Misc improvements (#117)

aiqm · Oct 6, 2018 · 3913717 · 3913717
1 parent e4fe2a5
commit 3913717
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Showing 3 changed files with 5 additions and 10 deletions.
diff --git a/tests/test_ensemble.py b/tests/test_ensemble.py
@@ -16,7 +16,7 @@ def setUp(self):
 
     def _test_molecule(self, coordinates, species):
         builtins = torchani.neurochem.Builtins()
-        coordinates = torch.tensor(coordinates, requires_grad=True)
+        coordinates.requires_grad_(True)
         aev = builtins.aev_computer
         ensemble = builtins.models
         models = [torch.nn.Sequential(aev, m) for m in ensemble]

diff --git a/tests/test_forces.py b/tests/test_forces.py
@@ -22,7 +22,7 @@ def testIsomers(self):
             datafile = os.path.join(path, 'test_data/{}'.format(i))
             with open(datafile, 'rb') as f:
                 coordinates, species, _, _, _, forces = pickle.load(f)
-                coordinates = torch.tensor(coordinates, requires_grad=True)
+                coordinates.requires_grad_(True)
                 _, energies = self.model((species, coordinates))
                 derivative = torch.autograd.grad(energies.sum(),
                                                  coordinates)[0]
@@ -36,7 +36,7 @@ def testPadding(self):
             datafile = os.path.join(path, 'test_data/{}'.format(i))
             with open(datafile, 'rb') as f:
                 coordinates, species, _, _, _, forces = pickle.load(f)
-                coordinates = torch.tensor(coordinates, requires_grad=True)
+                coordinates.requires_grad_(True)
                 species_coordinates.append((species, coordinates))
                 coordinates_forces.append((coordinates, forces))
         species, coordinates = torchani.utils.pad_coordinates(

diff --git a/torchani/aev.py b/torchani/aev.py
@@ -155,11 +155,7 @@ def _terms_and_indices(self, species, coordinates):
         """Shape (conformations, atoms, atoms) storing Rij distances"""
 
         padding_mask = (species == -1).unsqueeze(1)
-        distances = torch.where(
-            padding_mask,
-            torch.tensor(math.inf, dtype=self.EtaR.dtype,
-                         device=self.EtaR.device),
-            distances)
+        distances = distances.masked_fill(padding_mask, math.inf)
 
         distances, indices = distances.sort(-1)
 
@@ -172,11 +168,10 @@ def _terms_and_indices(self, species, coordinates):
         radial_terms = self._radial_subaev_terms(distances)
 
         indices_a = indices.index_select(-1, inRca)
-        new_shape = list(indices_a.shape) + [3]
 
         # TODO: remove this workaround when gather support broadcasting
         # https://github.com/pytorch/pytorch/pull/9532
-        _indices_a = indices_a.unsqueeze(-1).expand(*new_shape)
+        _indices_a = indices_a.unsqueeze(-1).expand(-1, -1, -1, 3)
         vec = vec.gather(-2, _indices_a)
 
         vec = self._combinations(vec, -2)