Changelog

v2.1.3

Improvements

  • Add kmag_detuning_correction keyword argument to Cell.add_single_coupling. Default behavior is to only use the atomic transition frequency to calculate the k-vector magnitude for a coupling with kunit provided, but this leads to inaccurate doppler averages if the coupling detuning is large relative to Doppler shifts. This new argument allows passing in a detuning to be applied to the calculation of the k-vector magnitude for a coupling.

Bug Fixes

  • Fix issue where Solution.coupling_rabi would fail for a coupling group that contains non-dipole-allowed transitions (as common in Cell with sublevel structure).

  • Fix incorrect Sensor.dm_basis labels. E.g. 01_real, 01_imag is actually 10_real, 10_imag. For real terms, change is purely cosmetic, but imaginary terms there is a sign difference. This change brings dm_basis labels to agree with the actual basis definitions (ie Solution.rho_ij).

v2.1.2

Improvements

  • Improved documentation based on JOSS reviewer @a-eghrari feedback. Biggest additions include more detailed contribution guidelines and a quantitative discussion of rydiqule performance (largely lifted from Comp Sci Comms article).

  • Added the Solution.complex_rho property which provides ready conversion of the solved density matrices into the complex basis with ground state present.

  • Made project uv compatible and added installation docs describing how to use it.

  • Updated license metadata to follow PEP 639 standard

  • Improve scannable parameter handling so that all sequences are saved to the graph as numpy arrays. Also ensures proper handling of length-1 and length-0 sequences.

  • Modified the about function to provide numpy’s BLAS/LAPACK backend information.

  • Updates stale example notebooks to incorporate v2.1.1 bugfixes

  • Improved documentation based on JOSS reviewer @nikolasibalic feedback.

Bug Fixes

  • Fix convert_complex_to_dm to properly return arrays with real dtype.

  • Fix Cell.kappa and Cell.eta to properly introspect q when first edge on the graph happens to not be dipole-allowed.

  • Fix draw_diagram to handle complex time-dependent functions correctly.

  • Fix cyrk_solve flat diffEq backend to properly handle EOM stacks in both steady-state and time-dependent problems.

Deprecations

v2.1.1

Improvements

  • leveldiagram and arc dependencies are now lazy loaded at first use (draw_diagram and Cell instantiation, respectively). This improves import rydiqule as rq time by about a second and ensures second-order dependencies such as matplotlib and sympy are not imported unless explicitly needed.

  • Expand Observables documentation to describe generalized paradigm in version 2, including how to calculate custom observables.

Bug Fixes

  • Minor changes to the precision of hard-coded values in unit tests. ARC v3.9.0 updated the precision of a constant used in its internal calculations that shifts calculated dipole moment values by a small amount. It is expected that other plots and values will differ by small amounts when using Cell and ARC v3.9.0

  • Fixed bug where solve_doppler_analytic ignored parameter time-dependence. It now follows the behavior of other steady-state solvers by constructing the Hamiltonian and equations of motion at t=0.

  • Ensure that Cell.eta, Cell.kappa, and Cell.probe_freq properly cache their values as intended.

  • Fix bug where Cell would not add transit broadening automatically, as intended.

  • Fix errors in gamma_mismatch calculations when coupling groups are used. Also fix issue that prevented gamma_mismatch='all' from working if only 1 dephasing is present that needs modification.

  • Update RF heterodyne example notebook to use new Cell syntax.

  • Properly mark slow/high-memory analytic doppler test.

v2.1.0

Improvements

  • Fully support 1D/2D/3D doppler solves using the analytic-enabled solver, solve_doppler_analytic. The analytic average is applied to a single dimension, with other present dimensions treated numerically. This provides notable decreases in computation times and memory footprints and increases in solution accuracy in all spatial dimensions.

  • Added an example notebook, Analytic Doppler Solver, showcasing the new solve_doppler_analytic.

  • Extended documentation and unit unit-testing to include hybrid solver implementation.

Deprecations

  • doppler_1d_exact has been deprecated in favor of the more complete solve_doppler_analytic which handles 1D/2D/3D analytic-enabled averaging

v2.0.0

Improvements

  • Added ability to use arbitrary tuples to define a state.

  • Added concept of StateSpec, which is a tuple with a nested list for at least one element. Rydiqule will interpret this as a list of state tuples expanded along the nested element. For example, (0, [-1, 0, 1]) is interpreted as the group of states [(0, -1), (0, 0), (0, 1)].

  • Added ability to couple groups of states to a single field using a single function. This involves several modifications:

    • The Sensor.add_coupling_group has been added which takes two lists of states and couples all combinations of states. Relative scaling of each sub-coupling is controlled via a coupling_coefficients dictionary. If an entry is missing from this dictionary, that sub-coupling will not be added.

    • The previous Sensor.add_coupling has has been renamed to Sensor.add_single_coupling.

    • The new Sensor.add_coupling function now takes either a pair of states or a pair of StateSpec (which define multiple states), and dispatches appropriately.

    • Identical functionality now exists for the add_decoherence, add_self_broadening, and add_energy_shift functions.

    • Added a string representation of Sensor so that a summary of the data on its graph is shown when calling print(<sensor>).

  • Complete overhaul of Cell.

    • States are now specified using the named tuple class A_QState, which tracks quantum numbers explicitly.

    • Cell now supports calculations with and without sublevels defined.

      • If sublevels are not defined (the NLJ basis), results now use an averaged dipole moment. Otherwise, calculations should be identical to Cell from v1. See Migrating Cell from v1 to v2 for further details.

      • Sublevels can now be defined, in either the fine structure (FS) or hyperfine structure (HFS) bases. Couplings between bases are also supported. This support heavily relies on new coupling group functionality of Sensor described above.

    • A new interface to ARC calculations has been defined, RQ_AlkaliAtom, which defines methods for calculating atomic parameters between pairs of A_QState.

    • The kvec parameter for couplings is replaced with kunit, the unit propagation axis. Necessary prefactors for calculation are automatically applied using ARC functionality. See Migrating Doppler averaging from v1 to v2 for details.

  • Definition of kvec has been redefined to be the field k-vector, instead of the most probable velocity vector. The most probable speed vP must now be provided separately either via init keyword argument (i.e. Sensor(4, vP=250)) or by setting the Sensor.vP attribute. See Migrating Doppler averaging from v1 to v2 for details.

  • Allow the about function to optionally print numpy backend information.

  • Created custom RydiquleError and RydiquleWarning classes and subclasses to denote errors and warnings specific to Rydiqule. By default, RydiquleError will suppress the raise statement in the traceback via patches to exception hooks. This can be disabled by calling rq.set_debug_state(True). rq.set_debug_state also controls debugging print statements during Sensor/Cell creation.

  • Added utility functions for converting density matrices between a standard complex basis and rydiqule’s real with ground removed computational basis (convert_dm_to_complex and convert_complex_to_dm). Added utility to add ground state to real computational basis results convert_to_full_dm. Also added utility to confirm density matrices are physical (check_positive_semi_definite). This functionality is now used in solve_time to ensure user-provided init_cond are physical.

  • Improved the ergonomics of Sensor.zip_parameters so that parameters to be zipped are specified by a dictionary keyed by coupling with entries that specify the parameter.

  • Changed Sensor.add_energy_shift to to be more in line with couplings, so that it works as a dispatch function for single shifts or groups. Also added add_energy_shift_group which will add and zip a group of energy shifts.

  • Package versioning is now handled by setuptools_scm which introspects the version based on git tags (if present). We also use this functionality to dynamically update the version on import when running an from an editable install, to account for local development.

  • Overhaul of the observable functions of sensor_solution to use a more physical definition of observable defined by the trace of the density matrix times an operator. Additionally, those functions are transparent to allow more flexible definitions of observables.

  • sensor_solution now stores the Sensor.couplings graph directly.

  • Added Sensor.get_time_hamiltonian method which returns the system hamiltonian at a specific time t.

  • Reworked Sensor’s time hamiltonian generation function structure to be more clear.

  • draw_diagram now scales the linewidth of coupling arrows based on the magnitude of the Rabi frequency.

  • Improved accuracy of language regarding rotating frame choices in rydiqule’s physics documentation.

  • Greatly over-hauled and expanded example notebooks and documentation to cover new features and clarify old ones.

  • Added a Sensor.zip_zips method to zip axes already containing multiple zipped parameters.

  • Updated CyRK timesolver backend to use pysolve_ivp. Added an improved differential equation generation method 'flat' which improves performance by ~30%. This new method is currently not compatible with doppler solves.

  • Extended the automated test suite to check docstring examples.

  • Added an analytic 1D doppler-averaged steady-state solver doppler_1d_exact. This solver is significantly faster for Doppler-averaged solves. For now, this solver is considered experimental.

Bug Fixes

  • Fix bug where re-adding a coupling that had a zipped parameter did not invalidate the zip.

  • transition_frequency is now correctly marked as a non-scannable parameter

  • Fixed bugs in draw_diagram with un-coupled states and dephasings not toggling correctly.

  • Fixed issue where passing the same numpy array to two zipped parameters would result in incorrect tensor broadcasts.

Deprecations

  • Overhaul of Cell is likely to change results of code that used Cell in v1, if not fail outright. Please see documentation for migration guide between v1 and v2.

  • Previously deprecated experiment functions have been deleted from rydiqule.experiments. These deprecated functions are: get_transmission_coef, get_susceptibility, get_phase_shift, get_solution_element, and get_OD. Since v1.1.0, this functionality has been incorporated directly into Sensor_Solution.

  • Internally-used utility functions have been removed from the top-level namespace. All these functions can still be accessed by importing from their sub-module locations. Functions removed from the top-level namespace are generate_eom, get_basis_transform, solve_eom_stack, generate_eom_time, get_doppler_equations, generate_doppler_shift_eom, doppler_classes, doppler_mesh, apply_doppler_weights, compute_grid, matrix_slice, memory_size, get_slice_num, and get_slice_num_t

  • Removed deprecated Cell.add_states method.

  • suppress_rwa_warn kwarg for Sensor.add_coupling is deprecated. Now use warnings.simplefilter('ignore', rq.RWAWarning) to suppress the warning.

  • Renamed Sensor.get_time_couplings to Sensor.get_time_hamiltonian_components.

  • Removed Sensor.get_time_hamiltonians. Instead call Sensor.get_hamiltonian and Sensor.get_time_hamiltonian_components directly.

  • suppress_dipole_warn kwarg for Cell.add_coupling is deprecated. It is no longer possible to add a non-dipole allowed coupling in Cell.

  • Solution object is no longer a bunch/dict object.

  • Dropped support for numba-only timesolver backends.

    • numbakit-ode was never much of an improvement, if any for our types of problems

    • nbrk_ode (and it’s modern replacement nbsolve_ivp) are not actively being maintained by CyRK. They also have not provided significant improvements for our types of problems.

v1.2.3

  • Minor hotfix release to pin down incompatible versions of numpy and cyrk dependencies.

v1.2.2

Improvements

Bug Fixes

  • Fixed bug where t=0 time-dependent hamiltonians calculated in solve_steady_state were double counted if more than one time-dependent coupling was present.

v1.2.1

Bug Fixes

  • Fixed bug in energy level shifts where shifts overwrote detunings instead of adding.

v1.2.0

Improvements

  • Level diagrams now use Sensor.get_rotating_frames to provide better plotting of energy ordering of levels.

  • Level diagrams now allow for optional control of plotting parameters by manually specifying ld_kw options on nodes and edges.

  • Added the ability to specify energy level shifts (additional Hamiltonian diagonal terms) not accounted for by the coupling infrastructure.

Bug Fixes

  • Sensor.make_real now returns correct sized const array when ground is not removed.

  • Many updates to type hints to improve their accuracy.

Deprecations

  • Remove Solution._variable_parameters in favor of property checking the observable parameters.

  • Renamed Sensor.basis() and Solution.basis to Sensor.dm_basis() and Solution.dm_basis to disambiguate physical basis from computational basis.

v1.1.0

Improvements

  • Added the ability to specify hyperfine states in a Cell. They are distinguished by having 5 quantum numbers [n, l, j, f, m_f].

  • kappa and eta are now properties of Cell which are calculated on the fly.

  • Separated rotating frame logic from hamiltonian diagonal generation into a new function Sensor.get_rotating_frames(). Allows for simple inspection of what rotating frame rydiqule is using in a solve.

  • Reworked the under-the-hood parameter zipping framework. This should have minimal impact on user-facing functionality.

    • Hamiltonians with zipped parameters are no longer generated with a diag operation.

    • Zipped parameters are now handled with a dictionary rather than a list.

    • Zipped parameters can now be given a shorthand label rather than the default behavior of concatenating individual labels.

  • The rearrangement of axes in a stack is now defined completely by the behavior of axis_labels().

  • Added a diff_nearest boolean argument to get_snr. When true, calculates SNR based on nearest neighbor diff. This is in contrast to the default behavior of taking the difference relative to the first element. One case where this is necessary is when getting SNR vs LO Rabi frequency of a heterodyne measurement.

  • Added the ability to label states of a sensor with the label_states method. States with a label matching a particular pattern can be accessed with the states_with_label function.

  • Timesolver now allows for returning doppler-averaged solutions without applying the doppler weight factors. This is mostly useful for internal testing.

  • solve_steady_state now treats time-dependent couplings as having their \(t=0\) value. Most importantly, this affects the default behavior for timesolve initial condition generation and should limit large transient behavior. This also allows the user to specify if time-dependent couplings should be solved with field on or off in steady-state by altering their \(t=0\) value (eg changing between sin and cos).

  • Added unit tests for observables, (susceptibility, optical depth, transmission coefficient, and phase shift).

  • All Observables (susceptibility, optical depth, etc) now only require a Solution object to run.

  • rq.D1_states and rq.D2_states can now specify the atom via string with any isotope specification (including none)

  • get_snr now warns if any couplings have time-dependence, which are ignored.

  • Zipped parameter labels may now include underscores

  • about function now conceals the user’s home directory by default when printing paths

  • Moved level diagram plotting to use an external library

Bug Fixes

  • Fixed return units of get_snr to actually return in 1s BW. Previously was returning in 1us BW.

  • Sign errors when specifying detunings both in and out of the rotating frame have been fixed. All detuning signs now follow the convention that positive = blue detuned from atomic resonance, so long as the couplings are added correctly (ie second state of states tuple is always the higher energy one).

  • Fixed potential issue in get_snr where output results could be overwritten to views of intermediate arrays

  • Fixed numerical bugs in observables: phase shift, susceptibility, optical depth, transmission coef. Now unit tested against Steck Quantum Optics notes.

  • Ensure that non-dipole-allowed transitions are properly warned about in Cell.add_coupling with ARC==3.4

Deprecations

  • The new kappa and eta properties of Cell directly calculate from Cell properties.

  • Time-solver backends (except scipy) are now optional dependencies that are no longer installed by default. To install them, use the pip install rydiqule[backends] command.

  • The uncollapsed stack shape can no longer be accessed to avoid confusion.

  • Removed the ability to pass additional parameters to np.meshgrid through the get_parameter_mesh function.

  • get_snr no longer returns in units of 1us.

  • Default timesolver initial conditions no longer assume time-dependent couplings have the value of rabi_frequency. It is now rabi_frequency times the time_dependence.

  • Multiple sign errors have been corrected in Sensor and Cell with regards to detunings. Results that are asymmetric about zero detuning are likely to change. Please ensure all couplings are following correct sign conventions for consistent results (ie second state of states tuple has higher energy).

  • most of the functions in experiments.py have been moved to become methods of Solution class.

v1.0.0

Improvements

  • Steady-state behavior for time-dependent fields (and thus initial conditions for time solves) is now computed as a static value rather than zero (previous behavior).

  • Added a flag in scipy_solve to specify how to define the right-hand function of the differential equation, to use either loops (the newer method) or list comprehension (the older method).

  • Implemented ruff linting rules as an action for new PRs to help enforce good coding practices.

  • Implemented unit-testing action for new PRs to help automate catching regression bugs.

Bug Fixes

  • Fixed a broken uinit test that did not affect package functionality.

  • Fixed issue where level diagrams don’t draw correctly if all non-zero dephasings are equal.

Deprecations

v1.0.0rc2

Improvements

  • Added a copy method to solution.

  • Expanded the Solution object to include more clear axis labels and the basis of the sensor used.

  • Begin hosting public documentation on readthedocs.

Bug Fixes

  • Changed an isinstance check to hasattr, fixing an occasional issue with reloading rydiqule in jupyter notebooks.

  • Fixed issue where submodules were not installed outside of editable mode.

  • Fixed a bug where additional arguments like warning suppression could not be passed to Sensor.add_couplings

Deprecations

v1.0.0rc1

Improvements

  • Added a warning in cell if add_coupling is called a dipole-forbidden transition.

  • The zip_parameters function can now be called on parameters of different types (e.g. detuning with rabi_frequency)

  • The time solver now can call ivp solvers outside its own module. This allows for more quickly using different backend solvers for time-dependent problems.

  • Implement timesolver backends based on CyRK’s cython and numba ode solvers

  • Optimize scipy backend of the timesolver for smaller dimensional problems

Bug Fixes

  • Fixed issue where solvers would save doppler axes labels and values even when they are summed over to the solution object

  • Fixed a bug where energy level diagrams broke when decoherence rates were scanned.

  • Fixed issue where compiled timesolvers could not solve doppler averaged problems.

  • Fixed issue where certain doppler solves could not be sliced correctly

Deprecations

v0.5.0

Improvements

  • Add isometric-population meshing option to doppler_mesh

  • Allow get_rho_ij to accept a Solution object directly, in addition to solution numpy arrays

  • Add get_rho_populations helper function to efficiently get the trace of density matrix solutions

  • Allow beam_power or beam_waist to be scanned parameters in a Cell coupling

  • Add more information to Solution objects returned by the solvers

  • Allow dephasings to be scannable parameters.

  • Updated the framework for scanning parameters to generate relevant lists on the fly

    • Note: This changes the order of axes in a stack. Previously, the axes would be ordered based on the order they were added to the system. They are now ordered based on python’s sort() applied to a tuple of ((low_state, high_state), parameter_name). As a result, they will be ordered first by lower state, then by upper state, then alphabetically by parameter name (e.g. “detuning”, “rabi_frequency”) In cases where the code was being used for simulations, this may affect cases where axes were defined specifically by number, and these may need to be updated.

  • Added a distinction between stack shapes in steady-state vs time-dependent. For example, a steady-state hamiltonian stack may have shape (10,1,3,3) while the time dependent portion may have shape (1,25,3,3).

  • Renamed the ham_slice function to matrix_slice and allowed it to iterate over any number of matrices. - Updated internals of solver functions to use this framework.

  • zip_parameters function no longer enforces parameters be the same type.

Bug Fixes

  • Fixed several issues with parameter zipping functionality producing errors when sensor methods were called multiple times.

  • Fixed issue where get_rho_ij incorrectly calculated the rho_00 element

  • Allow Cell.add_coupling to accept a list of e-field values

  • Fixed an bug where specifying a list of rabi_frequency in a coupling with time-dependence would raise an error when solved

  • Fixed issue with dephasing broadcasting preventing hamiltonian slices for large solves

Deprecations

  • Removed all sensor_management functionality as too difficult to maintain generally and securely.

  • Removed the internal _variable_couplings, _variable_parameters, and _variable_values attributes from sensor.

v0.4.0

Improvements

  • Changed the handling of decoherent transitions to be stored on graph edges rather than as a separate attribute.

    • Gamma matrix is now calculated on the fly with the decoherence__matrix() method.

    • Decoherent transitions are now added with with the add_decoherence() function in Sensor.

    • Cell now calculates transition frequencies and decay rates automatically and places them on the appropriate graph edges.

  • Changed the Sensor.couplings attribute from a nx.Graph to an nx.DiGraph. This has multiple advantages:

    • A less vague definition of detuning convention.

    • Precise definition of energy ordering: couplings now always point from lower to higher absolute energy.

    • More flexibility in decoherence. Decoherent transitions now point “from” one state “to” another rather than just “between” 2 states. This fixes a limitation where gamma matrices no longer must be lower triangular.

  • get_snr() function in rq.experiments now takes kappa and eta as optional arguments to allow for running on any Sensor object. They can still be inferred from a Sensor subclass that has them as attributes if unspecified.

  • time solver now properly handles complex time dependencies in the rotating wave approximation

  • Added type hints to code base that can be used to static type check with mypy

  • Added functions rq.calc_kappa and rq.calc_eta to properly calculate kappa and eta constants for experimental parameters.

  • Added function rq.get_OD that calculates the optical depth of a solution

  • Improved accuracy of the solver memory estimates

  • Increased input validation unit test coverage

  • Generalized handling of transit broadening to allow for multiple repopulation states with varying branching ratios

Bug Fixes

  • Fixed an issue with time dependence in the probe laser

  • Modified solver to allow for complex time dependence

  • Fixed non-hermitian hamiltonians in time solver

  • Fixed error with multiple time-dependencies in time solver

  • Added functionality to solver error with complex time dependencies

  • Modified experimental return functions (get_transmission_coef(), get_phase_shift(), and get_susceptibility()`) to allow scanning of probe rabi frequency

  • Fixed get_rho_ij so that it correctly calculates the (0,0) population element

  • Fix error in test_sensor_management which fails if temporary directory does not exist.

  • Tighten test_decoherences tolerances to the 2pi*100Hz level to catch errors in decoherence matrix generation.

  • Fixed issue where get_snr ignored the optical path length input parameter

  • Fixed issue where calling solve_steady_state with sum_doppler=False would double memory footprint.

  • Fixed issue where solve_steady_state could be called with weight_doppler=False and sum_doppler=True.

Deprecations

  • get_snr no longer allows manually specifying Sensor.eta and Sensor.kappa, these values must be passed as args for Sensor input

  • Removed unused gamma_transit argument from Sensor init

  • Re-ordered argument list to Cell.add_coupling to match order of Sensor.add_coupling

  • Sensor.add_fields has been fully removed and no longer works as a deprecated alias of Sensor.add_couplings

v0.3.0

Improvements

  • Expanded documentation

  • Removed restrictions on ARC and numpy versions during installation.

  • Vectorized equation of motion generation to support prepending axes to a hamiltonian

  • Updated the internal mechanism for sensor handling fields of various type

    • Fields are now internally called couplings

    • Fields are specified as either having rabi_frequency or transition_frequency, corresponding to RWA or non-RWA fields

    • Fields are specified as either having detuning or transition_frequency, corresponding to steady-state or time-dependent fields

    • Fields with specific traits can be accessed with the couplings_with() function

  • Added a feature to save/load sensors/cells

  • Implemented NumbaKitODE which considerably speeds up solve_time. This feature can be enabled by setting parameter compile=True of solve_time.

  • Improved logic for building diagonal terms of Hamiltonian using NetworkX graph library that allows for diagonal terms to be built from any set of values.

  • Generalized doppler averaging to support prepended axes on hamiltonians.

  • Improved time solver logic for improved modularity across doppler solving and multivalue parameters.

  • Added a feature to draw level diagram

  • Seamlessly generate all Hamiltonians from lists of parameters in sensor.

  • Added ability to label couplings.

  • Added capability to make any coupling time-dependent

  • Sped up time solving considerably by simultaneously solving all equations rather than looping.

  • Allow for user to specify fields by beam power, beam waist, and electric field, in the Cell framework.

  • Solve functions now return a bunch-type object rather than a tuple.

  • Added functionality that breaks equations into slices based on memory requirements

  • Quantum numbers and absolute energies are now stored on the nodes of a Cell couplings graph

  • Cell now adds decay rates and decoherences to the nodes and edges of the Cell couplings graph

  • Cell now calculates the gamma matrix in an arbitrary way, and is no longer limited to two laser, ladder schemes

  • Added function to calculate sensor SNR with respect to any varied sensor coupling parameter

  • Added function to return sensor parameter mesh

Bug Fixes

  • Fixed example notebook.

  • Fixed issue where doppler averaging breaks if there are uncoupled levels.

  • Fixed doppler averaging so that doppler shifts are applied with signs consistent with the hamiltonian.

  • Fixed a bug where doppler averaging did not properly solve separately for each doppler class.

  • Fixed issue where spatial dimension of doppler averaging is not introspected correctly in the presence of round-off errors.

Deprecations

  • All “field” functionality are being deprecated in favor of “coupling”

  • The rf_couplings, target_state, and rf_dipole_matrix arguments of solve_time()

  • All functions relating to sensor.transition_map are deprecated

  • Cell now does not accept gamma_excited or gamma_Rydberg as these are always calculated or Sensor can be used with a given gamma matrix

  • Cell now does not accept gamma_doppler as Doppler broadening width is given by multiplying the most probable velocity and the laser k-vector

v0.2.0

Beta release. Contains very large number of backwards-incompatible changes over alpha release.

v0.1.0

Alpha release. Minimum viable product release that does basic modeling tasks slowly.