improve analytical stress calculation (#387)

aiqm · Nov 12, 2019 · d400d8f · d400d8f
1 parent e784666
commit d400d8f
Showing 1 changed file with 6 additions and 20 deletions.
diff --git a/torchani/ase.py b/torchani/ase.py
@@ -52,13 +52,6 @@ def __init__(self, species, aev_computer, model, energy_shifter, dtype=torch.flo
             self.energy_shifter
         ).to(dtype)
 
-    @staticmethod
-    def strain(tensor, displacement, surface_normal_axis):
-        displacement_of_tensor = torch.zeros_like(tensor)
-        for axis in range(3):
-            displacement_of_tensor[..., axis] = tensor[..., surface_normal_axis] * displacement[axis]
-        return displacement_of_tensor
-
     def calculate(self, atoms=None, properties=['energy'],
                   system_changes=ase.calculators.calculator.all_changes):
         super(Calculator, self).calculate(atoms, properties, system_changes)
@@ -70,7 +63,7 @@ def calculate(self, atoms=None, properties=['energy'],
         species = self.species_to_tensor(self.atoms.get_chemical_symbols()).to(self.device)
         species = species.unsqueeze(0)
         coordinates = torch.tensor(self.atoms.get_positions())
-        coordinates = coordinates.unsqueeze(0).to(self.device).to(self.dtype) \
+        coordinates = coordinates.to(self.device).to(self.dtype) \
                                  .requires_grad_('forces' in properties)
 
         if pbc_enabled:
@@ -79,20 +72,13 @@ def calculate(self, atoms=None, properties=['energy'],
                 atoms.set_positions(coordinates.detach().cpu().reshape(-1, 3).numpy())
 
         if 'stress' in properties:
-            displacements = torch.zeros(3, 3, requires_grad=True,
-                                        dtype=self.dtype, device=self.device)
-            displacement_x, displacement_y, displacement_z = displacements
-            strain_x = self.strain(coordinates, displacement_x, 0)
-            strain_y = self.strain(coordinates, displacement_y, 1)
-            strain_z = self.strain(coordinates, displacement_z, 2)
-            coordinates = coordinates + strain_x + strain_y + strain_z
+            scaling = torch.eye(3, requires_grad=True, dtype=self.dtype, device=self.device)
+            coordinates = coordinates @ scaling
+        coordinates = coordinates.unsqueeze(0)
 
         if pbc_enabled:
             if 'stress' in properties:
-                strain_x = self.strain(cell, displacement_x, 0)
-                strain_y = self.strain(cell, displacement_y, 1)
-                strain_z = self.strain(cell, displacement_z, 2)
-                cell = cell + strain_x + strain_y + strain_z
+                cell = cell @ scaling
             aev = self.aev_computer((species, coordinates), cell=cell, pbc=pbc).aevs
         else:
             aev = self.aev_computer((species, coordinates)).aevs
@@ -108,5 +94,5 @@ def calculate(self, atoms=None, properties=['energy'],
 
         if 'stress' in properties:
             volume = self.atoms.get_volume()
-            stress = torch.autograd.grad(energy.squeeze(), displacements)[0] / volume
+            stress = torch.autograd.grad(energy.squeeze(), scaling)[0] / volume
             self.results['stress'] = stress.cpu().numpy()