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Update docs for new Chemistry functionality (#1359)
* Update docs for new chemistry content * Delete blank lines * fix lint and spell Co-authored-by: Manoel Marques <Manoel.Marques@ibm.com>
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‎.pylintdict

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ancilla
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ancillae
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ancillas
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ang
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anharmonic
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annealers
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ansatz
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plesset
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pmatrix
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pooya
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Popovas
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postoracle
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powell
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pre
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prepend
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prepending
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preprint
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Preprocesses
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preprocessing
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priori
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probs
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seeley
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sergey
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setia
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setted
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sgn
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shanno
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shor

‎docs/apidocs/qiskit.chemistry.algorithms.pes_samplers.rst

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.. _qiskit-chemistry-algorithms-pes_samplers:
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.. automodule:: qiskit.chemistry.algorithms.pes_samplers
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:no-members:
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:no-inherited-members:
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:no-special-members:

‎docs/apidocs/qiskit.chemistry.results.rst

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.. _qiskit-chemistry-results:
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.. automodule:: qiskit.chemistry.results
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:no-members:
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:no-inherited-members:
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:no-special-members:

‎docs/apidocs/qiskit.chemistry.transformations.rst

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.. _qiskit-chemistry-transformations:
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.. automodule:: qiskit.chemistry.transformations
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:no-members:
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:no-inherited-members:
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:no-special-members:

‎qiskit/chemistry/__init__.py

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.. autosummary::
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:toctree:
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applications
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algorithms
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applications
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components
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core
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drivers
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results
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transformations
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"""
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‎qiskit/chemistry/algorithms/__init__.py

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++++++++++++
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Algorithms that can find the eigenvalues of an operator, i.e. excited states for chemistry.
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**DEPRECATED** See the Excited States Solvers section below
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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QEomVQE
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QEomEE
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Excited State Solvers
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+++++++++++++++++++++
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Algorithms that can find the eigenvalues of an operator, i.e. excited states for chemistry.
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The interface for such solvers,
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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ExcitedStatesSolver
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the solvers themselves
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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ExcitedStatesEigensolver
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QEOM
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and factories to provision Quantum and/or Classical algorithms upon which the above solvers may
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depend
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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EigensolverFactory
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NumPyEigensolverFactory
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Ground State Solvers
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++++++++++++++++++++
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Algorithms that can find the minimum eigenvalue of an operator, i.e. ground state for chemistry.
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The interface for such solvers,
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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GroundStateSolver
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the solvers themselves
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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AdaptVQE
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GroundStateEigensolver
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OrbitalOptimizationVQE
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and factories to provision Quantum and/or Classical algorithms upon which the above solvers may
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depend
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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MinimumEigensolverFactory
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NumPyMinimumEigensolverFactory
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VQEUCCSDFactory
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VQEUVCCSDFactory
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Minimum Eigensolvers
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++++++++++++++++++++
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Algorithms that can find the minimum eigenvalue of an operator, i.e. ground state for chemistry.
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**DEPRECATED** See the Ground State Solvers section above
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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VQEAdapt
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Potential Energy Surface Samplers
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+++++++++++++++++++++++++++++++++
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Algorithms that can compute potential energy surfaces.
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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BOPESSampler
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The samplers include extrapolators to facilitate convergence across a set of points and support
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of various potentials. More detail may be found in the sub-module linked below
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.. autosummary::
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:toctree:
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pes_samplers
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"""
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from .eigen_solvers import QEomVQE, QEomEE
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from .minimum_eigen_solvers import VQEAdapt, VQEAdaptResult
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from .excited_states_solvers import (ExcitedStatesEigensolver, ExcitedStatesSolver, QEOM,
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EigensolverFactory, NumPyEigensolverFactory)
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from .ground_state_solvers import (AdaptVQE, GroundStateEigensolver, GroundStateSolver,
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OrbitalOptimizationVQE, MinimumEigensolverFactory,
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NumPyMinimumEigensolverFactory, VQEUCCSDFactory,
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VQEUVCCSDFactory)
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from .pes_samplers import BOPESSampler
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__all__ = [
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'QEomVQE',
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'QEomEE',
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'VQEAdapt',
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'VQEAdaptResult',
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'ExcitedStatesEigensolver',
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'ExcitedStatesSolver',
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'QEOM',
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'EigensolverFactory',
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'NumPyEigensolverFactory',
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'AdaptVQE',
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'GroundStateEigensolver',
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'GroundStateSolver',
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'OrbitalOptimizationVQE',
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'MinimumEigensolverFactory',
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'NumPyMinimumEigensolverFactory',
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'VQEUCCSDFactory',
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'VQEUVCCSDFactory',
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'BOPESSampler',
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]

‎qiskit/chemistry/algorithms/excited_states_solvers/eigensolver_factories/__init__.py

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"""Factories that create an eigensolver based on a qubit transformation."""
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from .eigensolver_factory import EigensolverFactory
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from .numpy_eigensolver_factory import NumPyEigensolverFactory
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‎qiskit/chemistry/algorithms/excited_states_solvers/excited_states_solver.py

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aux_operators: Optional[Union[List[FermionicOperator],
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"""Compute the excited states energies of the molecule that was supplied via the driver.
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r"""Compute the excited states energies of the molecule that was supplied via the driver.
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driver: a chemistry driver object which defines the chemical problem that is to be
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solved by this calculation.
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solved by this calculation.
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aux_operators: Additional auxiliary operators to evaluate. Must be of type
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``FermionicOperator`` if the qubit transformation is fermionic and of type
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``BosonicOperator`` it is bosonic.
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an eigenstate result
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"""

‎qiskit/chemistry/algorithms/ground_state_solvers/adapt_vqe.py

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solver: a factory for the VQE solver employing a UCCSD variational form.
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threshold: the energy convergence threshold. It has a minimum value of 1e-15.
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delta: the finite difference step size for the gradient computation. It has a minimum
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value of 1e-5.
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max_iterations: the maximum number of iterations of the AdaptVQE algorithm.
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"""
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aux_operators: Additional auxiliary ``FermionicOperator``s to evaluate at the
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aux_operators: Additional auxiliary ``FermionicOperator`` instances to evaluate at the
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ground state.
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Raises:
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AquaError: if a solver other than VQE or a variational form other than UCCSD is provided
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or if the algorithm finishes due to an unforeseen reason.
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AquaError: if a solver other than VQE or a variational form other than UCCSD is
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provided or if the algorithm finishes due to an unforeseen reason.
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An AdaptVQEResult which is an ElectronicStructureResult but also includes runtime

‎qiskit/chemistry/algorithms/pes_samplers/__init__.py

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# copyright notice, and modified files need to carry a notice indicating
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# that they have been altered from the originals.
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"""Potential energy surface samplers"""
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"""
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Potential energy surface samplers (:mod:`qiskit.chemistry.algorithms.pes_samplers`)
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===================================================================================
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Potential energy surface samplers.
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.. currentmodule:: qiskit.chemistry.algorithms.pes_samplers
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Algorithms that can compute potential energy surfaces.
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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BOPESSampler
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When used with variational solvers, such as VQE, when computing a set of points there is support
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for extrapolation from prior solution(s) to bootstrap the algorithm with a better starting point
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to facilitate convergence. Extrapolators are:
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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Extrapolator
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DifferentialExtrapolator
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PCAExtrapolator
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PolynomialExtrapolator
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SieveExtrapolator
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WindowExtrapolator
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There is also a set of support function for potentials:
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.. autosummary::
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:toctree: ../stubs/
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:nosignatures:
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EnergySurface1DSpline
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HarmonicPotential
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MorsePotential
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EnergySurfaceBase
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PotentialBase
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VibronicStructureBase
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"""
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from .bopes_sampler import BOPESSampler
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from .extrapolator import (Extrapolator, DifferentialExtrapolator, PCAExtrapolator,
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PolynomialExtrapolator, SieveExtrapolator, WindowExtrapolator)
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from .potentials import (EnergySurface1DSpline, HarmonicPotential, MorsePotential,
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EnergySurfaceBase, PotentialBase, VibronicStructureBase)
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__all__ = ['BOPESSampler'
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]
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__all__ = [
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'BOPESSampler',
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'Extrapolator',
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'DifferentialExtrapolator',
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'PCAExtrapolator',
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'PolynomialExtrapolator',
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'SieveExtrapolator',
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'WindowExtrapolator',
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'EnergySurface1DSpline',
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'HarmonicPotential',
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'MorsePotential',
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'EnergySurfaceBase',
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'PotentialBase',
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'VibronicStructureBase',
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]

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