Vibrational Structure Problems with v0.5#

Further resources#

Be sure to check out the vibrational structure tutorial for more details on how to use the new code.

TL;DR#

This section gives you one cell with a v0.4 code followed by one cell with v0.5 code doing the same things. Hopefully this already gives you all the information which you were looking for.

Previously#

from qiskit_nature.drivers.second_quantization import GaussianForcesDriver
from qiskit_nature.problems.second_quantization import VibrationalStructureProblem
from qiskit_nature.settings import settings

settings.dict_aux_operators = True

driver = GaussianForcesDriver(logfile="aux_files/CO2_freq_B3LYP_631g.log")

problem = VibrationalStructureProblem(driver, num_modals=[2, 2, 3, 4], truncation_order=2)

# Note: at this point, `driver.run()` has NOT been called yet. We can trigger this indirectly like so:
second_q_ops = problem.second_q_ops()

hamiltonian = second_q_ops["VibrationalEnergy"]
print("\n".join(str(hamiltonian).splitlines()[:10] + ["..."]))

  NIIIIIIIIII * (1268.0676746875001+0j)
+ INIIIIIIIII * (3813.8767834375008+0j)
+ IINIIIIIIII * (705.8633818750001+0j)
+ II+-IIIIIII * (-46.025705898886045+0j)
+ II-+IIIIIII * (-46.025705898886045+0j)
+ IIINIIIIIII * (2120.1145593750007+0j)
+ IIIINIIIIII * (238.31540750000005+0j)
+ IIII+I-IIII * (19.820422279761104+0j)
+ IIIIINIIIII * (728.9613775000003+0j)
+ IIII-I+IIII * (19.820422279761104+0j)
...

New#

from qiskit_nature.second_q.drivers import GaussianForcesDriver
from qiskit_nature.second_q.problems import HarmonicBasis

driver = GaussianForcesDriver(logfile="aux_files/CO2_freq_B3LYP_631g.log")
basis = HarmonicBasis(num_modals=[2, 2, 3, 4])

# this is now done explicitly and already requires the basis
problem = driver.run(basis=basis)
problem.hamiltonian.truncation_order = 2

hamiltonian = problem.hamiltonian.second_q_op()
print("\n".join(str(hamiltonian).splitlines()[:10] + ["..."]))

Vibrational Operator
number modes=4, number modals=[2, 2, 3, 4], number terms=177
  (1268.0676746875001+0j) * ( +_0_0 -_0_0 )
+ (3813.8767834375008+0j) * ( +_0_1 -_0_1 )
+ (705.8633818750002+0j) * ( +_1_0 -_1_0 )
+ (-46.025705898886045+0j) * ( +_1_0 -_1_1 )
+ (-46.025705898886045+0j) * ( +_1_1 -_1_0 )
+ (2120.1145593750007+0j) * ( +_1_1 -_1_1 )
+ (238.31540750000005+0j) * ( +_2_0 -_2_0 )
+ (19.82042227976109+0j) * ( +_2_0 -_2_2 )
...

`qiskit_nature.drivers`#

This section deals exclusively with the migration of the vibrational structure-related drivers.

The table below summarizes where each of the vibrational structure components of qiskit_nature.drivers.second_quantization has ended up.

Legacy component	New location
BaseDriver	`qiskit_nature.second_q.drivers.BaseDriver`
VibrationalStructureDriver	`qiskit_nature.second_q.drivers.VibrationalStructureDriver`
VibrationalStructureDriverType	removed
VibrationalStructureMoleculeDriver	removed
GaussianForcesDriver	`qiskit_nature.second_q.drivers.GaussianForcesDriver`
GaussianLogDriver	`qiskit_nature.second_q.drivers.GaussiaLogDriver`
GaussianLogResult	`qiskit_nature.second_q.drivers.GaussianLogResult`

Furthermore, the two components from qiskit_nature.drivers were moved like so:

Legacy component	New location
Molecule	`qiskit_nature.second_q.formats.molecule_info.MoleculeInfo`
UnitsType	`qiskit_nature.units.DistanceUnit`

A few notes are worth adding:

The VibrationalStructureMoleculeDriver was removed because we are steering towards a future with tighter, plugin-like integration with classical codes, making the concept of drivers where Qiskit starts a classical simulation outdated. You can still use the .from_molecule(...) methods of the remaining drivers in combination with the MoleculeInfo class.
The MoleculeInfo has become a pure data container and no longer supports degrees of freedom.

Vibrational Structure Drivers#

Vibrational structure drivers work slightly differently than their electronic structure counterparts, because you must supply a basis upon running the driver, which maps the real-space Watson hamiltonian into second-quantized space. This was treated inconsistently in Qiskit Nature v0.4 as explained below.

Previously#

In Qiskit Nature v0.4 the stack implementation was actually inconsistent because the VibrationalIntegrals (which were part of the second_quantization stack) were actually storing the coefficients of the real-space Watson hamiltonian. Only later would these get mapped to a specified basis:

from qiskit_nature.drivers.second_quantization import GaussianLogResult
from qiskit_nature.properties.second_quantization.vibrational.bases import HarmonicBasis
from qiskit_nature.settings import settings

settings.dict_aux_operators = True

log_result = GaussianLogResult("aux_files/CO2_freq_B3LYP_631g.log")

hamiltonian = log_result.get_vibrational_energy()
print(hamiltonian)

hamiltonian.basis = HarmonicBasis([2, 2, 3, 4])
op = hamiltonian.second_q_ops()["VibrationalEnergy"]
print("\n".join(str(op).splitlines()[:10] + ["..."]))

VibrationalEnergy:
    None
    1-Body Terms:
            <sparse integral list with 13 entries>
            (2, 2) = 352.3005875
            (-2, -2) = -352.3005875
            (1, 1) = 631.6153975
            (-1, -1) = -631.6153975
            (4, 4) = 115.653915
            ... skipping 8 entries
    2-Body Terms:
            <sparse integral list with 11 entries>
            (1, 1, 2) = -88.2017421687633
            (4, 4, 2) = 42.675273102831454
            (3, 3, 2) = 42.675273102831454
            (1, 1, 2, 2) = 4.9425425
            (4, 4, 2, 2) = -4.194299375
            ... skipping 6 entries
    3-Body Terms:
            <sparse integral list with 0 entries>
  NIIIIIIIIII * (1268.0676746875001+0j)
+ INIIIIIIIII * (3813.8767834375008+0j)
+ IINIIIIIIII * (705.8633818750001+0j)
+ II+-IIIIIII * (-46.025705898886045+0j)
+ II-+IIIIIII * (-46.025705898886045+0j)
+ IIINIIIIIII * (2120.1145593750007+0j)
+ IIIINIIIIII * (238.31540750000005+0j)
+ IIII+I-IIII * (19.820422279761104+0j)
+ IIIIINIIIII * (728.9613775000003+0j)
+ IIII-I+IIII * (19.820422279761104+0j)
...

New#

As of Qiskit Nature v0.5 the design is now consistently separating the treatment of the real-space Watson hamiltonian from the second-quantized coefficients. This is achieved by introducing a dedicated dataclass storing a WatsonHamiltonian:

from qiskit_nature.second_q.drivers import GaussianLogResult
from qiskit_nature.second_q.formats import watson_to_problem
from qiskit_nature.second_q.problems import HarmonicBasis

log_result = GaussianLogResult("aux_files/CO2_freq_B3LYP_631g.log")

watson = log_result.get_watson_hamiltonian()
print(watson)

basis = HarmonicBasis(num_modals=[2, 2, 3, 4])

problem = watson_to_problem(watson, basis)

hamiltonian = problem.hamiltonian.second_q_op()
print("\n".join(str(hamiltonian).splitlines()[:10] + ["..."]))

WatsonHamiltonian(quadratic_force_constants=<COO: shape=(4, 4), dtype=float64, nnz=4, fill_value=0.0>, cubic_force_constants=<COO: shape=(4, 4, 4), dtype=float64, nnz=4, fill_value=0.0>, quartic_force_constants=<COO: shape=(4, 4, 4, 4), dtype=float64, nnz=12, fill_value=0.0>, kinetic_coefficients=<COO: shape=(4, 4), dtype=float64, nnz=4, fill_value=-0.0>)
Vibrational Operator
number modes=4, number modals=[2, 2, 3, 4], number terms=177
  (1268.0676746875001+0j) * ( +_0_0 -_0_0 )
+ (3813.8767834375008+0j) * ( +_0_1 -_0_1 )
+ (705.8633818750002+0j) * ( +_1_0 -_1_0 )
+ (-46.025705898886045+0j) * ( +_1_0 -_1_1 )
+ (-46.025705898886045+0j) * ( +_1_1 -_1_0 )
+ (2120.1145593750007+0j) * ( +_1_1 -_1_1 )
+ (238.31540750000005+0j) * ( +_2_0 -_2_0 )
+ (19.82042227976109+0j) * ( +_2_0 -_2_2 )
...

The `VibrationalStructureProblem` (`qiskit_nature.problems`)#

This section details all the changes around the VibrationalStructureProblem.

The table below summarizes the vibrational components of the new qiskit_nature.second_q.problems module, and shows from where these parts originated in the old code:

New component	Legacy location
`BaseProblem`	`qiskit_nature.problems.second_quantization.BaseProblem`
`EigenstateResult`	`qiskit_nature.results.EigenstateResult`
`PropertiesContainer`	similar to `qiskit_nature.properties.GroupedProperty`
`VibrationalBasis`	`qiskit_nature.properties.second_quantization.vibrational.bases.VibrationalBasis`
`HarmonicBasis`	`qiskit_nature.properties.second_quantization.vibrational.bases.HarmonicBasis`
`VibrationalStructureProblem`	`qiskit_nature.problems.second_quantization.vibrational.VibrationalStructureProblem`
`VibrationalPropertiesContainer`	did not exist yet
`VibrationalStructureResult`	`qiskit_nature.results.VibrationalStructureResult`

Previously#

from qiskit_nature.drivers.second_quantization import GaussianForcesDriver
from qiskit_nature.problems.second_quantization import VibrationalStructureProblem

driver = GaussianForcesDriver(logfile="aux_files/CO2_freq_B3LYP_631g.log")

problem = VibrationalStructureProblem(driver, num_modals=[2, 2, 3, 4], truncation_order=2)

# we trigger driver.run() implicitly like so:
second_q_ops = problem.second_q_ops()

hamiltonian_op = second_q_ops.pop("VibrationalEnergy")
aux_ops = second_q_ops

New#

from qiskit_nature.second_q.drivers import GaussianForcesDriver
from qiskit_nature.second_q.problems import HarmonicBasis

driver = GaussianForcesDriver(logfile="aux_files/CO2_freq_B3LYP_631g.log")
basis = HarmonicBasis(num_modals=[2, 2, 3, 4])

problem = driver.run(basis=basis)
problem.hamiltonian.truncation_order = 2

hamiltonian_op, aux_ops = problem.second_q_ops()

For more information on the new and improved VibrationalStructureProblem, please refer to the vibrational structure tutorial.

`qiskit_nature.properties`#

The properties module has been refactored and split into multiple locations. In this section, we will only be focusing on its vibrational components.

The following table lists where each component of qiskit_nature.properties has been moved to.

Legacy component	New location
`Property`	`qiskit_nature.second_q.properties.SparseLabelOpsFactory`
`GroupedProperty`	succeeded by `qiskit_nature.second_q.problems.PropertiesContainer`
`second_quantization.DriverMetadata`	removed
`second_quantization.vibrational.VibrationalEnergy`	`qiskit_nature.second_q.hamiltonians.VibrationalEnergy`
`second_quantization.vibrational.OccupiedModals`	`qiskit_nature.second_q.properties.OccupiedModals`
`second_quantization.vibrational.bases.VibrationalBasis`	`qiskit_nature.second_q.problems.VibrationalBasis`
`second_quantization.vibrational.bases.HarmonicBasis`	`qiskit_nature.second_q.problems.HarmonicBasis`
`second_quantization.vibrational.integrals.VibrationalIntegrals`	succeeded by `qiskit_nature.second_q.operators.VibrationalIntegrals`

We suggest that you look at the vibrational structure tutorial for more in-depth explanations, but we will leave a few comments here:

the VibrationalBasis is now only tracked on the VibrationalStructureProblem and not for each operator individually
the VibrationalEnergy (which has always been a_special_ Property) is in the new second_q.hamiltonians module to highlight this special role

Vibrational Structure Problems with v0.5#

Further resources#

TL;DR#

Previously#

New#

qiskit_nature.drivers#

Vibrational Structure Drivers#

Previously#

New#

The VibrationalStructureProblem (qiskit_nature.problems)#

Previously#

New#

qiskit_nature.properties#

`qiskit_nature.drivers`#

The `VibrationalStructureProblem` (`qiskit_nature.problems`)#

`qiskit_nature.properties`#