qc2.ase

qc2 ASE package.

Submodules

Package Contents

Classes

DIRAC

A general ASE calculator for the relativistic qchem DIRAC code.
class qc2.ase.DIRAC(restart: bool | None = None, ignore_bad_restart_file: bool | None = FileIOCalculator._deprecated, label: str | None = None, atoms: ase.Atoms | None = None, command: str | None = None, **kwargs)[source]

Bases: ase.calculators.calculator.FileIOCalculator, qc2.ase.qc2_ase_base_class.BaseQc2ASECalculator

A general ASE calculator for the relativistic qchem DIRAC code.

Parameters:

  • FileIOCalculator (FileIOCalculator) – Base class for calculators that write/read input/output files.

  • BaseQc2ASECalculator (BaseQc2ASECalculator) – Base class for ase calculartors in qc2.

implemented_properties: List[str] = ['energy']
label: str = 'dirac'
command: str = 'pam --inp=PREFIX.inp --mol=PREFIX.xyz --silent --get="AOMOMAT MRCONEE MDCINT"'
check_dirac_attributes() → None[source]

Checks for any missing and/or mispelling DIRAC input attribute.

Notes

it can also be used to eventually set specific options in the near future.

calculate(*args, **kwargs) → None[source]

Execute DIRAC workflow.

write_input(atoms: ase.Atoms | None = None, properties: List[str] | None = None, system_changes: List[str] | None = None) → None[source]

Generate all necessary inputs for DIRAC.

read_results()[source]

Read energy from DIRAC output file.

save(datafile: h5py.File) → None[source]

Dumps qchem data to a datafile using QCSchema or FCIDump formats.

Parameters:

datafile (Union[h5py.File, str]) – file to save the data to.

Returns:

None

Notes

files are written following the QCSchema or FCIDump formats.

Example

>>> from ase.build import molecule
>>> from qc2.ase import DIRAC
>>>
>>> molecule = molecule('H2')
>>> molecule.calc = DIRAC()  # => RHF/STO-3G
>>> molecule.calc.schema_format = "qcschema"
>>> molecule.calc.get_potential_energy()
>>> molecule.calc.save('h2.h5')
>>>
>>> molecule = molecule('H2')
>>> molecule.calc = DIRAC()  # => RHF/STO-3G
>>> molecule.calc.schema_format = "fcidump"
>>> molecule.calc.get_potential_energy()
>>> molecule.calc.save('h2.fcidump')
load(datafile: h5py.File | str) → qiskit_nature.second_q.formats.qcschema.QCSchema | qiskit_nature.second_q.formats.fcidump.FCIDump[source]

Loads electronic structure data from a datafile.

Parameters:

datafile (Union[h5py.File, str]) – file to read the data from.

Returns:

Instances of QCSchema or FCIDump dataclasses containing qchem data.

Notes

files are read following the qcschema or fcidump formats.

Example

>>> from ase.build import molecule
>>> from qc2.ase import DIRAC
>>>
>>> molecule = molecule('H2')
>>> molecule.calc = DIRAC()     # => RHF/STO-3G
>>> molecule.calc.schema_format = "qcschema"
>>> qcschema = molecule.calc.load('h2.h5')
>>>
>>> molecule = molecule('H2')
>>> molecule.calc = DIRAC()     # => RHF/STO-3G
>>> molecule.calc.schema_format = "fcidump"
>>> fcidump = molecule.calc.load('h2.fcidump')
get_integrals_mo_basis() → Tuple[float | complex, Dict[int, float | complex], Dict[Tuple[int, int], float | complex], Dict[Tuple[int, int, int, int], float | complex]][source]

Retrieves 1- and 2-body integrals in MO basis from FCIDUMP.

Returns:

  • e_core (Union[float, complex]): Nuclear repulsion energy.

  • spinor (Dict[int, Union[float, complex]]): Dictionary of spinor values with their corresponding indices.

  • one_body_int (Dict[Tuple[int, int], Union[float, complex]]): Dictionary of one-body integrals with their corresponding indices as tuples.

  • two_body_int (Dict[Tuple[int, int, int, int], Union[float, complex]]): Dictionary of two-body integrals with their corresponding indices as tuples.

Return type:

A tuple containing np.ndarray types

Notes

Adapted from Openfermion-Dirac: see: https://github.com/bsenjean/Openfermion-Dirac.

abstract get_integrals_ao_basis() → Tuple[Any, Ellipsis][source]

Calculates one- and two-electron integrals in AO basis.

TODO: after Luuks’s python interface

abstract get_molecular_orbitals_coefficients() → Tuple[Any, Ellipsis][source]

Reads alpha and beta molecular orbital coefficients.

TODO: after Luuks’s python interface

abstract get_molecular_orbitals_energies() → Tuple[Any, Ellipsis][source]

Reads alpha and beta orbital energies.

TODO: after Luuks’s python interface

abstract get_overlap_matrix() → Tuple[Any, Ellipsis][source]

Reads overlap matrix.

TODO: after Luuks’s python interface

_get_from_dirac_hdf5_file(property_name) → Any[source]

Helper routine to open dirac HDF5 output and extract property.

_get_dirac_fcidump() → None[source]

Helper routine to generate DIRAC FCIDUMP file.

Raises:

  • EnvironmentError – If the command execution fails.

  • CalculationFailed – If the calculator fails with a non-zero error code.

Notes

Requires MRCONEE and MDCINT files obtained using **DIRAC .4INDEX, **MOLTRA .ACTIVE all and pam ... --get="MRCONEE MDCINT" options.

_format_fcidump_mo_integrals(one_body_integrals: Dict[Tuple[int, int], float | complex], two_body_integrals: Dict[Tuple[int, int, int, int], float | complex], nmo: int) → Tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray, numpy.ndarray, numpy.ndarray, numpy.ndarray][source]

Helper routine to format DIRAC FCIDUMP integrals.

Returns:

  • one_body_coefficients_a & one_body_coefficients_b: Numpy arrays containing alpha and beta components of the one-body integrals.

  • two_body_coefficients_aa, two_body_coefficients_bb, two_body_coefficients_ab & two_body_coefficients_ba: Numpy arrays containing alpha-alpha, beta-beta, alpha-beta & beta-alpha components of the two-body integrals.

Return type:

A tuple containing np.ndarray types

Notes

Adapted from Openfermion-Dirac: see: https://github.com/bsenjean/Openfermion-Dirac.