QCSchema (`qiskit_nature.second_q.formats.qcschema`)¶

The documentation of this schema can be found [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

In our Python implementation of this schema, we are handling optional attributes of the schema a bit differently than how they work in a JSON or HDF5 container. Whereas in these latter cases, the attributes might not simply exist at all, in our Python data classes, the attributes will always be available but might simply take the value None. When dumping a Python instance of this schema to either file format, attributes which are None will be filtered, in order to ensure that loading and dumping the same data subsequently, does not change the available attributes.

It should also be noted, that optional attributes will not take “default” values on the schema object. Thus, it is up to the code reading from a schema instance, to handle None i.e. undefined values for a specific variable, for example using in its place a suitable default value instead.

Classes

`QCBasisSet`(center_data, atom_map, name[, ...])	A dataclass to store the information of the basis set used in the original calculation.
`QCCenterData`([electron_shells, ...])	A dataclass to store the information of a single atom/center in the basis set.
`QCECPPotential`(ecp_type, angular_momentum, ...)	A dataclass to store the information of an ECP in a basis set.
`QCElectronShell`(angular_momentum, ...)	A dataclass to store the information of a single electron shell in a basis set.
`QCError`(error_type, error_message)	A dataclass to store the failure information contained in a QCSchema.
`QCModel`(method, basis)	A dataclass to store the mathematical model information used in the original calculation.
`QCProperties`([calcinfo_nbasis, ...])	A dataclass to store the computed properties of the original calculation.
`QCProvenance`(creator, version, routine)	A dataclass to store the program information that generated the QCSchema file.
`QCSchema`(schema_name, schema_version, ...[, ...])	The full QCSchema as a dataclass.
`QCSchemaInput`(schema_name, schema_version, ...)	A dataclass containing all classical input components of the QCSchema.
`QCTopology`(symbols, geometry, schema_name, ...)	A dataclass to store the topological information of the physical system.
`QCWavefunction`(basis[, overlap, orbitals_a, ...])	A dataclass to store any additional computed wavefunction properties.

class QCBasisSet(center_data, atom_map, name, schema_version=None, schema_name=None, description=None)[source]¶

A dataclass to store the information of the basis set used in the original calculation.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/auto_basis.html#basis-set-schema).

atom_map: Sequence[str]¶: The list of atomic kinds, indicating the keys used to store the basis in center_data.

center_data: Mapping[str, QCCenterData]¶: A dictionary mapping the keys provided by atom_map to their basis center data.

description: str | None = None¶: A description of this basis set.

classmethod from_dict(data)[source]¶

Constructs a schema object from a dictionary of data.

The dictionary provided to this method corresponds to the format as obtained by json.load from a JSON representation of the schema object according to the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: QCBasisSet

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

While the QCSchema is officially tailored to support JSON, HDF5 is supported as a more high-performance alternative and considered the standard within Qiskit Nature. Due to its similarities with JSON a 1-to-1 correspondence can be made between the two.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

name: str¶: The name of the basis set.

schema_name: str | None = None¶: The name of this schema. This value is expected to be qcschema_basis.

schema_version: int | None = None¶: The version of this specific schema.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)[source]¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCCenterData(electron_shells=None, ecp_electrons=None, ecp_potentials=None)[source]¶

A dataclass to store the information of a single atom/center in the basis set.

For more information refer to [here](https://github.com/MolSSI/QCSchema/blob/1d5ff3baa5/qcschema/dev/definitions.py#L146).

ecp_electrons: int | None = None¶: The number of electrons replaced by an ECP.

ecp_potentials: Sequence[QCECPPotential] | None = None¶: The list of effective core potentials for this element.

electron_shells: Sequence[QCElectronShell] | None = None¶: The list of electronic shells for this element.

classmethod from_dict(data)[source]¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: QCCenterData

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)[source]¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCECPPotential(ecp_type, angular_momentum, r_exponents, gaussian_exponents, coefficients)[source]¶

A dataclass to store the information of an ECP in a basis set.

For more information refer to [here](https://github.com/MolSSI/QCSchema/blob/1d5ff3baa5/qcschema/dev/definitions.py#L90).

angular_momentum: Sequence[int]¶: The angular momenta of this potential as a list of integers.

coefficients: Sequence[Sequence[float | str]]¶: The general contraction coefficients of this potential. The official spec stores these values as strings.

ecp_type: str¶: The type of this potential.

classmethod from_dict(data)¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

gaussian_exponents: Sequence[float | str]¶: The exponents of the gaussian terms. The official spec stores these values as strings.

r_exponents: Sequence[int]¶: The exponents of the r term.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)[source]¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCElectronShell(angular_momentum, harmonic_type, exponents, coefficients)[source]¶

A dataclass to store the information of a single electron shell in a basis set.

For more information refer to [here](https://github.com/MolSSI/QCSchema/blob/1d5ff3baa5/qcschema/dev/definitions.py#L43).

angular_momentum: Sequence[int]¶: The angular momenta of this electron shell as a list of integers.

coefficients: Sequence[Sequence[float | str]]¶: The general contraction coefficients of this contracted shell. The official spec stores these values as strings.

exponents: Sequence[float | str]¶: The exponents of this contracted shell. The official spec stores these values as strings.

classmethod from_dict(data)¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

harmonic_type: str¶: The type of this shell.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)[source]¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCError(error_type, error_message)[source]¶

A dataclass to store the failure information contained in a QCSchema.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/spec_components.html#success).

error_message: str¶: A description of the error that was raised.

error_type: str¶: The type of error that was raised.

classmethod from_dict(data)¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCModel(method, basis)[source]¶

A dataclass to store the mathematical model information used in the original calculation.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/spec_components.html#model).

basis: str | QCBasisSet¶: The basis set used during the computation. This can be either a simple string or a full QCBasisSet specification.

classmethod from_dict(data)[source]¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: QCModel

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

method: str¶: The method used for the computation of this object.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)[source]¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCProperties(calcinfo_nbasis=None, calcinfo_nmo=None, calcinfo_nalpha=None, calcinfo_nbeta=None, calcinfo_natom=None, return_energy=None, scf_one_electron_energy=None, scf_two_electron_energy=None, nuclear_repulsion_energy=None, nuclear_dipole_moment=None, scf_vv10_energy=None, scf_xc_energy=None, scf_dispersion_correction_energy=None, scf_dipole_moment=None, scf_total_energy=None, scf_iterations=None, mp2_same_spin_correlation_energy=None, mp2_opposite_spin_correlation_energy=None, mp2_singles_energy=None, mp2_doubles_energy=None, mp2_correlation_energy=None, mp2_total_energy=None, mp2_dipole_moment=None, ccsd_same_spin_correlation_energy=None, ccsd_opposite_spin_correlation_energy=None, ccsd_singles_energy=None, ccsd_doubles_energy=None, ccsd_correlation_energy=None, ccsd_total_energy=None, ccsd_prt_pr_correlation_energy=None, ccsd_prt_pr_total_energy=None, ccsdt_correlation_energy=None, ccsdt_total_energy=None, ccsdtq_correlation_energy=None, ccsdtq_total_energy=None, ccsd_dipole_moment=None, ccsd_prt_pr_dipole_moment=None, ccsdt_dipole_moment=None, ccsdtq_dipole_moment=None, ccsd_iterations=None, ccsdt_iterations=None, ccsdtq_iterations=None)[source]¶

A dataclass to store the computed properties of the original calculation.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/auto_props.html#properties-schema).

calcinfo_nalpha: int | None = None¶: The number of alpha-spin electrons in the computation.

calcinfo_natom: int | None = None¶: The number of atoms in the computation.

calcinfo_nbasis: int | None = None¶: The number of basis functions in the computation.

calcinfo_nbeta: int | None = None¶: The number of beta-spin electrons in the computation.

calcinfo_nmo: int | None = None¶: The number of molecular orbitals in the computation.

ccsd_correlation_energy: float | None = None¶: The total CCSD correlation energy.

ccsd_dipole_moment: tuple[float, float, float] | None = None¶: The total CCSD X, Y, and Z dipole components.

ccsd_doubles_energy: float | None = None¶: The total CCSD doubles correlation energy.

ccsd_iterations: int | None = None¶: The number of CCSD iterations taken during the computation.

ccsd_opposite_spin_correlation_energy: float | None = None¶: The CCSD doubles correlation energy contribution from opposite-spin (e.g. singlet) correlations, without any user scaling.

ccsd_prt_pr_correlation_energy: float | None = None¶: The total CCSD(T) correlation energy.

ccsd_prt_pr_dipole_moment: tuple[float, float, float] | None = None¶: The total CCSD(T) X, Y, and Z dipole components.

ccsd_prt_pr_total_energy: float | None = None¶: The total CCSD(T) energy (i.e. the sum of the SCF energy and CCSD(T) correlation energy).

ccsd_same_spin_correlation_energy: float | None = None¶: The CCSD doubles correlation energy contribution from same-spin (e.g. triplet) correlations, without any user scaling.

ccsd_singles_energy: float | None = None¶: The CCSD singles correlation energy. This value is 0.0 except in ROHF.

ccsd_total_energy: float | None = None¶: The total CCSD energy (i.e. the sum of the SCF energy and CCSD correlation energy).

ccsdt_correlation_energy: float | None = None¶: The total CCSDT correlation energy.

ccsdt_dipole_moment: tuple[float, float, float] | None = None¶: The total CCSDT X, Y, and Z dipole components.

ccsdt_iterations: int | None = None¶: The number of CCSDT iterations taken during the computation.

ccsdt_total_energy: float | None = None¶: The total CCSDT energy (i.e. the sum of the SCF energy and CCSDT correlation energy).

ccsdtq_correlation_energy: float | None = None¶: The total CCSDTQ correlation energy.

ccsdtq_dipole_moment: tuple[float, float, float] | None = None¶: The total CCSDTQ X, Y, and Z dipole components.

ccsdtq_iterations: int | None = None¶: The number of CCSDTQ iterations taken during the computation.

ccsdtq_total_energy: float | None = None¶: The total CCSDTQ energy (i.e. the sum of the SCF energy and CCSDTQ correlation energy).

classmethod from_dict(data)¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

mp2_correlation_energy: float | None = None¶: The total MP2 correlation energy.

mp2_dipole_moment: tuple[float, float, float] | None = None¶: The total MP2 X, Y, and Z dipole components.

mp2_doubles_energy: float | None = None¶: The total MP2 doubles correlation energy.

mp2_opposite_spin_correlation_energy: float | None = None¶: The MP2 doubles correlation energy contribution from opposite-spin (e.g. singlet) correlations, without any user scaling.

mp2_same_spin_correlation_energy: float | None = None¶: The MP2 doubles correlation energy contribution from same-spin (e.g. triplet) correlations, without any user scaling.

mp2_singles_energy: float | None = None¶: The MP2 singles correlation energy. This value is 0.0 except in ROHF.

mp2_total_energy: float | None = None¶: The total MP2 energy (i.e. the sum of the SCF energy and MP2 correlation energy).

nuclear_dipole_moment: tuple[float, float, float] | None = None¶: The nuclear X, Y, and Z dipole components.

nuclear_repulsion_energy: float | None = None¶: The nuclear repulsion energy contribution to the total SCF energy.

return_energy: float | None = None¶: The returned energy of the computation. When QCSchemaInput.driver is energy, this value is identical to QCSchema.return_result.

scf_dipole_moment: tuple[float, float, float] | None = None¶: The total SCF X, Y, and Z dipole components.

scf_dispersion_correction_energy: float | None = None¶: The dispersion correction appended to the underlying functional in a DFT-D method.

scf_iterations: int | None = None¶: The number of SCF iterations taken during the computation.

scf_one_electron_energy: float | None = None¶: The one-electron energy contribution to the total SCF energy.

scf_total_energy: float | None = None¶: The total SCF energy.

scf_two_electron_energy: float | None = None¶: The two-electron energy contribution to the total SCF energy.

scf_vv10_energy: float | None = None¶: The VV10 functional energy contribution to the total SCF energy.

scf_xc_energy: float | None = None¶: The XC functional energy contribution to the total SCF energy.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCProvenance(creator, version, routine)[source]¶

A dataclass to store the program information that generated the QCSchema file.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/spec_components.html#provenance).

creator: str¶: The name of the creator of this object.

classmethod from_dict(data)¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

routine: str¶: The routine that was used to create this object.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

version: str¶: The version of the creator of this object.

class QCSchema(schema_name, schema_version, molecule, driver, model, keywords, provenance, return_result, success, properties, error=None, wavefunction=None)[source]¶

The full QCSchema as a dataclass.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/spec_components.html#output-components).

driver: str¶: The type of computation. Example values are energy, gradient, and hessian.

error: QCError | None = None¶: An instance of QCError if the computation was not successful (success = False).

classmethod from_dict(data)[source]¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: QCSchema

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

keywords: Mapping[str, Any]¶: Any additional program-specific parameters.

model: QCModel¶: An instance of QCModel.

molecule: QCTopology¶: An instance of QCTopology.

properties: QCProperties¶: An instance of QCProperties.

provenance: QCProvenance¶: An instance of QCProvenance.

return_result: float | Sequence[float]¶: The primary result of the computation. Its value depends on the type of computation (see also driver).

schema_name: str¶: The name of this schema. This value is expected to be qcschema or qc_schema.

schema_version: int¶: The version of this specific schema.

success: bool¶: Whether the computation was successful.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)[source]¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

wavefunction: QCWavefunction | None = None¶: An instance of QCWavefunction.

class QCSchemaInput(schema_name, schema_version, molecule, driver, model, keywords)[source]¶

A dataclass containing all classical input components of the QCSchema.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/spec_components.html#input-components).

driver: str¶: The type of computation. Example values are energy, gradient, and hessian.

classmethod from_dict(data)[source]¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: QCSchemaInput

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

keywords: Mapping[str, Any]¶: Any additional program-specific parameters.

model: QCModel¶: An instance of QCModel.

molecule: QCTopology¶: An instance of QCTopology.

schema_name: str¶: The name of this schema. This value is expected to be qcschema or qc_schema.

schema_version: int¶: The version of this specific schema.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)[source]¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCTopology(symbols, geometry, schema_name, schema_version, molecular_charge=None, molecular_multiplicity=None, fix_com=None, real=None, connectivity=None, fix_orientation=None, atom_labels=None, fragment_multiplicities=None, fix_symmetry=None, fragment_charges=None, mass_numbers=None, name=None, masses=None, comment=None, provenance=None, fragments=None, atomic_numbers=None)[source]¶

A dataclass to store the topological information of the physical system.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/spec_components.html#topology).

atom_labels: Sequence[str] | None = None¶: A list of user-provided information for each atom. Its length must match that of the symbols list.

atomic_numbers: Sequence[int] | None = None¶: The atomic numbers of all atoms, indicating their nuclear charge. Its length must match that of the symbols list.

comment: str | None = None¶: Any additional (user-provided) comment.

connectivity: Sequence[tuple[int, int, int]] | None = None¶: A list indicating the bonds between the atoms in the molecule. Each item of this list must be a tuple of three integers, indicating the first atom index in the bond, the second atom index, and finally the order of the bond.

fix_com: bool | None = None¶: Whether translation of the geometry is allowed (False) or not (True).

fix_orientation: bool | None = None¶: Whether rotation of the geometry is allowed (False) or not (True).

fix_symmetry: str | None = None¶: The maximal point group symmetry at which the geometry should be treated.

fragment_charges: Sequence[float] | None = None¶: The list of charges associated with each fragment.

fragment_multiplicities: Sequence[int] | None = None¶: The list of multiplicities associated with each fragment.

fragments: Sequence[tuple[int, ...]] | None = None¶: The list of fragments. Each item of this list must be a tuple of integers with variable length (greater than 1). The first number indicates the fragment index, all following numbers refer to the (0-indexed) atom indices that constitute this fragment.

classmethod from_dict(data)[source]¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: QCTopology

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

geometry: Sequence[float]¶: The XYZ coordinates (in Bohr units) of the atoms. This is a flat list of three times the length of the symbols list.

mass_numbers: Sequence[int] | None = None¶: The mass numbers of all atoms. If it is an unknown isotope, the value should be -1. Its length must match that of the symbols list.

masses: Sequence[float] | None = None¶: The masses (in atomic units) of all atoms. Canonical weights are assumed if this is not given explicitly.

molecular_charge: int | None = None¶: The overall charge of the molecule.

molecular_multiplicity: int | None = None¶: The overall multiplicity of the molecule.

name: str | None = None¶: The (user-given) name of the molecule.

provenance: QCProvenance | None = None¶: An instance of QCProvenance.

real: Sequence[bool] | None = None¶: A list indicating whether each atom is real (True) or a ghost (False). Its length must match that of the symbols list.

schema_name: str¶: The name of this schema. This value is expected to be qcschema_molecule.

schema_version: int¶: The version of this specific schema.

symbols: Sequence[str]¶: The list of atom symbols in this topology.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

class QCWavefunction(basis, overlap=None, orbitals_a=None, orbitals_b=None, density_a=None, density_b=None, density_mo_a=None, density_mo_b=None, fock_a=None, fock_b=None, fock_mo_a=None, fock_mo_b=None, eigenvalues_a=None, eigenvalues_b=None, occupations_a=None, occupations_b=None, eri=None, eri_mo_aa=None, eri_mo_ab=None, eri_mo_ba=None, eri_mo_bb=None, dipole_x=None, dipole_y=None, dipole_z=None, dipole_mo_x_a=None, dipole_mo_y_a=None, dipole_mo_z_a=None, dipole_mo_x_b=None, dipole_mo_y_b=None, dipole_mo_z_b=None, scf_overlap=None, scf_orbitals_a=None, scf_orbitals_b=None, scf_density_a=None, scf_density_b=None, scf_density_mo_a=None, scf_density_mo_b=None, scf_fock_a=None, scf_fock_b=None, scf_fock_mo_a=None, scf_fock_mo_b=None, scf_coulomb_a=None, scf_coulomb_b=None, scf_exchange_a=None, scf_exchange_b=None, scf_eigenvalues_a=None, scf_eigenvalues_b=None, scf_occupations_a=None, scf_occupations_b=None, scf_eri=None, scf_eri_mo_aa=None, scf_eri_mo_ab=None, scf_eri_mo_ba=None, scf_eri_mo_bb=None, scf_dipole_x=None, scf_dipole_y=None, scf_dipole_z=None, scf_dipole_mo_x_a=None, scf_dipole_mo_y_a=None, scf_dipole_mo_z_a=None, scf_dipole_mo_x_b=None, scf_dipole_mo_y_b=None, scf_dipole_mo_z_b=None, localized_orbitals_a=None, localized_orbitals_b=None, localized_fock_a=None, localized_fock_b=None, h_core_a=None, h_core_b=None, h_effective_a=None, h_effective_b=None, restricted=None)[source]¶

A dataclass to store any additional computed wavefunction properties.

Matrix quantities are stored as flat, column-major arrays.

For more information refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/auto_wf.html#wavefunction-schema).

basis: str | QCBasisSet¶

The basis set used during the computation. This can be either a simple string or a full QCBasisSet specification.

Note: This deviates slightly from the official QCSchema spec, where a QCBasisSet instance is required. However, since this is data not relevant in the routines of Qiskit Nature, we are a bit more lenient here, in order to enable a migration path from legacy HDF5 files generated by Qiskit Nature.

density_a: str | None = None¶: The name of the alpha-spin density in the AO basis.

density_b: str | None = None¶: The name of the beta-spin density in the AO basis.

density_mo_a: str | None = None¶: The name of the alpha-spin density in the MO basis.

density_mo_b: str | None = None¶: The name of the beta-spin density in the MO basis.

dipole_mo_x_a: str | None = None¶: The name of alpha-spin x-axis dipole moment integrals in the MO basis.

dipole_mo_x_b: str | None = None¶: The name of beta-spin x-axis dipole moment integrals in the MO basis.

dipole_mo_y_a: str | None = None¶: The name of alpha-spin y-axis dipole moment integrals in the MO basis.

dipole_mo_y_b: str | None = None¶: The name of beta-spin y-axis dipole moment integrals in the MO basis.

dipole_mo_z_a: str | None = None¶: The name of alpha-spin z-axis dipole moment integrals in the MO basis.

dipole_mo_z_b: str | None = None¶: The name of beta-spin z-axis dipole moment integrals in the MO basis.

dipole_x: str | None = None¶: The name of x-axis dipole moment integrals in the AO basis.

dipole_y: str | None = None¶: The name of y-axis dipole moment integrals in the AO basis.

dipole_z: str | None = None¶: The name of z-axis dipole moment integrals in the AO basis.

eigenvalues_a: str | None = None¶: The name of the alpha-spin orbital eigenvalues.

eigenvalues_b: str | None = None¶: The name of the beta-spin orbital eigenvalues.

eri: str | None = None¶: The name of the electron-repulsion integrals in the AO basis.

eri_mo_aa: str | None = None¶: The name of the alpha-alpha electron-repulsion integrals in the MO basis.

eri_mo_ab: str | None = None¶: The name of the alpha-beta electron-repulsion integrals in the MO basis.

eri_mo_ba: str | None = None¶: The name of the beta-alpha electron-repulsion integrals in the MO basis.

eri_mo_bb: str | None = None¶: The name of the beta-beta electron-repulsion integrals in the MO basis.

fock_a: str | None = None¶: The name of the alpha-spin Fock matrix in the AO basis.

fock_b: str | None = None¶: The name of the beta-spin Fock matrix in the AO basis.

fock_mo_a: str | None = None¶: The name of the alpha-spin Fock matrix in the MO basis.

fock_mo_b: str | None = None¶: The name of the beta-spin Fock matrix in the MO basis.

classmethod from_dict(data)[source]¶

Constructs a schema object from a dictionary of data.

Parameters:: data (dict[str, Any]) – the data dictionary.
Returns:: An instance of the schema object.
Return type:: QCWavefunction

classmethod from_hdf5(h5py_data)¶

Constructs a schema object from an HDF5 object.

For more details refer to [here](https://molssi-qc-schema.readthedocs.io/en/latest/tech_discussion.html#json-and-hdf5).

Parameters:: h5py_data (str | Path | Group) – can be either the path to a file or an h5py.Group.
Returns:: An instance of the schema object.
Return type:: _QCBase

classmethod from_json(json_data)¶

Constructs a schema object from JSON.

The JSON data must match the latest standard as documented [here](https://molssi-qc-schema.readthedocs.io/en/latest/).

Parameters:: json_data (str | bytes | Path) – can be either the path to a file or the json data directly provided as a str.
Returns:: An instance of the schema object.
Return type:: _QCBase

h_core_a: Sequence[float] | None = None¶: The alpha-spin core (one-electron) Hamiltonian matrix in the AO basis.

h_core_b: Sequence[float] | None = None¶: The beta-spin core (one-electron) Hamiltonian matrix in the AO basis.

h_effective_a: Sequence[float] | None = None¶: The effective alpha-spin core (one-electron) Hamiltonian matrix in the AO basis.

h_effective_b: Sequence[float] | None = None¶: The effective beta-spin core (one-electron) Hamiltonian matrix in the AO basis.

localized_fock_a: Sequence[float] | None = None¶: The alpha-spin Fock matrix in the localized basis. All nmo orbitals are included, even if only a subset were localized.

localized_fock_b: Sequence[float] | None = None¶: The beta-spin Fock matrix in the localized basis. All nmo orbitals are included, even if only a subset were localized.

localized_orbitals_a: Sequence[float] | None = None¶: The localized alpha-spin orbitals. All nmo orbitals are included, even if only a subset were localized.

localized_orbitals_b: Sequence[float] | None = None¶: The localized beta-spin orbitals. All nmo orbitals are included, even if only a subset were localized.

occupations_a: str | None = None¶: The name of the alpha-spin orbital occupations.

occupations_b: str | None = None¶: The name of the beta-spin orbital occupations.

orbitals_a: str | None = None¶: The name of the alpha-spin orbitals in the AO basis.

orbitals_b: str | None = None¶: The name of the beta-spin orbitals in the AO basis.

overlap: str | None = None¶: The name of the overlap matrix in the AO basis.

restricted: bool | None = None¶: Whether the computation used restricted spin orbitals.

scf_coulomb_a: Sequence[float] | None = None¶: The SCF alpha-spin Coulomb matrix in the AO basis.

scf_coulomb_b: Sequence[float] | None = None¶: The SCF beta-spin Coulomb matrix in the AO basis.

scf_density_a: Sequence[float] | None = None¶: The SCF alpha-spin density in the AO basis.

scf_density_b: Sequence[float] | None = None¶: The SCF beta-spin density in the AO basis.

scf_density_mo_a: Sequence[float] | None = None¶: The SCF alpha-spin density in the MO basis.

scf_density_mo_b: Sequence[float] | None = None¶: The SCF beta-spin density in the MO basis.

scf_dipole_mo_x_a: Sequence[float] | None = None¶: The SCF alpha-spin x-axis dipole moment integrals in the MO basis.

scf_dipole_mo_x_b: Sequence[float] | None = None¶: The SCF beta-spin x-axis dipole moment integrals in the MO basis.

scf_dipole_mo_y_a: Sequence[float] | None = None¶: The SCF alpha-spin y-axis dipole moment integrals in the MO basis.

scf_dipole_mo_y_b: Sequence[float] | None = None¶: The SCF beta-spin y-axis dipole moment integrals in the MO basis.

scf_dipole_mo_z_a: Sequence[float] | None = None¶: The SCF alpha-spin z-axis dipole moment integrals in the MO basis.

scf_dipole_mo_z_b: Sequence[float] | None = None¶: The SCF beta-spin z-axis dipole moment integrals in the MO basis.

scf_dipole_x: Sequence[float] | None = None¶: The SCF x-axis dipole moment integrals in the AO basis.

scf_dipole_y: Sequence[float] | None = None¶: The SCF y-axis dipole moment integrals in the AO basis.

scf_dipole_z: Sequence[float] | None = None¶: The SCF z-axis dipole moment integrals in the AO basis.

scf_eigenvalues_a: Sequence[float] | None = None¶: The SCF alpha-spin orbital eigenvalues.

scf_eigenvalues_b: Sequence[float] | None = None¶: The SCF beta-spin orbital eigenvalues.

scf_eri: Sequence[float] | None = None¶: The SCF electron-repulsion integrals in the AO basis.

scf_eri_mo_aa: Sequence[float] | None = None¶: The SCF alpha-alpha electron-repulsion integrals in the MO basis.

scf_eri_mo_ab: Sequence[float] | None = None¶: The SCF alpha-beta electron-repulsion integrals in the MO basis.

scf_eri_mo_ba: Sequence[float] | None = None¶: The SCF beta-alpha electron-repulsion integrals in the MO basis.

scf_eri_mo_bb: Sequence[float] | None = None¶: The SCF beta-beta electron-repulsion integrals in the MO basis.

scf_exchange_a: Sequence[float] | None = None¶: The SCF alpha-spin Exchange matrix in the AO basis.

scf_exchange_b: Sequence[float] | None = None¶: The SCF beta-spin Exchange matrix in the AO basis.

scf_fock_a: Sequence[float] | None = None¶: The SCF alpha-spin Fock matrix in the AO basis.

scf_fock_b: Sequence[float] | None = None¶: The SCF beta-spin Fock matrix in the AO basis.

scf_fock_mo_a: Sequence[float] | None = None¶: The SCF alpha-spin Fock matrix in the MO basis.

scf_fock_mo_b: Sequence[float] | None = None¶: The SCF beta-spin Fock matrix in the MO basis.

scf_occupations_a: Sequence[float] | None = None¶: The SCF alpha-spin orbital occupations.

scf_occupations_b: Sequence[float] | None = None¶: The SCF beta-spin orbital occupations.

scf_orbitals_a: Sequence[float] | None = None¶: The SCF alpha-spin orbitals in the AO basis.

scf_orbitals_b: Sequence[float] | None = None¶: The SCF beta-spin orbitals in the AO basis.

scf_overlap: Sequence[float] | None = None¶: The SCF overlap matrix in the AO basis.

to_dict()¶

Converts the schema object to a dictionary.

Returns:: The dictionary representation of the schema object.
Return type:: dict[str, Any]

to_hdf5(group)[source]¶

Converts the schema object to HDF5.

Parameters:: group (Group) – the h5py group into which to store the object.

to_json()¶

Converts the schema object to JSON.

Returns:: The JSON representation of the schema object.
Return type:: str

QCSchema (qiskit_nature.second_q.formats.qcschema)¶

QCSchema (`qiskit_nature.second_q.formats.qcschema`)¶