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_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_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_convert(self):
pos_angstrom = Posinp.from_file(
os.path.join(pos_folder, "H2O_unrelaxed.xyz"))
pos_atomic = Posinp.from_file(
os.path.join(pos_folder, "H2O_atomic.xyz"))
job1 = Job(posinp=pos_angstrom, calculator=self.calc3)
job2 = Job(posinp=pos_atomic, calculator=self.calc3)
job1.run("energy")
job2.run("energy")
assert job1.results["energy"] == job2.results["energy"]
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],
)
with pytest.raises(ValueError):
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],
)
# They are obviously different if the cell size along the other
# directions are not the same
pos2_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=[20, "inf", 40],
)
assert pos_with_inf != pos2_with_inf
# They still have the same BC
assert pos2_with_inf.boundary_conditions == pos_with_inf.boundary_conditions
class TestEnsemble:
pos1 = Posinp.from_file(os.path.join(pos_folder, "H2O_unrelaxed.xyz"))
model1 = os.path.join(model_folder, "H2O_forces_model")
model2 = os.path.join(model_folder, "H2O_model")
def test_both_models(self):
ens = EnsembleCalculator(modelpaths=[self.model1, self.model2])
job1 = Job(posinp=self.pos1, calculator=ens)
job1.run("energy")
assert job1.results["energy"] == np.array(-1277.0513)
assert job1.results["energy_std"] == np.array(799.70636)
ref_forces = np.array(
[
[0, 0.7647542, -7.8656354],
[0, -2.2895808, 3.8240397],
[0, 1.5248268, 4.0415955],
],
dtype=np.float32,
)
ref_std = np.array(
[
[0, 0.03656149, 1.2570109],
[0, 0.8168775, 0.4650414],
[0, 0.8534391, 0.7919693],
],
dtype=np.float32,
)
job2 = Job(posinp=self.pos1, calculator=ens)
job2.run("forces")
assert np.isclose(job2.results["forces"], ref_forces, atol=1e-04).all()
assert np.isclose(job2.results["forces_std"], ref_std,
atol=1e-04).all()
def main(args):
function = get_function(args.function)
distances = np.linspace(args.range[0], args.range[1], args.ndata)
with connect(args.dbname) as db:
for d in distances:
pos_dict = {
"units":
"angstroem",
"boundary_conditions":
"free",
"positions": [
{
args.element: [0, 0, 0]
},
{
args.element: [d, 0, 0]
},
],
}
posinp = Posinp.from_dict(pos_dict)
atoms = posinp_to_ase_atoms(posinp)
energy = function.value(d)
forces = np.array([
[-1.0 * function.first_derivative(-d), 0, 0],
[-1.0 * function.first_derivative(d), 0, 0],
])
db.write(atoms, data={"energy": energy, "forces": forces})
def test_convert(self):
pos1 = self.periodic_pos.positions
assert self.periodic_pos.units == "angstroem"
self.periodic_pos.convert_units("atomic")
assert np.isclose(
self.periodic_pos.positions,
np.array(
[
[0.15747717, 0.94486299, 0.4724315],
[0.78738583, 0.94486299, 0.4724315],
[1.10234016, 0.94486299, 1.41729449],
[1.73224882, 0.94486299, 1.41729449],
]
),
).all()
assert self.periodic_pos.units == "atomic"
self.periodic_pos.convert_units("angstroem")
assert np.isclose(self.periodic_pos.positions, pos1).all()
assert self.periodic_pos.units == "angstroem"
self.periodic_pos.convert_units("angstroem")
assert np.isclose(self.periodic_pos.positions, pos1).all()
red = Posinp.from_file(tests_fol + "reduced.xyz")
red.convert_units("angstroem")
print(red.positions)
assert np.isclose(
red.positions,
np.array(
[
[0.4233418, 1.32294312, 0.95251905],
[3.81007619, 0.26458862, 0.47625952],
]
),
).all()
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=Cell([0.0, 0.0, 0.0]), angles=[90. 90. 90.])"
)
assert repr(new_pos) == msg
class TestSchnetPack:
pos1 = Posinp.from_file(os.path.join(pos_folder, "N2.xyz"))
model1 = os.path.join(model_folder, "ani1_N2_model")
model2 = os.path.join(model_folder, "wacsf_model")
model3 = os.path.join(model_folder, "H2O_model")
calc1 = SchnetPackCalculator(model_dir=model1)
calc2 = SchnetPackCalculator(model_dir=model2)
calc3 = SchnetPackCalculator(model_dir=model3)
job = Job(posinp=pos1, calculator=calc1)
jobwacsf = Job(posinp=pos1, calculator=calc2)
def test_only_energy(self):
self.job.run("energy")
assert np.array(-2979.6067) == self.job.results["energy"][0]
new_job = deepcopy(self.job)
new_job.calculator.units = {"energy": "hartree", "positions": "atomic"}
new_job.run("energy")
assert new_job.results["energy"][0] == np.array(-81079.228)
self.job.results["energy"] = None
def test_forces_from_deriv(self):
assert self.job.calculator.available_properties == ["energy"]
self.job.run("forces")
ref_forces = np.array([[-0.0, -0.0, -0.31532133],
[-0.0, -0.0, 0.31532133]])
assert np.isclose(self.job.results["forces"][0], ref_forces).all()
new_job = deepcopy(self.job)
new_job.calculator.units = {"energy": "hartree", "positions": "atomic"}
new_job.run("forces")
assert np.isclose(ref_forces * 51.42206334724,
new_job.results["forces"][0]).all()
def test_forces_from_finite_difference(self):
assert self.job.calculator.available_properties == ["energy"]
self.job.run("forces", finite_difference=True)
ref_forces = np.array([[-0.0, -0.0, -0.32416448],
[-0.0, -0.0, 0.32416448]])
assert np.isclose(self.job.results["forces"][0], ref_forces).all()
def test_wacsf(self):
self.jobwacsf.run("energy")
assert self.jobwacsf.results["energy"] is not None
def test_bad_property(self):
with pytest.raises(ValueError):
self.job.run("dipole")
def test_convert(self):
pos_angstrom = Posinp.from_file(
os.path.join(pos_folder, "H2O_unrelaxed.xyz"))
pos_atomic = Posinp.from_file(
os.path.join(pos_folder, "H2O_atomic.xyz"))
job1 = Job(posinp=pos_angstrom, calculator=self.calc3)
job2 = Job(posinp=pos_atomic, calculator=self.calc3)
job1.run("energy")
job2.run("energy")
assert job1.results["energy"] == job2.results["energy"]
class TestGeopt:
posN2 = Posinp.from_file(os.path.join(pos_folder, "N2_unrelaxed.xyz"))
posH2O = Posinp.from_file(os.path.join(pos_folder, "H2O_unrelaxed.xyz"))
calcN2 = SchnetPackCalculator(os.path.join(model_folder, "ani1_N2_model"))
calcH2O = SchnetPackCalculator(os.path.join(model_folder, "H2O_model"))
def test_N2(self, capsys):
init = Job(posinp=self.posN2, calculator=self.calcN2)
init.run("energy")
assert init.results["energy"][0] == -2978.2354
geo = Geopt(posinp=self.posN2, calculator=self.calcN2)
geo.run(recenter=True, verbose=2)
output = capsys.readouterr()
assert 1.101 < geo.final_posinp.distance(0, 1) < 1.103
assert np.isclose(
geo.final_posinp.positions[0, 2],
-geo.final_posinp.positions[1, 2],
atol=1e-6,
)
assert output.out is not None
final = Job(posinp=geo.final_posinp, calculator=self.calcN2)
final.run("energy")
assert final.results["energy"][0] == -2979.6070
def test_H2O(self):
init = Job(posinp=self.posH2O, calculator=self.calcH2O)
init.run("energy")
assert np.isclose(init.results["energy"][0], -2076.7576, atol=1e-4)
geo = Geopt(posinp=self.posH2O, calculator=self.calcH2O)
geo.run()
assert 0.964 < geo.final_posinp.distance(0, 1) < 0.965
assert (geo.final_posinp.distance(0, 1) -
geo.final_posinp.distance(0, 2)) < 0.0001
# TODO Check the angle
final = Job(posinp=geo.final_posinp, calculator=self.calcH2O)
final.run("energy")
assert np.isclose(final.results["energy"][0], -2078.6301, atol=1e-4)
def test_errors(self):
with pytest.raises(ValueError):
geo = Geopt(posinp=None, calculator=self.calcN2)
with pytest.raises(TypeError):
geo = Geopt(posinp=self.posN2, calculator=1)
class TestJob:
file1, file2, file3 = (
os.path.join(pos_folder, "free.xyz"),
os.path.join(pos_folder, "surface.xyz"),
os.path.join(pos_folder, "N2.xyz"),
)
pos1, pos2, pos3 = (
Posinp.from_file(file1),
Posinp.from_file(file2),
Posinp.from_file(file3),
)
dummy = Calculator(available_properties="",
units={
"positions": "atomic",
"energy": "eV"
})
badCalc = dict()
job = Job(name="test", posinp=[pos1, pos2, pos3], calculator=dummy)
def test_raises_no_positions(self):
with pytest.raises(ValueError):
j = Job(calculator=self.dummy)
def test_raises_posinp_types(self):
with pytest.raises(TypeError):
j = Job(posinp=[self.pos1, 1], calculator=self.dummy)
def test_raises_bad_calc(self):
with pytest.raises(TypeError):
j = Job(posinp=[self.pos1], calculator=self.badCalc)
def test_posinp_types(self):
job1 = Job(posinp=self.pos1, calculator=self.dummy)
job2 = Job(posinp=[self.pos1], calculator=self.dummy)
assert job1.posinp == job2.posinp
@pytest.mark.parametrize(
"value, expected",
[(job.name, "test"), (job.num_struct, 3), (job.posinp[1], pos2)],
)
def test_values(self, value, expected):
assert value == expected
class TestGrapheneAngles:
graphene2_name = os.path.join(pos_folder, "gra2.xyz")
pos_2at = Posinp.from_file(graphene2_name)
graphene4_name = os.path.join(pos_folder, "gra4_red.xyz")
pos_4at_red = Posinp.from_file(graphene4_name)
calc = SchnetPackCalculator(os.path.join(model_folder, "H2O_model"))
def test_same_result(self):
j1 = Job(posinp=self.pos_2at, calculator=self.calc)
j1.run("energy")
e1 = j1.results["energy"]
j2 = Job(posinp=self.pos_4at_red, calculator=self.calc)
j2.run("energy")
e2 = j2.results["energy"]
pos_4at = deepcopy(self.pos_4at_red)
pos_4at.convert_units("angstroem")
j3 = Job(posinp=pos_4at, calculator=self.calc)
j3.run("energy")
e3 = j3.results["energy"]
assert e2 == e3
assert np.isclose(e2, 2 * e1, atol=0.0002)
def test_cell_with_angles(self):
assert np.isclose(
self.pos_2at.cell.array,
np.array([[2.46, 0.0, 0.0], [0.0, 0.0, 0.0],
[1.23, 0.0, 2.13042249]]),
).all()
def test_verify_values(self):
assert np.isclose(self.pos_2at.angles, np.array([90.0, 60.0,
90.0])).all()
assert self.pos_4at_red.orthorhombic
assert not self.pos_2at.orthorhombic
assert np.isclose(self.pos_2at.cell.lengths(),
np.array([2.46, 0.0, 2.46])).all()
def main(args):
eval_name = args.modelpath.split("/")[-1]
eval_file = "evaluation_" + eval_name + ".txt"
if os.path.exists(eval_file):
if args.overwrite:
os.remove(eval_file)
else:
raise Exception(
"The evaluation file already exists. Delete it or add the overwrite flag."
)
device = "cuda" if args.cuda else "cpu"
calculator = mlcalcdriver.calculators.SchnetPackCalculator(args.modelpath,
device=device)
with connect(args.dbpath) as db:
answers, results = (
[[] for _ in range(len(args.properties))],
[[] for _ in range(len(args.properties))],
)
posinp = []
for row in db.select():
for i, prop in enumerate(args.properties):
answers[i].append(row.data[prop])
posinp.append(Posinp.from_ase(row.toatoms()))
if len(posinp) == args.batch_size:
job = Job(posinp=posinp, calculator=calculator)
for i, prop in enumerate(args.properties):
job.run(prop, batch_size=args.batch_size)
results[i].append(job.results[prop].tolist())
posinp = []
if len(posinp) > 0:
job = Job(posinp=posinp, calculator=calculator)
for i, prop in enumerate(args.properties):
job.run(prop, batch_size=args.batch_size)
results[i].append(job.results[prop])
posinp = []
header, error = [], []
for prop in args.properties:
header += ["MAE_" + prop, "%Error_" + prop, "RMSE_" + prop]
for l1, l2 in zip(answers, results):
an, re = np.array(l1).flatten(), np.concatenate(l2).flatten()
error.append(np.abs(an - re).mean())
error.append(np.abs((an - re) / an).mean() * 100)
error.append(np.sqrt(np.mean((an - re)**2)))
with open(eval_file, "w") as file:
wr = csv.writer(file)
wr.writerow(header)
wr.writerow(error)
def get_dos(
model,
posinp,
device="cpu",
supercell=(6, 6, 6),
qpoints=[30, 30, 30],
npts=1000,
width=0.004,
):
if isinstance(posinp, str):
atoms = posinp_to_ase_atoms(Posinp.from_file(posinp))
elif isinstance(posinp, Posinp):
atoms = posinp_to_ase_atoms(posinp)
else:
raise ValueError("The posinp variable is not recognized.")
if isinstance(model, str):
model = load_model(model, map_location=device)
elif isinstance(model, torch.nn.Module):
pass
else:
raise ValueError("The model variable is not recognized.")
# Bugfix to make older models work with PyTorch 1.6
# Hopefully temporary
for mod in model.modules():
if not hasattr(mod, "_non_persistent_buffers_set"):
mod._non_persistent_buffers_set = set()
assert len(supercell) == 3, "Supercell should be a length 3 object."
assert len(qpoints) == 3, "Qpoints should be a length 3 object."
supercell = tuple(supercell)
cutoff = float(model.state_dict()
["representation.interactions.0.cutoff_network.cutoff"])
calculator = SpkCalculator(
model,
device=device,
energy="energy",
forces="forces",
environment_provider=AseEnvironmentProvider(cutoff),
)
ph = Phonons(atoms, calculator, supercell=supercell, delta=0.02)
ph.run()
ph.read(acoustic=True)
dos = ph.get_dos(kpts=qpoints).sample_grid(npts=npts, width=width)
ph.clean()
return Dos(dos.energy * 8065.6, dos.weights[0])
def generate_graphene_cell(xsize, zsize):
base_cell = np.array([2.4674318, 0, 4.2737150])
positions = []
reduced_pos = np.array([[0, 0, 0], [0, 0, 1.0 / 3], [0.5, 0, 0.5],
[0.5, 0, 5.0 / 6]])
for i in range(xsize):
for j in range(zsize):
p = (np.array([i, 0, j]) + reduced_pos) * base_cell
for pi in p:
positions.append({"C": pi})
pos_dict = {
"units": "angstroem",
"cell": base_cell * np.array([xsize, 0, zsize]),
"positions": positions,
}
pos = Posinp.from_dict(pos_dict)
return pos
class TestPhononAutoGrad:
posH2O = Posinp.from_file(os.path.join(pos_folder, "H2Orelaxed.xyz"))
calc_ener = SchnetPackCalculator(os.path.join(model_folder, "H2O_model"))
calc_for = SchnetPackCalculator(
os.path.join(model_folder, "H2O_forces_model"))
def test_ph_h2o_autograd_2nd_derivative(self):
ph1 = Phonon(posinp=self.posH2O, calculator=self.calc_ener)
ph1.run()
ph1.energies.sort()
assert np.allclose(ph1.energies[6:9], [1726, 3856, 3942], atol=1)
def test_ph_h2o_autograd_1st_derivative(self):
ph1 = Phonon(posinp=self.posH2O, calculator=self.calc_for)
ph1.run()
ph1.energies.sort()
assert np.allclose(ph1.energies[6:9], [1589, 3703, 3812], atol=1)
def get_orthonormal_basis(modes=None, model=None, posinp=None, write=False):
if modes:
with h5py.File(modes, "r") as f:
normal_modes = f["modes"][:]
orthonormal_basis = gramschmidt(normal_modes)
else:
calculator = SchnetPackCalculator(model)
posinp = Posinp.from_file(posinp)
ph = Phonon(posinp=posinp, calculator=calculator)
ph.run()
normal_modes = ph.normal_modes.copy()
orthonormal_basis = gramschmidt(normal_modes)
if write:
fx = h5py.File("orthonormal_basis.h5", "w")
fx.create_dataset("basis", data=orthonormal_basis)
fx.close()
return orthonormal_basis
class TestPhononFinite:
posN2 = Posinp.from_file(os.path.join(pos_folder, "N2_unrelaxed.xyz"))
calcN2 = SchnetPackCalculator(os.path.join(model_folder, "myN2_model"))
def test_ph_N2(self):
ph1 = Phonon(posinp=self.posN2,
calculator=self.calcN2,
finite_difference=True)
ph1.run(batch_size=1)
assert np.isclose(ph1.energies.max(), 2339.53, atol=0.01)
assert all(
np.abs(np.delete(ph1.energies, np.argmax(ph1.energies))) < 30)
ph2 = Phonon(
posinp=ph1._ground_state,
calculator=ph1.calculator,
relax=False,
finite_difference=True,
translation_amplitudes=0.03,
)
ph2.run()
assert np.allclose(ph1.energies, ph2.energies)
ph3 = Phonon(
posinp=self.posN2,
calculator=self.calcN2,
finite_difference=True,
relax=False,
)
ph3.run()
assert not np.allclose(ph3.energies, ph1.energies, atol=100)
def test_phonon_posinp_error(self):
with pytest.raises(TypeError):
ph = Phonon(posinp=None, calculator=self.calcN2)
def test_phonon_calc_error(self):
with pytest.raises(TypeError):
ph = Phonon(posinp=self.posN2, calculator=None)
def get_normal_modes(posinp, model, device="cpu", rotate=False):
calculator = SchnetPackCalculator(model, device=device)
posinp = Posinp.from_file(posinp)
ph = Phonon(posinp=posinp, calculator=calculator)
ph.run()
if rotate:
ndim = 3 * len(posinp)
final_modes = np.zeros((ndim, ndim))
idx = np.arange(ndim)
for i in range(ndim):
init = ph.normal_modes[:, i]
final = np.empty_like(init)
final[np.where(idx % 3 == 0)[0]] = init[np.where(idx % 3 == 0)[0]]
final[np.where(idx % 3 == 1)[0]] = init[np.where(idx % 3 == 2)[0]]
final[np.where(idx %
3 == 2)[0]] = -1.0 * init[np.where(idx % 3 == 1)[0]]
final_modes[:, i] = final
return ph.energies, final_modes
else:
return ph.energies, ph.normal_modes
def main(args):
with connect(args.dbname) as db:
db.metadata = DEFAULT_METADATA
if args.run_mode == "bigdft":
files = [f for f in os.listdir() if f.endswith(".xyz")]
for f in files:
atoms = posinp_to_ase_atoms(Posinp.from_file(f))
with open(f, "r") as posinp_file:
energy = float(
posinp_file.readline().split()[2]) * 27.21138602
forces = None
for line in posinp_file:
if "forces" not in line:
continue
else:
forces = []
for _ in range(len(atoms)):
forces.append([
float(force) for force in
posinp_file.readline().split()[-3:]
])
forces = np.array(
forces) * 27.21138602 / 0.529177249
break
db.write(atoms, data={"energy": energy, "forces": forces})
elif args.run_mode == "abinit":
files = [f for f in os.listdir() if f.endswith(".out")]
for f in files:
atoms = read(f, format="abinit-out")
about = AbinitOutputFile(f)
energy = float(about.final_vars_global["etotal"]) * 27.21138602
forces = (np.array([
float(g) for g in about.final_vars_global["fcart"].split()
]).reshape(-1, 3) * 27.21138602 / 0.529177249)
db.write(atoms, data={"energy": energy, "forces": forces})
def test_surface(self):
pos1 = Posinp.from_file(os.path.join(pos_folder, "surface2.xyz"))
atoms = posinp_to_ase_atoms(pos1)
pos2 = Posinp.from_ase(atoms)
assert pos1 == pos2
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)
periodic_filename = os.path.join(tests_fol, "periodic.xyz")
periodic_pos = Posinp.from_file(periodic_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 1.000000000 3.461304757
C 7.327412521 0.000000000 3.461304757"""
str_pos = Posinp.from_string(string)
value = [len(pos), pos.units, pos.boundary_conditions, pos.cell, pos[0], pos.angles]
expected = [
4,
"reduced",
"surface",
Cell.new(np.array([8.07007483423, 0.0, 4.65925987792])),
Atom("C", [0.08333333333, 0.5, 0.25]),
np.array([90.0, 90.0, 90.0]),
]
def test_from_file(self):
for v, e in zip(self.value, self.expected):
if isinstance(v, np.ndarray) or isinstance(v, Cell):
assert np.allclose(v, e)
else:
assert v == e
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=Cell([0.0, 0.0, 0.0]), angles=[90. 90. 90.])"
)
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 == Cell.new()).all()
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],
)
with pytest.raises(ValueError):
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],
)
# They are obviously different if the cell size along the other
# directions are not the same
pos2_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=[20, "inf", 40],
)
assert pos_with_inf != pos2_with_inf
# They still have the same BC
assert pos2_with_inf.boundary_conditions == pos_with_inf.boundary_conditions
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_distance(self):
assert np.isclose(self.free_pos.distance(0, 2), 4.722170992308181)
def test_convert(self):
pos1 = self.periodic_pos.positions
assert self.periodic_pos.units == "angstroem"
self.periodic_pos.convert_units("atomic")
assert np.isclose(
self.periodic_pos.positions,
np.array(
[
[0.15747717, 0.94486299, 0.4724315],
[0.78738583, 0.94486299, 0.4724315],
[1.10234016, 0.94486299, 1.41729449],
[1.73224882, 0.94486299, 1.41729449],
]
),
).all()
assert self.periodic_pos.units == "atomic"
self.periodic_pos.convert_units("angstroem")
assert np.isclose(self.periodic_pos.positions, pos1).all()
assert self.periodic_pos.units == "angstroem"
self.periodic_pos.convert_units("angstroem")
assert np.isclose(self.periodic_pos.positions, pos1).all()
red = Posinp.from_file(tests_fol + "reduced.xyz")
red.convert_units("angstroem")
print(red.positions)
assert np.isclose(
red.positions,
np.array(
[
[0.4233418, 1.32294312, 0.95251905],
[3.81007619, 0.26458862, 0.47625952],
]
),
).all()
def test_angles(self):
h2o = Posinp.from_file(tests_fol + "H2Orelaxed.xyz")
a = h2o.angle(1, 0, 2) * 180 / np.pi
assert np.isclose(a, 104.1219, atol=10 ** -4)
a1, a2 = h2o.angle(0, 1, 2), h2o.angle(2, 1, 0)
assert a1 == a2
def test_periodic(self):
pos1 = Posinp.from_file(os.path.join(pos_folder, "periodic.xyz"))
atoms = posinp_to_ase_atoms(pos1)
pos2 = Posinp.from_ase(atoms)
assert pos1 == pos2
def get_normal_modes(posinp, model, device="cpu"):
calculator = SchnetPackCalculator(model, device=device)
posinp = Posinp.from_file(posinp)
ph = Phonon(posinp=posinp, calculator=calculator)
ph.run()
return ph.energies, ph.normal_modes
import numpy as np
from mlcalcdriver import Posinp
import matplotlib.pyplot as plt
pos = Posinp.from_file("data/posinp.xyz")
translations = (
np.array(
[
[0, 0, 0],
[1, 0, 0],
[-1, 0, 0],
[0, 0, 1],
[0, 0, -1],
[1, 0, 1],
[1, 0, -1],
[-1, 0, 1],
[-1, 0, -1],
]
)
* pos.cell
)
results = []
n = 50000
n_at = len(pos)
for _ in range(n):
i,j = np.random.choice(n_at, 2, replace=False)
atom1, atom2 = pos[i], pos[j]
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)
def test_angles(self):
h2o = Posinp.from_file(tests_fol + "H2Orelaxed.xyz")
a = h2o.angle(1, 0, 2) * 180 / np.pi
assert np.isclose(a, 104.1219, atol=10 ** -4)
a1, a2 = h2o.angle(0, 1, 2), h2o.angle(2, 1, 0)
assert a1 == a2
from mlcalcdriver import Posinp
import numpy as np
import os
from copy import copy
import matplotlib.pyplot as plt
pos_folder = "positions/"
positions = [
Posinp.from_file(pos_folder + file) for file in os.listdir(pos_folder)
if file.endswith(".xyz")
]
distances, angles = [], []
for pos in positions:
az_idx = [i for i, at in enumerate(pos) if at.type == "N"]
if len(az_idx) == 2:
distances.append(pos.distance(az_idx[0], az_idx[1]))
angles.append(np.pi)
elif len(az_idx) == 3:
mid = np.array(pos.cell) / 2
d = np.array(
[np.linalg.norm(pos[idx].position - mid) for idx in az_idx])
mid_idx = az_idx[np.argmin(d)]
other_idx = copy(az_idx)
del other_idx[np.argmin(d)]
distances.append(pos.distance(mid_idx, other_idx[0]))
distances.append(pos.distance(mid_idx, other_idx[1]))
angles.append(pos.angle(other_idx[0], mid_idx, other_idx[1]))
else: