def run(self, batch_size=128, **kwargs):
r"""
Parameters
----------
batch_size : int
Batch size used when passing the structures to the model
**kwargs :
Optional arguments for the geometry optimization.
Only useful if the relaxation is unstable.
"""
if self.relax:
geopt = Geopt(posinp=self.posinp,
calculator=self.calculator,
**kwargs)
geopt.run(batch_size=batch_size)
self._ground_state = deepcopy(geopt.final_posinp)
if self.finite_difference:
job = Job(posinp=self._create_displacements(),
calculator=self.calculator)
job.run(property="forces", batch_size=batch_size)
else:
job = Job(posinp=self._ground_state, calculator=self.calculator)
job.run(property="hessian", batch_size=batch_size)
self._post_proc(job)
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 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 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 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_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_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("angstrom")
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)