def main(args):
param = InputParams()
for filename in [f for f in os.listdir() if f.endswith(".yaml")]:
try:
param = InputParams.from_file(filename)
break
except:
continue
pseudos = not (args.no_pseudos)
positions = [
Posinp.from_file(args.positions_dir + file)
for file in os.listdir(args.positions_dir) if file.endswith(".xyz")
]
# Create directories
os.makedirs("run_dir/", exist_ok=True)
os.makedirs("saved_results/", exist_ok=True)
os.chdir("run_dir/")
for i in range(args.n_structs):
j = int(np.random.choice(len(positions), 1))
posinp = generate_random_structure(positions[j])
run(posinp, i, args, param, pseudos)
def post_proc(self):
r"""
Read the final posinp from a file.
"""
job = self.queue[0]
directory = os.path.join(job.init_dir, job.run_dir)
filename = "final_" + job.posinp_name
final_posinp_path = os.path.join(directory, filename)
self._final_posinp = Posinp.from_file(final_posinp_path)
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
def prepare_calculations(overwrite=False):
r"""
Determines which files are present and which need to be generated.
Parameters:
-------------
overwrite : bool
(default : False) if True, the present files are ignored
Returns:
base_inp : InputParams
base input parameters for the calculation
base_pos : Posinp
base atomic positions for the calculation
jobname : string
Name of the calculation if there is a pos file,
string "jobname" if no position file.
"""
files = [f for f in os.listdir() if f.endswith((".xyz", ".yaml"))]
posinp_is_present, jobname = verify_posinp(files)
if verify_input(files):
base_inp = InputParams.from_file("input.yaml")
else:
base_inp = InputParams()
if posinp_is_present:
base_pos = Posinp.from_file(jobname + ".xyz")
elif base_inp.posinp is not None:
base_pos = base_inp.posinp
jobname = "jobname"
base_pos.write(jobname + ".xyz")
else:
raise ValueError("No atomic positions are available.")
return base_inp, base_pos, jobname
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"))
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()
def test_init_raises_ValueError(self, fname):
with pytest.raises(ValueError):
Posinp.from_file(os.path.join(tests_fol, fname))
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)
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