pyscivr.potentials module

Potential energy calculators.

All calculators take positions in Angstrom and return energies in eV, forces in eV/Angs and Hessians in eV/Angs^2.

Notation:

  • N: number of atoms.

class pyscivr.potentials.Calculator[source]

Bases: ABC

Base class for potential energy calculators.

Subclasses implement _energy_forces_batch() and optionally _hessian_batch() for a batch of geometries. The public methods accept either a single geometry (N, 3) or a batch of geometries (n_batch, N, 3), and return the results without the batch axis for a single geometry.

energy_forces(positions)[source]

Compute the energy and forces for a single geometry or a batch of geometries.

Parameters:

positions (ArrayLike) – (N, 3) or (n_batch, N, 3) positions [Angs].

Returns:

(energy, forces) [eV, eV/Angs], with shapes () and (N, 3) for a single geometry, or (n_batch,) and (n_batch, N, 3) for a batch.

Return type:

tuple[NDArray[np.float64], NDArray[np.float64]]

energy(positions)[source]

Compute the energy [eV] (see energy_forces()).

Parameters:

positions (ArrayLike)

Return type:

NDArray[np.float64]

forces(positions)[source]

Compute the forces [eV/Angs] (see energy_forces()).

Parameters:

positions (ArrayLike)

Return type:

NDArray[np.float64]

hessian(positions)[source]

Compute the analytical Hessian.

Parameters:

positions (ArrayLike) – (N, 3) or (n_batch, N, 3) positions [Angs].

Returns:

(3N, 3N) Hessian [eV/Angs^2] for a single geometry, or (n_batch, 3N, 3N) for a batch.

Raises:

NotImplementedError – If the subclass does not implement an analytic Hessian. Use pyscivr.hessian.eval_hess_active() instead.

Return type:

NDArray[np.float64]

class pyscivr.potentials.ZeroPotential[source]

Bases: Calculator

Zero potential. The energies, forces and Hessians are all zero.

class pyscivr.potentials.H2SplinePotential[source]

Bases: Calculator

H2 potential by cubic spline interpolation of CCSD(T)/aug-cc-pV5Z scan computed with Gaussian 16.

The potential \(V(r)\) depends only on the bond length \(r\) between the two atoms. The forces and Hessians are the exact derivatives of the spline, with the Hessian blocks H_ii = H_jj = H_BB and H_ij = H_ji = -H_BB, where

\[H_{BB} = V''(r) \hat{u}\hat{u}^T + \frac{V'(r)}{r} (I - \hat{u}\hat{u}^T), \quad \hat{u} = \frac{q_j - q_i}{r}\]

Warning

The scan covers only 0.4 to 1.5 Angs (0.02 Angs spacing). The spline is not reliable outside this range.

class pyscivr.potentials.ASEPotential(symbols, calc)[source]

Bases: Calculator

Wrapper for ASE calculators.

Geometries in a batch are evaluated sequentially. The analytical Hessian is not available.

Parameters:

  • symbols (Sequence[str]) – (N,) atomic symbols.

  • calc (ASECalculator) – ASE calculator.

pyscivr.potentials.mace_anicc_potential(symbols, *, device=None, num_threads=1)[source]

Make a calculator with the pre-trained MACE-ANICC model.

Parameters:

  • symbols (Sequence[str]) – (N,) atomic symbols.

  • device (str | None) – Device to run the model on. If None, use GPU if available, otherwise CPU.

  • num_threads (int) – Number of threads to use for CPU inference.

Returns:

Calculator wrapping the MACE-ANICC model.

Return type:

ASEPotential

Note

Requires the torch, mace and ase packages. On the CPU, torch.jit.load is patched to load the model onto the CPU.

class pyscivr.potentials.DFTPotential(symbols, *, basis='def2-svp', xc='b3lyp', charge=0, spin=0, conv_tol=1e-10)[source]

Bases: Calculator

Potential by DFT calculations with PySCF.

Geometries in a batch are evaluated sequentially. The analytical Hessian is not available.

Parameters:

  • symbols (Sequence[str]) – (N,) atomic symbols.

  • basis (str) – Basis set.

  • xc (str) – Exchange-correlation functional.

  • charge (int) – Total charge.

  • spin (int) – Number of unpaired electrons (2S). Restricted Kohn-Sham is used if spin == 0, otherwise unrestricted Kohn-Sham.

  • conv_tol (float) – Convergence threshold of the SCF energy [Hartree].

class pyscivr.potentials.ArgonPotential(calc, root=None, fname_qc_base=None)[source]

Bases: Calculator

Wrapper for Argon (Unpublished) calculators.

Geometries in a batch are evaluated sequentially. The analytical Hessian is not available.

Parameters:

  • calc – Argon calculator.

  • root – tuple that specifying the bra (and ket) state of the property will be returned.

  • fname_qc_base – File name (w/o extension) of QC input/output file.