fix new dataset reshape bug (#405)

torchani/data/new.py

@@ -554,7 +554,7 @@ def collate_fn(data, chunk_threshold, properties_info):
                                                     padding_value=-1)
     batch_coordinates = torch.nn.utils.rnn.pad_sequence(batch_coordinates,
                                                         batch_first=True,
-                                                        padding_value=0)
+                                                        padding_value=np.inf)
 
     # sort - time: 0.7s
     atoms = torch.sum(~(batch_species == -1), dim=-1, dtype=torch.int32)
@@ -574,7 +574,7 @@ def collate_fn(data, chunk_threshold, properties_info):
 
     # truncate redundant padding - time: 1.3s
     chunks_batch_species = trunc_pad(list(chunks_batch_species), padding_value=-1)
-    chunks_batch_coordinates = trunc_pad(list(chunks_batch_coordinates))
+    chunks_batch_coordinates = trunc_pad(list(chunks_batch_coordinates), padding_value=np.inf)
 
     for i, c in enumerate(chunks_batch_coordinates):
         chunks_batch_coordinates[i] = c.reshape(c.shape[0], -1, 3)