Vibrational Analysis

A vibrational analysis computes a Cartesian Hessian and harmonic frequencies for the input geometry. It is usually run after a geometry optimization or transition-state search.

Your First Vibrational Analysis

import atomiverse
from atomiverse import Atoms, JobFailedError, Vibrations
from atomiverse.levels import GFN2_XTB

atomiverse.configure(api_key="your-api-key")

water = Atoms.from_smiles("O")

job = Vibrations(
    atoms=water,
    level_of_theory=GFN2_XTB,
)

job.submit()

try:
    result = job.require_result()
except JobFailedError as exc:
    print(f"Job failed: {exc.failure.error}")
else:
    print(f"Hessian dimension: {len(result.hessian)}")
    for freq in result.frequencies:
        print(f"{freq:10.2f} cm^-1")

Result

job.require_result() returns a VibrationsResult with two fields:

Field	Type	Units	Shape
hessian	list[list[float]]	Hartree/Angstrom^2	(3 * n_atoms, 3 * n_atoms)
frequencies	list[float]	cm^-1	variable

Imaginary modes are returned as negative frequencies. For a transition state, the reaction-coordinate mode should usually appear as a negative value.

Charge, Multiplicity, and Level of Theory

These work exactly as for single point energy calculations:

job = Vibrations(
    atoms=molecule,
    charge=-1,
    multiplicity=2,
    level_of_theory=GFN2_XTB,
)

See Levels of Theory for all available methods and Single Point Energy for charge/multiplicity details.

Handling Failures

The most common failures are unsupported elements or charge/multiplicity combinations, unreasonable geometries, and methods that cannot evaluate the requested structure.

from atomiverse import JobFailedError

job.submit()

try:
    result = job.require_result()
except JobFailedError as exc:
    print(f"Vibrational analysis failed: {exc.failure.error}")
else:
    print(result.frequencies)
    print(result.hessian[0][0])

For best results, start from an optimized minimum or a converged transition-state geometry.