
repr(lin); str(lin)
assert lin.to_string(verbose=2)
lin.set_basis_functions_from_abinit_pseudos([abidata.pseudo("Al.GGA_PBE-JTH.xml")])
# XML parser does not guarantee order.
assert sorted(lin.basis_functions[0].split()) == sorted("Al 3s 3p".split())
lin.write(self.mkdtemp())
def get_pseudos(structure, extension='oncvpsp'):
"""
returns a list of pseudos names for structure. This list should be fed to abidata.pseudos like
abidata.pseudos(get_pseudos(structure))
"""
pseudos = []
for element in structure.composition.elements:
pseudos.append(abidata.pseudo(str(element) + '.' + extension))
#todo test if the pseudo potential file exists
return pseudos
def get_pseudos(structure, extension="oncvpsp"):
"""
returns a list of pseudos names for structure. This list should be fed to abidata.pseudos like
abidata.pseudos(get_pseudos(structure))
"""
pseudos = []
for element in structure.composition.elements:
pseudos.append(abidata.pseudo(str(element) + "." + extension))
# todo test if the pseudo potential file exists
return pseudos
def test_psps_nc_silicon(self):
"""Very preliminary test for PSPS.nc file with Ga.oncvpsp"""
pseudo = abidata.pseudo("Ga.oncvpsp")
with pseudo.open_pspsfile(ecut=10) as psps:
print(psps)
r = psps.reader
assert r.usepaw == 0 and r.ntypat == 1
if has_matplotlib():
psps.plot(what="all", show=False)
psps.compare(psps, show=False)
def test_psps_nc_silicon(self):
"""Test PSPS.nc file with Ga.oncvpsp"""
pseudo = abidata.pseudo("Ga.oncvpsp")
with pseudo.open_pspsfile(ecut=10) as psps:
print(psps)
r = psps.reader
assert r.usepaw == 0 and r.ntypat == 1
if has_matplotlib():
psps.plot(what="all", show=False)
psps.compare(psps, show=False)
def itest_gbrv_flow(fwp, tvars):
"""The the GBRV flow: relaxation + EOS computation."""
factory = GbrvFactory()
#pseudo = "si_pbe_v1_abinit.paw"
pseudo = abidata.pseudo("Si.GGA_PBE-JTH-paw.xml")
ecut = 2
pawecutdg = 2 * ecut if pseudo.ispaw else None
flow = abilab.Flow(workdir=fwp.workdir,
manager=fwp.manager,
pickle_protocol=0)
struct_types = ["fcc"] #, "bcc"]
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.allocate()
flow.build_and_pickle_dump()
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
#work = flow[0]
#t0 = work[0]
#assert len(work) == 1
#t0.start_and_wait()
#flow.check_status()
# At this point on_all_ok is called.
#assert t0.status == t0.S_OK
#assert len(flow) == 2
#assert len(flow[1]) == 9
#assert not flow.all_ok
#for task in flow[1]:
# task.start_and_wait()
flow.check_status()
flow.show_status()
assert all(work.finalized for work in flow)
assert flow.all_ok
def test_helper_functions(self):
"""Testing AbinitInput helper functions."""
pseudo = abidata.pseudo("14si.pspnc")
pseudo_dir = os.path.dirname(pseudo.filepath)
inp = AbinitInput(structure=abidata.cif_file("si.cif"), pseudos=pseudo.basename, pseudo_dir=pseudo_dir)
nval_atoms = inp.valence_electrons_per_atom
assert len(nval_atoms) == 2
assert nval_atoms == [4, 4]
inp.set_kmesh(ngkpt=(1, 2, 3), shiftk=(1, 2, 3, 4, 5, 6))
assert inp["kptopt"] == 1 and inp["nshiftk"] == 2
assert inp.uses_ktimereversal
inp.set_gamma_sampling()
assert inp["kptopt"] == 1 and inp["nshiftk"] == 1
assert np.all(inp["shiftk"] == 0)
inp.set_autokmesh(nksmall=2)
assert inp["kptopt"] == 1 and np.all(inp["ngkpt"] == [2, 2, 2]) and inp["nshiftk"] == 4
inp.set_kpath(ndivsm=3, kptbounds=None)
assert inp["ndivsm"] == 3 and inp["iscf"] == -2 and len(inp["kptbounds"]) == 12
inp.set_qpath(ndivsm=3, qptbounds=None)
assert len(inp["ph_qpath"]) == 12 and inp["ph_nqpath"] == 12 and inp["ph_ndivsm"] == 3
inp.set_phdos_qmesh(nqsmall=16, method="tetra")
assert inp["ph_intmeth"] == 2 and np.all(inp["ph_ngqpt"] == 16) and np.all(inp["ph_qshift"] == 0)
inp.set_kptgw(kptgw=(1, 2, 3, 4, 5, 6), bdgw=(1, 2))
assert inp["nkptgw"] == 2 and np.all(inp["bdgw"].ravel() == np.array(len(inp["kptgw"]) * [1,2]).ravel())
linps = inp.linspace("ecut", 2, 6, num=3, endpoint=True)
assert len(linps) == 3 and (linps[0]["ecut"] == 2 and (linps[-1]["ecut"] == 6))
ranginps = inp.arange("ecut", start=3, stop=5, step=1)
assert len(ranginps) == 2 and (ranginps[0]["ecut"] == 3 and (ranginps[-1]["ecut"] == 4))
with self.assertRaises(inp.Error):
inp.product("ngkpt", "tsmear", [[2, 2, 2], [4, 4, 4]])
prod_inps = inp.product("ngkpt", "tsmear", [[2, 2, 2], [4, 4, 4]], [0.1, 0.2, 0.3])
assert len(prod_inps) == 6
assert prod_inps[0]["ngkpt"] == [2, 2, 2] and prod_inps[0]["tsmear"] == 0.1
assert prod_inps[-1]["ngkpt"] == [4, 4, 4] and prod_inps[-1]["tsmear"] == 0.3
inp["kptopt"] = 4
assert not inp.uses_ktimereversal
def test_expand(self):
"""
Testing helper function to extend the convergence grid
"""
self.maxDiff = None
spec = get_spec('GW')
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
tests = SingleAbinitGWWork(struc, spec).convs
tests_out = {'nscf_nbands': {'test_range': (40,),
'control': 'gap', 'method': 'set_bands', 'level': 'nscf'},
'ecut': {'test_range': (50, 48, 46, 44),
'control': 'e_ks_max', 'method': 'direct', 'level': 'scf'},
'ecuteps': {'test_range': (4, 8, 12, 16, 20),
'control': 'gap', 'method': 'direct', 'level': 'sigma'}}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
if "VASP_PSP_DIR" in os.environ:
spec.update_code_interface()
tests = GWG0W0VaspInputSet(struc, spec).convs
tests_out = {'ENCUTGW': {'test_range': (200, 400, 600, 800), 'control': 'gap', 'method': 'incar_settings'}}
self.assertEqual(expand(tests, 1), tests_out)
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def itest_gbrv_flow(fwp, tvars):
"""The the GBRV flow: relaxation + EOS computation."""
from pseudo_dojo.dojo.dojo_workflows import GbrvFactory
factory = GbrvFactory()
#pseudo = "si_pbe_v1_abinit.paw"
pseudo = abidata.pseudo("Si.GGA_PBE-JTH-paw.xml")
ecut = 2
pawecutdg = 2 * ecut if pseudo.ispaw else None
flow = abilab.Flow(workdir=fwp.workdir, manager=fwp.manager, pickle_protocol=0)
struct_types = ["fcc"] #, "bcc"]
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.allocate()
flow.build_and_pickle_dump()
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start()
assert not fwp.scheduler.exceptions
#work = flow[0]
#t0 = work[0]
#assert len(work) == 1
#t0.start_and_wait()
#flow.check_status()
# At this point on_all_ok is called.
#assert t0.status == t0.S_OK
#assert len(flow) == 2
#assert len(flow[1]) == 9
#assert not flow.all_ok
#for task in flow[1]:
# task.start_and_wait()
flow.check_status()
flow.show_status()
assert all(work.finalized for work in flow)
assert flow.all_ok
def test_data_api(self):
"""Testing abipy.data API."""
ncpseudo_h = abidata.pseudo("01h.pspgth")
assert ncpseudo_h.isnc
paw_table = abidata.pseudos("1h.paw", "28ni.paw")
assert paw_table.allpaw
assert os.path.isfile(abidata.cif_file("al.cif"))
assert os.path.isfile(abidata.pyscript("plot_bz.py"))
d = abidata.get_mp_structures_dict()
assert isinstance(d, dict) and d is abidata.get_mp_structures_dict()
structure = abidata.structure_from_cif("gan2.cif")
assert hasattr(structure, "to_abivars")
structure = abidata.structure_from_mpid("mp-4820")
assert hasattr(structure, "to_abivars")
with self.assertRaises(KeyError):
abidata.structure_from_mpid("foobar")
def test_data_api(self):
"""Testing abipy.data API."""
ncpseudo_h = abidata.pseudo("01h.pspgth")
assert ncpseudo_h.isnc
paw_table = abidata.pseudos("1h.paw", "28ni.paw")
assert paw_table.allpaw
assert os.path.isfile(abidata.cif_file("al.cif"))
assert os.path.isfile(abidata.pyscript("plot_bz.py"))
d = abidata.get_mp_structures_dict()
assert isinstance(d, dict) and d is abidata.get_mp_structures_dict()
structure = abidata.structure_from_cif("gan2.cif")
assert hasattr(structure, "to_abivars")
structure = abidata.structure_from_mpid("mp-4820")
assert hasattr(structure, "to_abivars")
with self.assertRaises(KeyError):
abidata.structure_from_mpid("foobar")
def test_expand(self):
"""
Testing helper function to extend the convergence grid
"""
self.maxDiff = None
spec = get_spec('GW')
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'simple_scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
temp_ABINIT_PS_EXT = os.environ.get('ABINIT_PS_EXT', None)
temp_ABINIT_PS = os.environ.get('ABINIT_PS', None)
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
tests = SingleAbinitGWWork(struc, spec).convs
tests_out = {'nscf_nbands': {'test_range': (25,),
'control': 'gap', 'method': 'set_bands', 'level': 'nscf'},
'ecut': {'test_range': (50, 48, 46, 44),
'control': 'e_ks_max', 'method': 'direct', 'level': 'scf'},
'ecuteps': {'test_range': (4, 6, 8, 10, 12),
'control': 'gap', 'method': 'direct', 'level': 'sigma'}}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def delta_flow(workdir="tmp_deltafactor"):
# Path of the pseudopotential to test.
#pseudo = data.pseudo("14si.pspnc")
pseudo = data.pseudo("Si.GGA_PBE-JTH-paw.xml")
# Manager used to submit the jobs.
manager = abilab.TaskManager.from_user_config()
# Initialize the flow.
# FIXME Abistructure is not pickleable with protocol -1
flow = abilab.AbinitFlow(workdir=workdir, manager=manager, pickle_protocol=0)
# Build the workflow for the computation of the deltafactor.
# The calculation is done with the parameters and the cif files
# used in the original paper. We only have to specify
# the cutoff energy ecut (Ha) for the pseudopotential.
# 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.
factory = DeltaFactory()
kppa = 6750 # Use this to have the official k-point sampling
kppa = 50 # this value is for testing purpose.
#extra = {}
ecut = 8
pawecutdg = ecut * 2 #if pseudo.ispaw else None
work = factory.work_for_pseudo(pseudo, accuracy="normal", kppa=kppa,
ecut=ecut, pawecutdg=pawecutdg,
toldfe=1.e-8, smearing="fermi_dirac:0.0005")
# Register the workflow.
flow.register_work(work)
return flow.allocate()
def itest_deltafactor(fwp, tvars):
"""Test the flow used for the computation of the deltafactor."""
# Path of the pseudopotential to test.
pseudo = abidata.pseudo("Si.GGA_PBE-JTH-paw.xml")
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
work = DeltaFactory().work_for_pseudo(pseudo,
kppa=kppa,
ecut=ecut,
pawecutdg=pawecutdg,
paral_kgb=tvars.paral_kgb)
# Register the workflow.
flow.register_work(work)
flow.allocate()
flow.build_and_pickle_dump()
for task in flow[0]:
task.start_and_wait()
flow.check_status()
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
results = flow[0].get_results()
def test_api(self):
"""Testing MultiDataset API."""
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudo = abidata.pseudo("14si.pspnc")
pseudo_dir = os.path.dirname(pseudo.filepath)
multi = MultiDataset(structure=structure, pseudos=pseudo)
with self.assertRaises(ValueError):
MultiDataset(structure=structure, pseudos=pseudo, ndtset=-1)
multi = MultiDataset(structure=structure,
pseudos=pseudo.basename,
pseudo_dir=pseudo_dir)
assert len(multi) == 1 and multi.ndtset == 1
assert multi.isnc
for i, inp in enumerate(multi):
assert list(inp.keys()) == list(multi[i].keys())
multi.addnew_from(0)
assert multi.ndtset == 2 and multi[0] is not multi[1]
assert multi[0].structure == multi[1].structure
assert multi[0].structure is not multi[1].structure
multi.set_vars(ecut=2)
assert all(inp["ecut"] == 2 for inp in multi)
self.assert_equal(multi.get("ecut"), [2, 2])
df = multi.get_vars_dataframe("ecut", "foobar")
assert "ecut" in df
self.assert_equal(df["ecut"].values, [2, 2])
multi[1].set_vars(ecut=1)
assert multi[0]["ecut"] == 2 and multi[1]["ecut"] == 1
self.assert_equal(multi.get("ecut"), [2, 1])
self.assert_equal(multi.get("foo", "default"), ["default", "default"])
multi[1].set_vars(paral_kgb=1)
assert "paral_kgb" not in multi[0]
self.assert_equal(multi.get("paral_kgb"), [None, 1])
pert_structure = structure.copy()
pert_structure.perturb(distance=0.1)
assert structure != pert_structure
assert multi.set_structure(structure) == multi.ndtset * [structure]
assert all(s == structure for s in multi.structure)
assert multi.has_same_structures
multi[1].set_structure(pert_structure)
assert multi[0].structure != multi[1].structure and multi[
1].structure == pert_structure
assert not multi.has_same_structures
split = multi.split_datasets()
assert len(split) == 2 and all(split[i] == multi[i]
for i in range(multi.ndtset))
repr(multi)
str(multi)
assert multi.to_string(mode="text")
assert multi._repr_html_()
inp.write(filepath=self.tmpfileindir("run.abi"))
multi.write(filepath=self.tmpfileindir("run.abi"))
new_multi = MultiDataset.from_inputs([inp for inp in multi])
assert new_multi.ndtset == multi.ndtset
assert new_multi.structure == multi.structure
for old_inp, new_inp in zip(multi, new_multi):
assert old_inp is not new_inp
self.assertDictEqual(old_inp.as_dict(), new_inp.as_dict())
ref_input = multi[0]
new_multi = MultiDataset.replicate_input(input=ref_input, ndtset=4)
assert new_multi.ndtset == 4
for inp in new_multi:
assert ref_input is not inp
self.assertDictEqual(ref_input.as_dict(), inp.as_dict())
# Compatible with Pickle and MSONable?
self.serialize_with_pickle(multi, test_eq=False)
#self.assertMSONable(multi)
# Test tags
new_multi.add_tags([GROUND_STATE, RELAX], [0, 2])
assert len(new_multi[0].tags) == 2
sub_multi = new_multi.filter_by_tags(GROUND_STATE)
assert len(sub_multi) == 2
new_multi.remove_tags([RELAX])
assert len(new_multi[0].tags) == 1
def test_helper_functions(self):
"""Testing AbinitInput helper functions."""
pseudo = abidata.pseudo("14si.pspnc")
pseudo_dir = os.path.dirname(pseudo.filepath)
inp = AbinitInput(structure=abidata.cif_file("si.cif"),
pseudos=pseudo.basename,
pseudo_dir=pseudo_dir)
nval_atoms = inp.valence_electrons_per_atom
assert len(nval_atoms) == 2
assert nval_atoms == [4, 4]
inp.set_kmesh(ngkpt=(1, 2, 3), shiftk=(1, 2, 3, 4, 5, 6))
assert inp["kptopt"] == 1 and inp["nshiftk"] == 2
assert inp.uses_ktimereversal
inp.set_gamma_sampling()
assert inp["kptopt"] == 1 and inp["nshiftk"] == 1
assert np.all(inp["shiftk"] == 0)
inp.set_autokmesh(nksmall=2)
assert inp["kptopt"] == 1 and np.all(
inp["ngkpt"] == [2, 2, 2]) and inp["nshiftk"] == 4
inp.set_kpath(ndivsm=3, kptbounds=None)
assert inp["ndivsm"] == 3 and inp["iscf"] == -2 and len(
inp["kptbounds"]) == 12
inp.set_qpath(ndivsm=3, qptbounds=None)
assert len(inp["ph_qpath"]
) == 12 and inp["ph_nqpath"] == 12 and inp["ph_ndivsm"] == 3
inp.set_phdos_qmesh(nqsmall=16, method="tetra")
assert inp["ph_intmeth"] == 2 and np.all(
inp["ph_ngqpt"] == 16) and np.all(inp["ph_qshift"] == 0)
inp.set_kptgw(kptgw=(1, 2, 3, 4, 5, 6), bdgw=(1, 2))
assert inp["nkptgw"] == 2 and np.all(
inp["bdgw"].ravel() == np.array(len(inp["kptgw"]) *
[1, 2]).ravel())
linps = inp.linspace("ecut", 2, 6, num=3, endpoint=True)
assert len(linps) == 3 and (linps[0]["ecut"] == 2 and
(linps[-1]["ecut"] == 6))
ranginps = inp.arange("ecut", start=3, stop=5, step=1)
assert len(ranginps) == 2 and (ranginps[0]["ecut"] == 3 and
(ranginps[-1]["ecut"] == 4))
with self.assertRaises(inp.Error):
inp.product("ngkpt", "tsmear", [[2, 2, 2], [4, 4, 4]])
prod_inps = inp.product("ngkpt", "tsmear", [[2, 2, 2], [4, 4, 4]],
[0.1, 0.2, 0.3])
assert len(prod_inps) == 6
assert prod_inps[0]["ngkpt"] == [2, 2, 2
] and prod_inps[0]["tsmear"] == 0.1
assert prod_inps[-1]["ngkpt"] == [4, 4, 4
] and prod_inps[-1]["tsmear"] == 0.3
inp["kptopt"] = 4
assert not inp.uses_ktimereversal
def test_setup(self):
"""
Testing the main functions called in the abiGWsetup script
"""
spec_in = get_spec('GW')
self.assertIsInstance(spec_in, GWSpecs)
self.assert_equal(spec_in.test(), 0)
self.assert_equal(len(spec_in.to_dict()), 10)
self.assert_equal(spec_in.get_code(), 'ABINIT')
spec_in.data['source'] = 'cif'
self.assert_equal(
spec_in.hash_str(),
"code:ABINIT;source:cifjobs:[u'prep', u'G0W0'];mode:ceci;functional:PBE;kp_grid_dens:500prec:m;tol:0.0001;test:False;converge:False"
)
wdir = tempfile.mkdtemp()
base = os.getcwd()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"),
os.path.join(wdir, 'si.cif'))
shutil.copyfile(
abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'),
os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
spec_in.data['source'] = 'cif'
print('dirpath', abidata.dirpath)
spec_in.write_to_file('spec.in')
self.assertTrue(os.path.isfile(os.path.join(wdir, 'spec.in')))
# broken due to strategy refactoring
# spec_in.loop_structures('i')
os.chdir(base)
shutil.rmtree(wdir)
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_setup_single(self):
"""
Testing the main functions called in the abiGWsetup script for a single shot calculation
"""
spec_in = get_spec('GW')
self.assertIsInstance(spec_in, GWSpecs)
self.assert_equal(spec_in.test(), 0)
self.assert_equal(len(spec_in.to_dict()), 10)
self.assert_equal(spec_in.get_code(), 'ABINIT')
spec_in.data['source'] = 'cif'
self.assert_equal(spec_in.hash_str(), "code:ABINIT;source:cifjobs:['prep', 'G0W0'];mode:ceci;functional:PBE;kp_grid_dens:500prec:m;tol:0.0001;test:False;converge:False")
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'), os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'simple_scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
temp_ABINIT_PS_EXT = os.environ.get('ABINIT_PS_EXT', None)
temp_ABINIT_PS = os.environ.get('ABINIT_PS', None)
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
spec_in.data['source'] = 'cif'
print('dirpath', abidata.dirpath)
spec_in.write_to_file('spec.in')
self.assertTrue(os.path.isfile(os.path.join(wdir, 'spec.in')))
spec_in.loop_structures('i')
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
ls = os.listdir('.')
print(ls)
self.assertEqual(ls, [u'job_collection', u'manager.yml', u'scheduler.yml', u'si.cif', u'Si.pspnc',
u'Si_si.cif', u'spec.in'])
ls2 = os.listdir('Si_si.cif/')
print(ls2)
self.assertEqual(ls2, [u'.nodeid', u'__AbinitFlow__.pickle', u'indata', u'outdata', u'tmpdata', u'w0'])
ls3 = os.listdir('Si_si.cif/w0/')
print(ls3)
self.assertEqual(ls3, [u'indata', u'outdata', u't0', u't1', u't2', u't3', u'tmpdata'])
with open('Si_si.cif/w0/t0/run.abi') as f:
abi = f.readlines()
for x in [' ecut 44\n', ' tolvrs 1e-08\n', ' kptopt 1\n', ' ngkpt 6 6 6\n', ' nshiftk 1\n', ' nband 26\n']:
self.assertIn(x, abi)
with open('Si_si.cif/w0/t1/run.abi') as f:
abi = f.readlines()
for x in [' ecut 44\n', ' tolwfr 1e-17\n', ' kptopt 1\n', ' iscf -2\n']:
self.assertIn(x, abi)
with open('Si_si.cif/w0/t2/run.abi') as f:
abi = f.readlines()
for x in [' kptopt 1\n', ' shiftk 0 0 0\n', ' ngkpt 6 6 6\n', ' nshiftk 1\n', ' iscf -2\n', ' nband 60\n',
' nsppol 1\n', ' ecut 44\n', ' toldfe 1e-08\n',' gwmem 10\n', ' inclvkb 2\n', '\n', ' symsigma 1\n',
' ecuteps 8\n']:
self.assertIn(x, abi)
with open('Si_si.cif/w0/t3/run.abi') as f:
abi = f.readlines()
for x in [' kptopt 1\n', ' shiftk 0 0 0\n', ' ngkpt 6 6 6\n', ' nshiftk 1\n', ' iscf -2\n', ' nband 60\n',
' nsppol 1\n', ' ecut 44\n', ' toldfe 1e-08\n', ' gwmem 10\n', ' inclvkb 2\n', '\n', ' symsigma 1\n',
' ecutsigx 44\n', ' ecuteps 8\n', ' gw_qprange 2\n', ' ppmodel 1\n', ' gwcalctyp 00\n']:
self.assertIn(x, abi)
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
#wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"),
os.path.join(wdir, 'si.cif'))
shutil.copyfile(
abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers',
'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'),
os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open(os.path.join(wdir, 'extra_abivars'), 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc),
work.get_electrons(struc) / 2,
'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow[0][0].__class__, ScfTask)
self.assertEqual(flow[0][1].__class__, ScfTask)
self.assertEqual(flow[0][2].__class__, ScfTask)
self.assertEqual(flow[0][3].__class__, ScfTask)
self.assertEqual(flow[0][4].__class__, NscfTask)
self.assertEqual(flow[0][5].__class__, ScrTask)
self.assertEqual(flow[0][6].__class__, SigmaTask)
ecuts = [
dict(task.input.as_dict()['abi_args'])['ecut'] for task in flow[0]
]
print('ecuts:', ecuts)
# it is essential that the first four are diffent, this is for the convergence study of ecut, and that
# after that is stays the same
self.assertEqual(ecuts, [
50, 48, 46, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44,
44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44,
44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44
])
nbands = [
dict(task.input.as_dict()['abi_args'])['nband'] for task in flow[0]
]
print('nbands:', nbands)
# the firs 4 should be 'low' these are self consistent
# the fifth should be the maximum of what follows
# the 6th and on should always be pairs that are the same, they are combinations of scr and sigma tasks
self.assertEqual(nbands, [
26, 26, 26, 26, 180, 30, 30, 60, 60, 120, 120, 180, 180, 30, 30,
60, 60, 120, 120, 180, 180, 30, 30, 60, 60, 120, 120, 180, 180, 30,
30, 60, 60, 120, 120, 180, 180, 30, 30, 60, 60, 120, 120, 180, 180
])
ecuteps = [
dict(task.input.as_dict()['abi_args']).get('ecuteps', None)
for task in flow[0]
]
print('ecuteps:', ecuteps)
self.assertEqual(ecuteps, [
None, None, None, None, None, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8,
8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16,
16, 16, 20, 20, 20, 20, 20, 20, 20, 20
])
inplens = [len(task.input.as_dict()['abi_args']) for task in flow[0]]
print(inplens)
self.assertEqual(inplens, [
17, 17, 17, 17, 18, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30,
27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27,
30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30
])
ngkpts = [
dict(task.input.as_dict()['abi_args'])['ngkpt'] for task in flow[0]
]
for ngkpt in ngkpts:
self.assertEqual(ngkpt, [2, 2, 2])
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open('extra_abivars', 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc), work.get_electrons(struc) / 2, 'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_expand(self):
"""
Testing helper function to extend the convergence grid
"""
self.maxDiff = None
spec = get_spec('GW')
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"),
os.path.join(wdir, 'si.cif'))
shutil.copyfile(
abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'),
os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
tests = SingleAbinitGWWork(struc, spec).convs
tests_out = {
'nscf_nbands': {
'test_range': (40, ),
'control': 'gap',
'method': 'set_bands',
'level': 'nscf'
},
'ecut': {
'test_range': (50, 48, 46, 44),
'control': 'e_ks_max',
'method': 'direct',
'level': 'scf'
},
'ecuteps': {
'test_range': (4, 8, 12, 16, 20),
'control': 'gap',
'method': 'direct',
'level': 'sigma'
}
}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
if "VASP_PSP_DIR" in os.environ:
spec.update_code_interface()
tests = GWG0W0VaspInputSet(struc, spec).convs
tests_out = {
'ENCUTGW': {
'test_range': (200, 400, 600, 800),
'control': 'gap',
'method': 'incar_settings'
}
}
self.assertEqual(expand(tests, 1), tests_out)
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_api(self):
"""Testing MultiDataset API."""
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
pseudo = abidata.pseudo("14si.pspnc")
pseudo_dir = os.path.dirname(pseudo.filepath)
multi = MultiDataset(structure=structure, pseudos=pseudo)
with self.assertRaises(ValueError):
MultiDataset(structure=structure, pseudos=pseudo, ndtset=-1)
multi = MultiDataset(structure=structure, pseudos=pseudo.basename, pseudo_dir=pseudo_dir)
assert len(multi) == 1 and multi.ndtset == 1
assert multi.isnc
for i, inp in enumerate(multi):
assert list(inp.keys()) == list(multi[i].keys())
multi.addnew_from(0)
assert multi.ndtset == 2 and multi[0] is not multi[1]
assert multi[0].structure == multi[1].structure
assert multi[0].structure is not multi[1].structure
multi.set_vars(ecut=2)
assert all(inp["ecut"] == 2 for inp in multi)
self.assert_equal(multi.get("ecut"), [2, 2])
df = multi.get_vars_dataframe("ecut", "foobar")
assert "ecut" in df
self.assert_equal(df["ecut"].values, [2, 2])
multi[1].set_vars(ecut=1)
assert multi[0]["ecut"] == 2 and multi[1]["ecut"] == 1
self.assert_equal(multi.get("ecut"), [2, 1])
self.assert_equal(multi.get("foo", "default"), ["default", "default"])
multi[1].set_vars(paral_kgb=1)
assert "paral_kgb" not in multi[0]
self.assert_equal(multi.get("paral_kgb"), [None, 1])
pert_structure = structure.copy()
pert_structure.perturb(distance=0.1)
assert structure != pert_structure
assert multi.set_structure(structure) == multi.ndtset * [structure]
assert all(s == structure for s in multi.structure)
assert multi.has_same_structures
multi[1].set_structure(pert_structure)
assert multi[0].structure != multi[1].structure and multi[1].structure == pert_structure
assert not multi.has_same_structures
split = multi.split_datasets()
assert len(split) == 2 and all(split[i] == multi[i] for i in range(multi.ndtset))
repr(multi); str(multi)
assert multi.to_string(mode="text")
assert multi._repr_html_()
inp.write(filepath=self.tmpfileindir("run.abi"))
multi.write(filepath=self.tmpfileindir("run.abi"))
new_multi = MultiDataset.from_inputs([inp for inp in multi])
assert new_multi.ndtset == multi.ndtset
assert new_multi.structure == multi.structure
for old_inp, new_inp in zip(multi, new_multi):
assert old_inp is not new_inp
self.assertDictEqual(old_inp.as_dict(), new_inp.as_dict())
ref_input = multi[0]
new_multi = MultiDataset.replicate_input(input=ref_input, ndtset=4)
assert new_multi.ndtset == 4
for inp in new_multi:
assert ref_input is not inp
self.assertDictEqual(ref_input.as_dict(), inp.as_dict())
# Compatible with Pickle and MSONable?
self.serialize_with_pickle(multi, test_eq=False)
#self.assertMSONable(multi)
# Test tags
new_multi.add_tags([GROUND_STATE, RELAX], [0,2])
assert len(new_multi[0].tags) == 2
sub_multi = new_multi.filter_by_tags(GROUND_STATE)
assert len(sub_multi) == 2
new_multi.remove_tags([RELAX])
assert len(new_multi[0].tags) == 1
def pseudos(self):
return [abidata.pseudo("14si.pspnc")]
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
#wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open(os.path.join(wdir, 'extra_abivars'), 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc), work.get_electrons(struc) / 2, 'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
