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Fix units. Model uses Angstrom and kcal/mol.
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@lohedges
lohedges committed Nov 14, 2024
1 parent 544e4e8 commit 96baa28
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 deletions emle/calculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1132,7 +1132,7 @@ def run(self, path=None):

# No backend.
else:
E_vac, grad_vac = 0.0, _np.zeros_like(xyz_qm)
E_vac, grad_vac = 0.0, _np.zeros_like(xyz_qm.detatch().cpu())

# External backend.
else:
Expand Down Expand Up @@ -1179,11 +1179,11 @@ def run(self, path=None):
# Compute energy and gradients.
try:
E = self._emle(atomic_numbers, charges_mm, xyz_qm, xyz_mm)
dE_dxyz_qm_bohr, dE_dxyz_mm_bohr = _torch.autograd.grad(
dE_dxyz_qm, dE_dxyz_mm = _torch.autograd.grad(
E.sum(), (xyz_qm, xyz_mm)
)
dE_dxyz_qm_bohr = dE_dxyz_qm_bohr.cpu().numpy()
dE_dxyz_mm_bohr = dE_dxyz_mm_bohr.cpu().numpy()
dE_dxyz_qm_bohr = dE_dxyz_qm.cpu().numpy() * _BOHR_TO_ANGSTROM
dE_dxyz_mm_bohr = dE_dxyz_mm.cpu().numpy() * _BOHR_TO_ANGSTROM
except Exception as e:
msg = f"Failed to compute EMLE energies and gradients: {e}"
_logger.error(msg)
Expand All @@ -1210,11 +1210,11 @@ def run(self, path=None):

# Compute the embedding contributions.
E = self._emle_mm(atomic_numbers, charges_mm, xyz_qm, xyz_mm)
dE_dxyz_qm_bohr, dE_dxyz_mm_bohr = _torch.autograd.grad(
dE_dxyz_qm, dE_dxyz_mm = _torch.autograd.grad(
E.sum(), (xyz_qm, xyz_mm)
)
dE_dxyz_qm_bohr = dE_dxyz_qm_bohr.cpu().numpy()
dE_dxyz_mm_bohr = dE_dxyz_mm_bohr.cpu().numpy()
dE_dxyz_qm_bohr = dE_dxyz_qm.cpu().numpy() * _BOHR_TO_ANGSTROM
dE_dxyz_mm_bohr = dE_dxyz_mm.cpu().numpy() * _BOHR_TO_ANGSTROM

# Store the the MM and EMLE energies. The MM energy is an approximation.
E_mm = E_mm_qm_vac + E.sum().detach().cpu().numpy()
Expand Down Expand Up @@ -1571,11 +1571,11 @@ def _sire_callback(self, atomic_numbers, charges_mm, xyz_qm, xyz_mm, idx_mm=None
# Compute energy and gradients.
try:
E = self._emle(atomic_numbers, charges_mm, xyz_qm, xyz_mm)
dE_dxyz_qm_bohr, dE_dxyz_mm_bohr = _torch.autograd.grad(
dE_dxyz_qm, dE_dxyz_mm = _torch.autograd.grad(
E.sum(), (xyz_qm, xyz_mm)
)
dE_dxyz_qm_bohr = dE_dxyz_qm_bohr.cpu().numpy()
dE_dxyz_mm_bohr = dE_dxyz_mm_bohr.cpu().numpy()
dE_dxyz_qm_bohr = dE_dxyz_qm.cpu().numpy() * _BOHR_TO_ANGSTROM
dE_dxyz_mm_bohr = dE_dxyz_mm.cpu().numpy() * _BOHR_TO_ANGSTROM
except Exception as e:
msg = f"Failed to compute EMLE energies and gradients: {e}"
_logger.error(msg)
Expand All @@ -1590,7 +1590,7 @@ def _sire_callback(self, atomic_numbers, charges_mm, xyz_qm, xyz_mm, idx_mm=None
if self._is_interpolate:
# Create the ASE atoms object if it wasn't already created by the backend.
if atoms is None:
atoms = _ase.Atoms(positions=xyz_qm, numbers=atomic_numbers)
atoms = _ase.Atoms(positions=xyz_qm.detach().cpu(), numbers=atomic_numbers.cpu())

# Compute the in vacuo MM energy and gradients for the QM region.
if self._backend != None:
Expand All @@ -1602,15 +1602,15 @@ def _sire_callback(self, atomic_numbers, charges_mm, xyz_qm, xyz_mm, idx_mm=None

# If no backend is specified, then the MM energy and gradients are zero.
else:
E_mm_qm_vac, grad_mm_qm_vac = 0.0, _np.zeros_like(xyz_qm)
E_mm_qm_vac, grad_mm_qm_vac = 0.0, _np.zeros_like(xyz_qm.detach().cpu())

# Compute the embedding contributions.
E = self._emle_mm(atomic_numbers, charges_mm, xyz_qm, xyz_mm)
dE_dxyz_qm_bohr, dE_dxyz_mm_bohr = _torch.autograd.grad(
dE_dxyz_qm, dE_dxyz_mm = _torch.autograd.grad(
E.sum(), (xyz_qm, xyz_mm)
)
dE_dxyz_qm_bohr = dE_dxyz_qm_bohr.cpu().numpy()
dE_dxyz_mm_bohr = dE_dxyz_mm_bohr.cpu().numpy()
dE_dxyz_qm_bohr = dE_dxyz_qm.cpu().numpy() * _BOHR_TO_ANGSTROM
dE_dxyz_mm_bohr = dE_dxyz_mm.cpu().numpy() * _BOHR_TO_ANGSTROM

# Store the the MM and EMLE energies. The MM energy is an approximation.
E_mm = E_mm_qm_vac + E.sum().detach().cpu().numpy()
Expand Down

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