def test_write(self):
ref_log = Logfile.from_file(os.path.join(tests_fol, "log-HCN.yaml"))
lname = "dummy.yaml"
ref_log.write(lname)
new_log = Logfile.from_file(lname)
for log1, log2 in zip(ref_log, new_log):
assert log1.inputparams == log2.inputparams
assert log1.posinp == log2.posinp
os.remove(lname)
def run(posinp, i, args, param, pseudos):
try:
os.makedirs("{}_{:06}".format(args.name, i))
os.chdir("{}_{:06}".format(args.name, i))
job = Job(name=args.name,
posinp=posinp,
inputparams=param,
pseudos=pseudos)
job.run(nmpi=args.nmpi)
copyfile(
"forces_{}.xyz".format(args.name),
"../../saved_results/{:06}.xyz".format(i),
)
os.chdir("../")
except OSError:
os.chdir("{}_{:06}".format(args.name, i))
try:
log = Logfile.from_file("log-" + args.name + ".yaml")
print("Calculation {:06} was complete.\n".format(i))
except:
job = Job(name=args.name,
posinp=posinp,
inputparams=param,
pseudos=pseudos)
job.run(args.nmpi, restart_if_incomplete=True)
copyfile(
"forces_{}.xyz".format(args.name),
"../../saved_results/{:06}.xyz".format(i),
)
os.chdir("../")
def test_run_with_dry_run(self):
with Job(inputparams=self.inp, name="dry_run", run_dir="tests") as job:
# Run the calculation
job.clean()
assert not job.is_completed
job.run(dry_run=True, nmpi=2, nomp=4)
assert job.is_completed
# There must be input and output files afterwards
new_inp = InputParams.from_file(job.input_name)
assert new_inp == self.inp
new_pos = Posinp.from_file(job.posinp_name)
assert new_pos == self.pos
bigdft_tool_log = Logfile.from_file(job.logfile_name)
assert bigdft_tool_log.energy is None
def test_run_with_dry_run_with_posinp(self):
with Job(inputparams=self.inp,
posinp=self.pos,
name="dry_run",
run_dir="tests") as job:
job.clean()
assert not job.is_completed
job.run(dry_run=True, nmpi=2, nomp=4)
assert job.is_completed
# Make sure that input, posinp and output files are created
new_inp = InputParams.from_file(job.input_name)
assert new_inp == self.inp
new_pos = Posinp.from_file(job.posinp_name)
assert new_pos == self.pos
bigdft_tool_log = Logfile.from_file(job.logfile_name)
assert bigdft_tool_log.energy is None
class TestJob:
# Extract the input and posinp from an N2 calculation of bad quality
logname = os.path.join("tests", "log-warnings.yaml")
log = Logfile.from_file(logname)
inp = log.inputparams
pos = log.posinp
job = Job(inputparams=inp, posinp=pos)
job_with_name = Job(inputparams=inp, posinp=pos, name="test")
@pytest.mark.parametrize("attr, expected", [("inputparams", inp),
("posinp", pos),
("is_completed", False),
("input_name", "input.yaml"),
("posinp_name", "posinp.xyz"),
("logfile", {}),
("logfile_name", "log.yaml"),
("data_dir", "data"),
("ref_data_dir", None),
("run_dir", "MyBigDFT")])
def test_init(self, attr, expected):
if "_dir" in attr and attr != "ref_data_dir":
value = getattr(self.job, attr)
value = os.path.basename(os.path.normpath(value))
assert value == expected
else:
assert getattr(self.job, attr) == expected
@pytest.mark.parametrize("attr, expected", [
("inputparams", inp),
("posinp", pos),
("is_completed", False),
("input_name", "test.yaml"),
("posinp_name", "test.xyz"),
("logfile", {}),
("logfile_name", "log-test.yaml"),
("data_dir", "data-test"),
("ref_data_dir", None),
("run_dir", "MyBigDFT"),
])
def test_init_with_name(self, attr, expected):
if "_dir" in attr and attr != "ref_data_dir":
value = getattr(self.job_with_name, attr)
value = os.path.basename(os.path.normpath(value))
assert value == expected
else:
assert getattr(self.job_with_name, attr) == expected
def test_init_with_posinp_only(self):
assert Job(posinp=self.pos).inputparams == {}
def test_init_with_skip(self):
j = Job(inputparams=self.inp, skip=True)
cmd = j.bigdft_cmd
to_str = "{} " * len(cmd)
cmd = to_str.format(*cmd)
assert "-s Yes" in cmd
def test_init_without_posinp_raises_ValueError(self):
with pytest.raises(ValueError, match="provide initial positions"):
Job()
def test_init_with_different_posinp_in_inputparams_raises_ValueError(self):
with pytest.raises(ValueError, match="do not define the same posinp."):
Job(inputparams=self.inp,
posinp=Posinp.from_file("tests/surface.xyz"))
@pytest.mark.parametrize("attr", [
"inputparams",
"posinp",
"logfile",
"ref_data_dir",
"is_completed",
"input_name",
"posinp_name",
"logfile_name",
"bigdft_cmd",
"bigdft_tool_cmd",
"init_dir",
"run_dir",
"data_dir",
])
def test_cannot_set_attributes(self, attr):
with pytest.raises(AttributeError):
setattr(self.job, attr, 1)
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_run(self):
with Job(inputparams=self.inp, run_dir="tests",
name='warnings') as job:
job.run()
assert job.is_completed
assert self.inp["dft"].get("inputpsiid") is None
assert np.isclose(job.logfile.energy, -191.74377352940274)
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_run_with_force_run(self):
new_inp = deepcopy(self.inp)
new_inp["output"] = {"orbitals": "binary"}
with Job(inputparams=new_inp, run_dir="tests",
name="write_orbs") as job:
assert not job.is_completed
job.run(force_run=True, nmpi=2, nomp=4)
assert job.is_completed
job.clean()
assert self.inp["dft"].get("inputpsiid") is None
assert np.isclose(job.logfile.energy, -191.74377352940274)
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_run_with_force_run_and_inp_and_pos(self):
with Job(inputparams=self.inp,
posinp=self.pos,
run_dir="tests",
name="runtest") as job:
assert not job.is_completed
job.run(force_run=True)
assert job.is_completed
assert self.inp["dft"].get("inputpsiid") is None
assert np.isclose(job.logfile.energy, -191.74377352940274)
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_run_with_ref_data_dir(self):
with Job(inputparams=self.inp,
posinp=self.pos,
ref_data_dir="data-write_orbs",
run_dir="tests",
name="with_ref_data_dir") as job:
assert self.inp["dft"].get("inputpsiid") is None
assert job.inputparams["dft"].get("inputpsiid") is None
assert not job.is_completed
job.run(force_run=True)
assert job.is_completed
assert job.inputparams["dft"].get("inputpsiid") == 2
assert self.inp["dft"].get("inputpsiid") is None
job.run(force_run=True)
assert job.is_completed
assert np.isclose(job.logfile.energy, -191.74377352940274)
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_run_with_non_existing_ref_data_dir(self):
with Job(inputparams=self.inp,
posinp=self.pos,
ref_data_dir="unknown_data_dir",
run_dir="tests",
name="with_unknown_ref_data_dir") as job:
assert self.inp["dft"].get("inputpsiid") is None
assert job.inputparams["dft"].get("inputpsiid") is None
assert not job.is_completed
assert job.ref_data_dir is not None
assert not os.path.exists(job.ref_data_dir)
job.run(force_run=True)
assert job.is_completed
assert np.isclose(job.logfile.energy, -191.74377352940274)
def test_run_raises_ValueError_when_incomplete_logfile(self):
with Job(inputparams=self.inp,
posinp=self.pos,
run_dir="tests",
name="incomplete") as job:
shutil.copyfile(job.logfile_name + ".ref", job.logfile_name)
with pytest.raises(ValueError,
message="The logfile is incomplete!"):
job.run(restart_if_incomplete=False)
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_run_restart_if_incomplete(self):
with Job(inputparams=self.inp,
posinp=self.pos,
run_dir="tests",
name="incomplete") as job:
shutil.copyfile(job.logfile_name + ".ref", job.logfile_name)
assert not job.is_completed
job.run(restart_if_incomplete=True)
assert job.is_completed
job.clean()
assert np.isclose(job.logfile.energy, -191.74377352940274)
def test_run_exceeds_timeout_raises_RuntimeError(self):
inp = InputParams({"dft": {"rmult": [9, 12], "hgrids": 0.25}})
with Job(inputparams=inp,
posinp=self.pos,
run_dir="tests",
name="long-run") as job:
job.clean()
assert not job.is_completed
with pytest.raises(RuntimeError):
job.run(timeout=1.5 / 60, force_run=True)
def test_clean(self):
with Job(inputparams=self.inp, name="dry_run", run_dir="tests") as job:
job.write_input_files()
job.clean(logfiles_dir=True, data_dir=True)
assert not os.path.exists(job.posinp_name)
assert not os.path.exists(job.input_name)
assert not os.path.exists(job.logfile_name)
assert not os.path.exists("logfiles")
assert not os.path.exists("data-dry_run")
assert not job.is_completed
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_run_with_dry_run(self):
with Job(inputparams=self.inp, name="dry_run", run_dir="tests") as job:
# Run the calculation
job.clean()
assert not job.is_completed
job.run(dry_run=True, nmpi=2, nomp=4)
assert job.is_completed
# There must be input and output files afterwards
new_inp = InputParams.from_file(job.input_name)
assert new_inp == self.inp
new_pos = Posinp.from_file(job.posinp_name)
assert new_pos == self.pos
bigdft_tool_log = Logfile.from_file(job.logfile_name)
assert bigdft_tool_log.energy is None
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_run_with_dry_run_with_posinp(self):
with Job(inputparams=self.inp,
posinp=self.pos,
name="dry_run",
run_dir="tests") as job:
job.clean()
assert not job.is_completed
job.run(dry_run=True, nmpi=2, nomp=4)
assert job.is_completed
# Make sure that input, posinp and output files are created
new_inp = InputParams.from_file(job.input_name)
assert new_inp == self.inp
new_pos = Posinp.from_file(job.posinp_name)
assert new_pos == self.pos
bigdft_tool_log = Logfile.from_file(job.logfile_name)
assert bigdft_tool_log.energy is None
def test__check_logfile_posinp(self):
pos_name = os.path.join("tests", "surface.xyz")
pos = Posinp.from_file(pos_name)
with pytest.raises(UserWarning):
with Job(posinp=pos, run_dir="tests") as job:
job.run()
@pytest.mark.filterwarnings("ignore::UserWarning")
def test__check_logfile_inputparams(self):
with pytest.raises(UserWarning):
with Job(inputparams=InputParams(),
posinp=self.pos,
name="warnings",
run_dir="tests") as job:
job.run()
def test_posinp_with_inf(self):
new_inp = InputParams({
"posinp": {
"units":
"angstroem",
"cell": [40, ".inf", 40],
"positions": [
{
'N': [
2.97630782434901e-23, 6.87220595204354e-23,
0.0107161998748779
]
},
{
'N': [
-1.10434491945017e-23, -4.87342174483075e-23,
1.10427379608154
]
},
]
}
})
with Job(inputparams=new_inp, name="test") as job:
job.run(nmpi=6, nomp=3, dry_run=True)
job.clean()
assert job.logfile.boundary_conditions == 'surface'
def test_run_raises_RuntimeError(self):
# Error because two ".inf" in cell
new_inp = InputParams({
"posinp": {
"units":
"angstroem",
"cell": [40, ".inf", ".inf"],
"positions": [
{
'N': [
2.97630782434901e-23, 6.87220595204354e-23,
0.0107161998748779
]
},
{
'N': [
-1.10434491945017e-23, -4.87342174483075e-23,
1.10427379608154
]
},
]
}
})
with pytest.raises(RuntimeError):
with Job(inputparams=new_inp, run_dir="tests/dummy") as job:
job.run(force_run=True)
def test_dry_run_raises_RuntimeError(self):
# Error because two ".inf" in cell
new_inp = InputParams({
"posinp": {
"units":
"angstroem",
"cell": [40, ".inf", ".inf"],
"positions": [
{
'N': [
2.97630782434901e-23, 6.87220595204354e-23,
0.0107161998748779
]
},
{
'N': [
-1.10434491945017e-23, -4.87342174483075e-23,
1.10427379608154
]
},
]
}
})
with pytest.raises(RuntimeError):
with Job(inputparams=new_inp, run_dir="tests/dummy") as job:
job.run(dry_run=True)
class TestPosinp:
# Posinp with surface boundary conditions
surface_filename = os.path.join(tests_fol, "surface.xyz")
pos = Posinp.from_file(surface_filename)
# Posinp with free boundary conditions
free_filename = os.path.join(tests_fol, "free.xyz")
free_pos = Posinp.from_file(free_filename)
# Posinp read from a string
string = """\
4 atomic
free
C 0.6661284109 0.000000000 1.153768252
C 3.330642055 0.000000000 1.153768252
C 4.662898877 0.000000000 3.461304757
C 7.327412521 0.000000000 3.461304757"""
str_pos = Posinp.from_string(string)
# Posinp read from an N2 calculation of bad quality
log_pos = Logfile.from_file(logname).posinp
# Posinp read from an InputParams instance with surface BC
surf_inp = InputParams({
'posinp': {
'units': 'angstroem',
'cell': [8.0, '.inf', 8.0],
'positions': [{
'C': [0.0, 0.0, 0.0]
}]
}
})
surf_pos = surf_inp.posinp
# Posinp read from an InputParams instance with periodic BC
per_inp = InputParams({
'posinp': {
'units': 'angstroem',
'cell': [8.0, 1.0, 8.0],
'positions': [{
'C': [0.0, 0.0, 0.0]
}]
}
})
per_pos = per_inp.posinp
@pytest.mark.parametrize("value, expected", [
(len(pos), 4),
(pos.units, "reduced"),
(len(pos), 4),
(pos.boundary_conditions, "surface"),
(pos.cell, [8.07007483423, 'inf', 4.65925987792]),
(pos[0], Atom('C', [0.08333333333, 0.5, 0.25])),
])
def test_from_file(self, value, expected):
assert value == expected
@pytest.mark.parametrize("value, expected", [
(len(log_pos), 2),
(log_pos.units, "angstroem"),
(len(log_pos), 2),
(log_pos.boundary_conditions, "free"),
(log_pos.cell, None),
(log_pos[0],
Atom('N', [
2.9763078243490115e-23, 6.872205952043537e-23, 0.01071619987487793
])),
])
def test_from_Logfile(self, value, expected):
assert value == expected
@pytest.mark.parametrize("value, expected", [
(len(surf_pos), 1),
(surf_pos.units, "angstroem"),
(len(surf_pos), 1),
(surf_pos.boundary_conditions, "surface"),
(surf_pos.cell, [8, "inf", 8]),
(surf_pos[0], Atom('C', [0, 0, 0])),
])
def test_from_surface_InputParams(self, value, expected):
assert value == expected
@pytest.mark.parametrize("value, expected", [
(len(per_pos), 1),
(per_pos.units, "angstroem"),
(len(per_pos), 1),
(per_pos.boundary_conditions, "periodic"),
(per_pos.cell, [8, 1.0, 8]),
(per_pos[0], Atom('C', [0, 0, 0])),
])
def test_from_periodic_InputParams(self, value, expected):
assert value == expected
def test_from_string(self):
assert self.str_pos == self.free_pos
def test_repr(self):
atoms = [Atom('C', [0, 0, 0]), Atom('N', [0, 0, 1])]
new_pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
msg = "Posinp([Atom('C', [0.0, 0.0, 0.0]), Atom('N', [0.0, 0.0, "\
"1.0])], 'angstroem', 'free', cell=None)"
assert repr(new_pos) == msg
def test_write(self):
fname = os.path.join(tests_fol, "test.xyz")
self.pos.write(fname)
assert self.pos == Posinp.from_file(fname)
os.remove(fname)
def test_free_boundary_conditions_has_no_cell(self):
assert self.free_pos.cell is None
def test_translate_atom(self):
new_pos = self.pos.translate_atom(0, [0.5, 0, 0])
assert new_pos != self.pos
assert new_pos[0] == Atom("C", [0.58333333333, 0.5, 0.25])
@pytest.mark.parametrize("fname", [
"free_reduced.xyz",
"missing_atom.xyz",
"additional_atom.xyz",
])
def test_init_raises_ValueError(self, fname):
with pytest.raises(ValueError):
Posinp.from_file(os.path.join(tests_fol, fname))
@pytest.mark.parametrize("to_evaluate", [
"Posinp([Atom('C', [0, 0, 0])], 'bohr', 'periodic')",
"Posinp([Atom('C', [0, 0, 0])], 'bohr', 'periodic', cell=[1, 1])",
"Posinp([Atom('C', [0, 0, 0])], 'bohr', 'periodic', cell=[1,'inf',1])",
])
def test_init_raises_ValueError2(self, to_evaluate):
with pytest.raises(ValueError):
eval(to_evaluate)
def test_positions(self):
expected = [7.327412521, 0.0, 3.461304757]
pos1 = Posinp([Atom('C', expected)],
units="angstroem",
boundary_conditions="free")
pos2 = pos1.translate_atom(0, [-7.327412521, 0.0, -3.461304757])
assert np.allclose(pos1.positions, expected)
assert np.allclose(pos2.positions, [0, 0, 0])
def test___eq__(self):
atom1 = Atom('N', [0.0, 0.0, 0.0])
atom2 = Atom('N', [0.0, 0.0, 1.1])
pos1 = Posinp([atom1, atom2], 'angstroem', 'free')
pos2 = Posinp([atom2, atom1], 'angstroem', 'free')
assert pos1 == pos2 # The order of the atoms in the list do not count
assert pos1 != 1 # No error if other object is not a posinp
def test_with_surface_boundary_conditions(self):
# Two Posinp instances with surface BC are the same even if they
# have a different cell size along y-axis
pos_with_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[40, ".inf", 40])
pos_wo_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[40, 40, 40])
assert pos_with_inf == pos_wo_inf
# They are obviously different if the cell size along the other
# directions are not the same
pos2_wo_inf = Posinp([
Atom('N', [
2.97630782434901e-23, 6.87220595204354e-23, 0.0107161998748779
]),
Atom('N', [
-1.10434491945017e-23, -4.87342174483075e-23, 1.10427379608154
])
],
'angstroem',
'surface',
cell=[20, "inf", 40])
assert pos_with_inf != pos2_wo_inf
# They still have the same BC
assert \
pos2_wo_inf.boundary_conditions == pos_with_inf.boundary_conditions
# You can only have a cell with ".inf" in 2nd positiion to
# initialize a calculation with surface BC without using a
# Posinp instance
inp_with_inf = InputParams({
"posinp": {
"units":
"angstroem",
"cell": [40, ".inf", 40],
"positions": [
{
'N': [
2.97630782434901e-23, 6.87220595204354e-23,
0.0107161998748779
]
},
{
'N': [
-1.10434491945017e-23, -4.87342174483075e-23,
1.10427379608154
]
},
]
}
})
assert pos_with_inf == inp_with_inf.posinp
def test_to_centroid(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
expected_atoms = [Atom('N', [0, 0, -0.55]), Atom('N', [0, 0, 0.55])]
expected_pos = Posinp(expected_atoms,
units="angstroem",
boundary_conditions="free")
assert pos.to_centroid() == expected_pos
def test_to_barycenter(self):
atoms = [Atom('N', [0, 0, 0]), Atom('N', [0, 0, 1.1])]
pos = Posinp(atoms, units="angstroem", boundary_conditions="free")
expected_atoms = [Atom('N', [0, 0, -0.55]), Atom('N', [0, 0, 0.55])]
expected_pos = Posinp(expected_atoms,
units="angstroem",
boundary_conditions="free")
assert pos.to_barycenter() == expected_pos
def test_test_GeoptLogfile_acceptable_though_incomplete(self):
fname = os.path.join(tests_fol,
"log-geopt-acceptable-though-incomplete.yaml")
log_H3CCN = Logfile.from_file(fname)
assert isinstance(log_H3CCN, GeoptLogfile)
assert len(log_H3CCN) == 15
def test_init_log_with_warnings_warns_UserWarnings(self):
with pytest.warns(UserWarning):
Logfile.from_file("tests/log-warnings.yaml")
def test_GeoptLogfile(self):
log_HCN = Logfile.from_file(os.path.join(tests_fol, "log-HCN.yaml"))
assert isinstance(log_HCN, GeoptLogfile)
assert len(log_HCN) == 9
assert all([pos != log_HCN[0].posinp for pos in log_HCN.posinps[1:]])
assert all([log_HCN.inputparams == doc.inputparams for doc in log_HCN])
def test_write(self):
fname = os.path.join(tests_fol, "log-test.yaml")
self.log.write(fname)
log2 = Logfile.from_file(fname)
assert log2 == self.log
def test_init_raises_ValueError(self):
incomplete_log = os.path.join(tests_fol, "log-incomplete.yaml.ref")
with pytest.raises(ValueError):
Logfile.from_file(incomplete_log)
def test_empty_logfile_attributes(self, attr, value):
empty = Logfile()
# Two asserts as one can get both attributes (say, _n_at and n_at)
assert getattr(empty, attr) == value
assert getattr(empty, attr[1:]) == value
class TestLogfile:
# Logfile of an N2 calculation of bad quality
log = Logfile.from_file(logname)
@pytest.mark.parametrize("key, value", [
("Energy (Hartree)", -191.74377352940274),
("Number of MPI tasks", 2),
("OpenMP parallelization", True),
("Maximal OpenMP threads per MPI task", 16),
("Force Norm (Hartree/Bohr)", 448.63530538041755),
("Walltime since initialization", 1.835567),
])
def test_from_file(self, key, value):
assert self.log[key] == value
@pytest.mark.parametrize("attr, value", [
("_walltime", 1.835567),
("_energy", -191.74377352940274),
("_n_at", 2),
("_boundary_conditions", "free"),
("_dipole", [0.69649, 0.69649, -2.4954]),
("_sdos", None),
("_magnetization", None),
("_pressure", None),
("_atom_types", ['N']),
])
def test_attributes(self, attr, value):
# Two asserts as one can get both attributes (say, _n_at and n_at)
assert getattr(self.log, attr) == value
assert getattr(self.log, attr[1:]) == value
@pytest.mark.parametrize("attr, value", [
("_walltime", None),
("_energy", None),
("_n_at", None),
("_boundary_conditions", None),
("_dipole", None),
("_sdos", None),
("_magnetization", None),
("_pressure", None),
("_atom_types", None),
])
def test_empty_logfile_attributes(self, attr, value):
empty = Logfile()
# Two asserts as one can get both attributes (say, _n_at and n_at)
assert getattr(empty, attr) == value
assert getattr(empty, attr[1:]) == value
@pytest.mark.parametrize("name", ["n_at", "forces", "walltime"])
def test_set_base_attributes_raises_AttributeError(self, name):
with pytest.raises(AttributeError):
setattr(self.log, name, getattr(self.log, name))
def test_init_raises_ValueError(self):
incomplete_log = os.path.join(tests_fol, "log-incomplete.yaml.ref")
with pytest.raises(ValueError):
Logfile.from_file(incomplete_log)
def test_cannot_set_values_of_log_attr(self):
with pytest.raises(TypeError):
self.log['Walltime since initialization'] = 0
def test_len(self):
assert len(self.log) == 90
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_write(self):
fname = os.path.join(tests_fol, "log-test.yaml")
self.log.write(fname)
log2 = Logfile.from_file(fname)
assert log2 == self.log
def test_init_wrong_ixc_warns_UserWarning(self):
self.log["dft"]["ixc"] = -101130
with pytest.warns(UserWarning):
self.log._check_psppar()
self.log["dft"]["ixc"] = 1
@pytest.mark.skipif(sys.version_info < (3, 0),
reason="requires python3 or higher; see: "
"https://github.com/pytest-dev/pytest/issues/2917")
def test_init_log_with_warnings_warns_UserWarnings(self):
with pytest.warns(UserWarning):
Logfile.from_file("tests/log-warnings.yaml")
@pytest.mark.parametrize("attr", [
"n_at", "dipole", "forces", "pressure", "sdos", "energy",
"boundary_conditions", "cell", "fermi_level", "astruct", "evals",
"kpts", "gnrm_cv"
])
def test___dir__(self, attr):
assert attr in dir(self.log) and "_" + attr not in dir(self.log)
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_inputparams(self):
inp = log.inputparams
expected = InputParams({
'dft': {
'rmult': [2, 4],
'hgrids': 2.5,
'itermax': 1,
'disablesym': True
},
'posinp': {
'units':
'angstroem',
'positions': [{
'N': [
2.9763078243490115e-23, 6.872205952043537e-23,
0.01071619987487793
]
}, {
'N': [
-1.1043449194501671e-23, -4.873421744830746e-23,
1.104273796081543
]
}],
'properties': {
'format': 'xyz',
'source': 'N2.xyz'
}
}
})
assert inp == expected
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_GeoptLogfile(self):
log_HCN = Logfile.from_file(os.path.join(tests_fol, "log-HCN.yaml"))
assert isinstance(log_HCN, GeoptLogfile)
assert len(log_HCN) == 9
assert all([pos != log_HCN[0].posinp for pos in log_HCN.posinps[1:]])
assert all([log_HCN.inputparams == doc.inputparams for doc in log_HCN])
@pytest.mark.filterwarnings("ignore::UserWarning")
def test_test_GeoptLogfile_acceptable_though_incomplete(self):
fname = os.path.join(tests_fol,
"log-geopt-acceptable-though-incomplete.yaml")
log_H3CCN = Logfile.from_file(fname)
assert isinstance(log_H3CCN, GeoptLogfile)
assert len(log_H3CCN) == 15
from __future__ import absolute_import
import os
import sys
import pytest
import numpy as np
from mybigdft import InputParams, Posinp, Logfile, Atom
from mybigdft.iofiles.logfiles import GeoptLogfile
tests_fol = "tests"
# Result of an N2 calculation of very bad quality
logname = os.path.join(tests_fol, "log-warnings.yaml")
log = Logfile.from_file(logname)
class TestInputParams:
filename = os.path.join(tests_fol, "test.yaml")
@pytest.mark.parametrize("params, expected", [
({
"dft": {
"hgrids": 0.35
}
}, {
"dft": {
"hgrids": 0.35
}
}),
({
"dft": {
"hgrids": [0.45] * 3,