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4 files changed

+29
-21
lines changed

4 files changed

+29
-21
lines changed

pyiron_potentialfit/atomistics/job/trainingcontainer.py

Lines changed: 12 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -353,7 +353,7 @@ def train_test_split(self, train_size, seed=None):
353353
brk = int(len(self) * train_size)
354354
if brk in (0, 1):
355355
raise ValueError(
356-
f"container not large enough to realize this split, only multiples of {1/len(self)} possible!"
356+
f"container not large enough to realize this split, only multiples of {1/len(self)} possible!"
357357
)
358358

359359
# somewhat inefficient, but probably good enough for normal training set sizes
@@ -362,8 +362,8 @@ def train_test_split(self, train_size, seed=None):
362362
test_idx = idx[:brk]
363363
train_idx = idx[brk:]
364364
return (
365-
self.sample(lambda f, i: i in test_idx),
366-
self.sample(lambda f, i: i in train_idx)
365+
self.sample(lambda f, i: i in test_idx),
366+
self.sample(lambda f, i: i in train_idx),
367367
)
368368

369369

@@ -624,9 +624,15 @@ def iter(self, *arrays, wrap_atoms=True):
624624
"""
625625
yield from self._container.iter(*arrays, wrap_atoms=wrap_atoms)
626626

627-
def train_test_split(self, train_size: float, seed=None,
628-
run: bool = True,
629-
train_name: str = None, test_name: str = None, project=None):
627+
def train_test_split(
628+
self,
629+
train_size: float,
630+
seed=None,
631+
run: bool = True,
632+
train_name: str = None,
633+
test_name: str = None,
634+
project=None,
635+
):
630636
"""
631637
Split into two random sub sets for training and testing.
632638

pyiron_potentialfit/ml/potentialfit.py

Lines changed: 8 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -114,7 +114,6 @@ def get_lammps_potential(self) -> pd.DataFrame:
114114
pass
115115

116116

117-
118117
class PotentialPlots:
119118
def __init__(self, training_data, predicted_data):
120119
self._training_data = training_data
@@ -317,37 +316,35 @@ def __init__(self, true_data: TrainingStorage, predicted_data: FlattenedStorage)
317316
self._predicted_data = predicted_data
318317

319318
def _rmse(self, a, b):
320-
return np.sqrt(np.mean((a-b)**2))
319+
return np.sqrt(np.mean((a - b) ** 2))
321320

322321
def _mae(self, a, b):
323-
return np.mean(np.abs(a-b))
322+
return np.mean(np.abs(a - b))
324323

325324
@property
326325
def energy_rmse(self):
327326
N = self._true_data["length"]
328327
return self._rmse(
329-
self._true_data["energy"]/N,
330-
self._predicted_data["energy"]/N
328+
self._true_data["energy"] / N, self._predicted_data["energy"] / N
331329
)
332330

333331
@property
334332
def energy_mae(self):
335333
N = self._true_data["length"]
336334
return self._mae(
337-
self._true_data["energy"]/N,
338-
self._predicted_data["energy"]/N
335+
self._true_data["energy"] / N, self._predicted_data["energy"] / N
339336
)
340337

341338
@property
342339
def force_rmse(self):
343340
return self._rmse(
344-
np.linalg.norm(self._true_data["forces"], axis=-1),
345-
np.linalg.norm(self._predicted_data["forces"], axis=-1)
341+
np.linalg.norm(self._true_data["forces"], axis=-1),
342+
np.linalg.norm(self._predicted_data["forces"], axis=-1),
346343
)
347344

348345
@property
349346
def force_mae(self):
350347
return self._mae(
351-
np.linalg.norm(self._true_data["forces"], axis=-1),
352-
np.linalg.norm(self._predicted_data["forces"], axis=-1)
348+
np.linalg.norm(self._true_data["forces"], axis=-1),
349+
np.linalg.norm(self._predicted_data["forces"], axis=-1),
353350
)

pyiron_potentialfit/spgfit/learn.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -254,7 +254,7 @@ def energy_mae(j):
254254
N = inpt.get_array("length")
255255
train = np.squeeze(inpt.get_array("energy")) / N
256256
pred = np.squeeze(j["output/training_efs"].to_object().get_array("energy")) / N
257-
return np.abs(train-pred).mean()
257+
return np.abs(train - pred).mean()
258258

259259

260260
def energy_max(j):

pyiron_potentialfit/spgfit/structures.py

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -857,9 +857,10 @@ def main():
857857
help="Retry the current step from scratch",
858858
)
859859
parser.add_argument(
860-
"--export", type=str,
860+
"--export",
861+
type=str,
861862
help="Optionally specify a directory where to dump POSCAR files with the generated structures after everything "
862-
"is finished."
863+
"is finished.",
863864
)
864865
args = parser.parse_args()
865866

@@ -892,7 +893,11 @@ def main():
892893
dir_path = os.path.join(args.export, cont.name)
893894
os.makedirs(dir_path, exist_ok=True)
894895
for i, s in enumerate(cont.iter_structures()):
895-
s.write(os.path.join(dir_path, cont._container["identifier", i]) + ".POSCAR", format="vasp")
896+
s.write(
897+
os.path.join(dir_path, cont._container["identifier", i])
898+
+ ".POSCAR",
899+
format="vasp",
900+
)
896901

897902

898903
if __name__ == "__main__":

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