hqs_nmr.hamiltonian_tools
Tools to obtain and manipulate a NMR Hamiltonian.
Functions
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Cluster the molecule into spin-dependent cluster. |
Extract the NMR parameters of a cluster from the NMR parameters of the molecule. |
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Extract the coupling matrices from a Struqture spin Hamiltonian. |
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Identify magnetically equivalent spins and return them as groups. |
Gyromagnetic ratios of each spin, normalized w.r.t. |
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Convert a Struqture spin Hamiltonian to its matrix representation. |
- hqs_nmr.hamiltonian_tools.extract_coupling(H: PauliHamiltonian) tuple[ndarray, ndarray, ndarray]
Extract the coupling matrices from a Struqture spin Hamiltonian.
- Parameters:
H – Struqture Spin Hamiltonian.
- Returns:
Array with S^z term with prefactor 2, array with the S^z-S^z coupling, array with the S^+-S^- coupling.
- hqs_nmr.hamiltonian_tools.extract_cluster_nmr_parameters(molecule_parameters: NMRParameters, cluster_indices: list[int]) NMRParameters
Extract the NMR parameters of a cluster from the NMR parameters of the molecule.
- Parameters:
molecule_parameters – The molecular isotopes, shifts and J-coupling values.
cluster_indices – Indices of the cluster.
- Returns:
An object storing the NMR data of the cluster Hamiltonian.
- hqs_nmr.hamiltonian_tools.sh_to_matrix(H: PauliHamiltonian) ndarray[tuple[Any, ...], dtype[complexfloating]]
Convert a Struqture spin Hamiltonian to its matrix representation.
- Parameters:
H – Struqture Spin Hamiltonian
- Returns:
The Spin Hamiltonian as a dense matrix (numpy array).
- hqs_nmr.hamiltonian_tools.cluster_molecule(molecule_parameters: NMRParameters, gyromagnetic_ratios: dict[Isotope, float], field: float, solver_settings: NMRSolverSettings, reference_isotope: Isotope) list[Dict[str, Any]]
Cluster the molecule into spin-dependent cluster.
- Parameters:
molecule_parameters – The molecular isotopes, shifts and J-coupling values.
gyromagnetic_ratios – Dictionary of gyromagnetic ratios in rad / (T s).
field – Magnetic field in T.
solver_settings – NMRSolverSettings object containing information on the clustering and solver methods.
reference_isotope – Isotope specified as Isotope(mass, symbol) to define the frequency (w=gamma*field) of the rotating frame. Defaults to Isotope(1, ‘H’).
- Returns:
List with a dictionary defining each spin-dependent cluster.
- hqs_nmr.hamiltonian_tools.magnetically_equivalent_spins(molecule_parameters: NMRParameters, calculation_parameters: NMRCalculationParameters, tolerance_couplings: float = 1.0, tolerance_shifts: float = 1.0, verbose: int = 0) list[ndarray]
Identify magnetically equivalent spins and return them as groups.
- Parameters:
molecule_parameters – The molecular isotopes, shifts and J-coupling values.
calculation_parameters – Object storing all parameters specifying how a calculation will run.
tolerance_couplings – Tolerance for the J-couplings in the group identifier in percent. Defaults to 1.
tolerance_shifts – Tolerance for the shifts in the group identifier in percent. Defaults to 1.
verbose – Verbosity level of output. Defaults to 0.
- Returns:
A list of integer arrays with the indices of spins in the individual groups.
- hqs_nmr.hamiltonian_tools.normalized_spin_dependent_gyromagnetic_ratios(molecule_parameters: NMRParameters, gyromagnetic_ratios: dict[Isotope, float] = {(1, 'H'): 267522128.0, (13, 'C'): 67282840.0, (15, 'N'): -27126180.4, (19, 'F'): 251814800.0, (31, 'P'): 108394000.0}, reference_isotope: Isotope = (1, 'H')) ndarray
Gyromagnetic ratios of each spin, normalized w.r.t. the gyromagnetic ratio of hydrogen.
- Parameters:
molecule_parameters – The molecular isotopes, shifts and J-coupling values.
gyromagnetic_ratios – Dictionary of gyromagnetic ratios in rad / (T s). Defaults to GyromagneticRatios.
reference_isotope – Isotope used for normalization of the gyromagnetic ratios appearing in the molecule. Defaults to DEFAULT_REFERENCE_ISOTOPE.
- Returns:
Scaled gyromagnetic ratios of each spin.