Fixed: symeig deprication (#627)

* Fixed: symeig deprication

This causes:
RuntimeError: This function was deprecated since version 1.9 and is now removed. Please use the `torch.linalg.eigh` function instead.

* Fix: slow tensor creation

This raises:
Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor.

Author: kfir4444

torchani/ase.py

@@ -50,7 +50,7 @@ def __init__(self, species, model, overwrite=False):
     def calculate(self, atoms=None, properties=['energy'],
                   system_changes=ase.calculators.calculator.all_changes):
         super().calculate(atoms, properties, system_changes)
-        cell = torch.tensor(self.atoms.get_cell(complete=True),
+        cell = torch.tensor(self.atoms.get_cell(complete=True).array,
                             dtype=self.dtype, device=self.device)
         pbc = torch.tensor(self.atoms.get_pbc(), dtype=torch.bool,
                            device=self.device)

torchani/utils.py

@@ -322,7 +322,7 @@ def vibrational_analysis(masses, hessian, mode_type='MDU', unit='cm^-1'):
     if mass_scaled_hessian.shape[0] != 1:
         raise ValueError('The input should contain only one molecule')
     mass_scaled_hessian = mass_scaled_hessian.squeeze(0)
-    eigenvalues, eigenvectors = torch.symeig(mass_scaled_hessian, eigenvectors=True)
+    eigenvalues, eigenvectors = torch.linalg.eigh(mass_scaled_hessian)
     angular_frequencies = eigenvalues.sqrt()
     frequencies = angular_frequencies / (2 * math.pi)
     # converting from sqrt(hartree / (amu * angstrom^2)) to cm^-1 or meV