From 8eb9ce3f51ce4603565b971ba15a75f5006f61ce Mon Sep 17 00:00:00 2001 From: Eric Giguere Date: Wed, 27 Mar 2024 07:36:31 +0900 Subject: [PATCH 1/5] Add v5 changelog --- doc/changelog.rst | 457 ++++++++++++++++++++++++++++++++++++++- doc/changes/2352.feature | 1 - doc/changes/2354.misc | 1 - 3 files changed, 456 insertions(+), 3 deletions(-) delete mode 100644 doc/changes/2352.feature delete mode 100644 doc/changes/2354.misc diff --git a/doc/changelog.rst b/doc/changelog.rst index a916a657c5..18f0a93a33 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -6,6 +6,461 @@ Change Log .. towncrier release notes start + +QuTiP 5.0.0 (2024-03-26) +======================== + + +QuTiP 5 is a redesign of many of the core components of QuTiP (``Qobj``, +``QobjEvo``, solvers) to make them more consistent and more flexible. + +``Qobj`` may now be stored in either sparse or dense representations, +and the two may be mixed sensibly as needed. ``QobjEvo`` is now used +consistently throughout QuTiP, and the implementation has been +substantially cleaned up. A new ``Coefficient`` class is used to +represent the time-dependent factors inside ``QobjEvo``. + +The solvers have been rewritten to work well with the new data layer +and the concept of ``Integrators`` which solve ODEs has been introduced. +In future, new data layers may provide their own ``Integrators`` +specialized to their representation of the underlying data. + +Much of the user-facing API of QuTiP remains familiar, but there have +had to be many small breaking changes. If we can make changes to +easy migrating code from QuTiP 4 to QuTiP 5, please let us know. + +Any extensive list of changes follows. + +Contributors +------------ + +QuTiP 5 has been a large effort by many people over the last three years. + +In particular: + +- Jake Lishman led the implementation of the new data layer and coefficients. +- Eric Giguère led the implementation of the new QobjEvo interface and solvers. +- Boxi Li led the updating of QuTiP's QIP support and the creation of ``qutip_qip``. + +Other members of the QuTiP Admin team have been heavily involved in reviewing, +testing and designing QuTiP 5: + +- Alexander Pitchford +- Asier Galicia +- Nathan Shammah +- Shahnawaz Ahmed +- Neill Lambert +- Simon Cross +- Paul Menczel + +Two Google Summer of Code contributors updated the tutorials and benchmarks to +QuTiP 5: + +- Christian Staufenbiel updated many of the tutorials (``). +- Xavier Sproken update the benchmarks (``). + +During an internship at RIKEN, Patrick Hopf created new quantum control method and +improved the existing methods interface: + +- Patrick Hopf created new quantum control package (``). + +Four experimental data layers backends were written either as part of Google Summer +of Code or as separate projects. While these are still alpha quality, the helped +significantly to test the data layer API: + +- ``qutip-tensorflow``: a TensorFlow backend by Asier Galicia (``) +- ``qutip-cupy``: a CuPy GPU backend by Felipe Bivort Haiek (``)` +- ``qutip-tensornetwork``: a TensorNetwork backend by Asier Galicia (``) +- ``qutip-jax``: a JAX backend by Eric Giguère (``) + +Finally, Yuji Tamakoshi updated the visualization function and added animation +functions as part of Google Summer of Code project. + +We have also had many other contributors, whose specific contributions are +detailed below: + +- Pieter Eendebak (updated the required SciPy to 1.5+, `#1982 `). +- Pieter Eendebak (reduced import times by setting logger names, `#1981 `) +- Pieter Eendebak (Allow scipy 1.12 to be used with qutip, `#2354 `) +- Xavier Sproken (included C header files in the source distribution, `#1971 `) +- Christian Staufenbiel (added support for multiple collapse operators to the Floquet solver, `#1962 `) +- Christian Staufenbiel (fixed the basis used in the Floquet Master Equation solver, `#1952 `) +- Christian Staufenbiel (allowed the ``bloch_redfield_tensor`` function to accept strings and callables for `a_ops`, `#1951 `) +- Christian Staufenbiel (Add a guide on Superoperators, Pauli Basis and Channel Contraction, `#1984 `) +- Henrique Silvéro (allowed ``qutip_qip`` to be imported as ``qutip.qip``, `#1920 `) +- Florian Hopfmueller (added a vastly improved implementations of ``process_fidelity`` and ``average_gate_fidelity``, `#1712 `, `#1748 `, `#1788 `) +- Felipe Bivort Haiek (fixed inaccuracy in docstring of the dense implementation of negation, `#1608 `) +- Rajath Shetty (added support for specifying colors for individual points, vectors and states display by `qutip.Bloch`, `#1335 `) +- Rochisha Agarwal (Add dtype to printed ouput of qobj, `#2352 `) +- Kosuke Mizuno (Add arguments of plot_wigner() and plot_wigner_fock_distribution() to specify parameters for wigner(), `#2057 `) +- Matt Ord (Only pre-compute density matrices if keep_runs_results is False, `#2303 `) +- Daniel Moreno Galán (Add the possibility to customize point colors as in V4 and fix point plot behavior for 'l' style, `#2303 `) +- Sola85 (Fixed simdiag not returning orthonormal eigenvectors, `#2269 `) +- Edward Thomas (Fix LaTeX display of Qobj state in Jupyter cell outputs, `#2272 `) +- Bogdan Reznychenko (Rework `kraus_to_choi` making it faster, `#2284 `) +- gabbence95 (Fix typos in `expect` documentation, `#2331 `) +- lklivingstone (Added __repr__ to QobjEvo, `#2111 `) +- Yuji Tamakoshi (Improve print(qutip.settings) by make it shorter, `#2113 `) +- khnikhil (Added fermionic annihilation and creation operators, `#2166 `) +- Daniel Weiss (Improved sampling algorithm for mcsolve, `#2218 `) +- SJUW (Increase missing colorbar padding for matrix_histogram_complex() from 0 to 0.05, `#2181 `) +- Valan Baptist Mathuranayagam (Changed qutip-notebooks to qutip-tutorials and fixed the typo in the link redirecting to the changelog section in the PR template, `#2107 `) +- Gerardo Jose Suarez (Added information on sec_cutoff to the documentation, `#2136 `) +- Cristian Emiliano Godinez Ramirez (Added inherited members to API doc of MESolver, SMESolver, SSESolver, NonMarkovianMCSolver, `#2167 `) +- Andrey Rakhubovsky (Corrected grammar in Bloch-Redfield master equation documentation, `#2174 `) +- Rushiraj Gadhvi (qutip.ipynbtools.version_table() can now be called without Cython installed, `#2110 `) +- Harsh Khilawala (Moved HTMLProgressBar from qutip/ipynbtools.py to qutip/ui/progressbar.py, `#2112 `) +- Avatar Srinidhi P V (Added new argument bc_type to take boundary conditions when creating QobjEvo, `#2114 `) +- NAME (DESCRIPTION, `#0000 `) + + +Qobj changes +------------ + +Previously ``Qobj`` data was stored in a SciPy-like sparse matrix. Now the +representation is flexible. Implementations for dense and sparse formats are +included in QuTiP and custom implementations are possible. QuTiP's performance +on dense states and operators is significantly improved as a result. + +Some highlights: + +- The data is still acessible via the ``.data`` attribute, but is now an + instance of the underlying data type instead of a SciPy-like sparse matrix. + The operations available in ``qutip.core.data`` may be used on ``.data``, + regardless of the data type. +- ``Qobj`` with different data types may be mixed in arithmetic and other + operations. A sensible output type will be automatically determined. +- The new ``.to(...)`` method may be used to convert a ``Qobj`` from one data type + to another. E.g. ``.to("dense")`` will convert to the dense representation and + ``.to("csr")`` will convert to the sparse type. +- Many ``Qobj`` methods and methods that create ``Qobj`` now accepted a ``dtype`` + parameter that allows the data type of the returned ``Qobj`` to specified. +- The new ``&`` operator may be used to obtain the tensor product. +- The new ``@`` operator may be used to obtain the matrix / operator product. + ``bar @ ket`` returns a scalar. +- The new ``.contract()`` method will collapse 1D subspaces of the dimensions of + the ``Qobj``. +- The new ``.logm()`` method returns the matrix logarithm of an operator. +- The methods ``.set_data``, ``.get_data``, ``.extract_state``, ``.eliminate_states``, + ``.evaluate`` and ``.check_isunitary`` have been removed. +- The property ``dtype`` return the representation of the data used. +- The new ``data_as`` allow to obtain the data as a common python formats: + numpy array, scipy sparse matrix, JAX Array, etc. + +QobjEvo changes +--------------- + +The ``QobjEvo`` type for storing time-dependent quantum objects has been +significantly expanded, standardized and extended. The time-dependent +coefficients are now represented using a new ``Coefficient`` type that +may be independently created and manipulated if required. + +Some highlights: + +- The ``.compile()`` method has been removed. Coefficients specified as + strings are automatically compiled if possible and the compilation is + cached across different Python runs and instances. +- Mixing coefficient types within a single ``Qobj`` is now supported. +- Many new attributes were added to ``QobjEvo`` for convenience. Examples + include ``.dims``, ``.shape``, ``.superrep`` and ``.isconstant``. +- Many old attributes such as ``.cte``, ``.use_cython``, ``.type``, ``.const``, + and ``.coeff_file`` were removed. +- A new ``Spline`` coefficient supports spline interpolations of different + orders. The old ``Cubic_Spline`` coefficient has been removed. +- The new ``.arguments(...)`` method allows additional arguments to the + underlying coefficient functions to be updated. +- The ``_step_func_coeff`` argument has been replaced by the ``order`` + parameter. ``_step_func_coeff=False`` is equivalent to ``order=3``. + ``_step_func_coeff=True`` is equivalent to ``order=0``. Higher values + of ``order`` gives spline interpolations of higher orders. +- The spline type can take ``bc_type`` to control the boundary conditions. +- QobjEvo can be creating from the multiplication of a Qobj with a coefficient: + ``oper * qutip.coefficient(f, args=args)`` is equivalent to + ``qutip.QobjEvo([[oper, f]], args=args)``. +- Coefficient function can be defined in a pythonic manner: ``def f(t, A, w)``. + The dictionary ``args`` second argument is no longer needed. + Function using the exact ``f(t, args)`` signature will use the old method for + backward compatibility. + +Solver changes +-------------- + +The solvers in QuTiP have been heavily reworked and standardized. +Under the hood solvers now make use of swappable ODE ``Integrators``. +Many ``Integrators`` are included (see the list below) and +custom implementations are possible. Solvers now consistently +accept a ``QobjEvo`` instance at the Hamiltonian or Liouvillian, or +any object which can be passed to the ``QobjEvo`` constructor. + +A breakdown of highlights follows. + +All solvers: + +- Solver options are now supplied in an ordinary Python dict. + ``qutip.Options`` is deprecated and returns a dict for backwards + compatibility. +- A specific ODE integrator may be selected by supplying a + ``method`` option. +- Each solver provides a class interface. Creating an instance + of the class allows a solver to be run multiple times for the + same system without having to repeatedly reconstruct the + right-hand side of the ODE to be integrated. +- A ``QobjEvo`` instance is accepted for most operators, e.g., + ``H``, ``c_ops``, ``e_ops``, ``a_ops``. +- The progress bar is now selected using the ``progress_bar`` option. + A new progess bar using the ``tqdm`` Python library is provided. +- Dynamic arguments, where the value of an operator depends on + the current state of the evolution interface reworked. Now a property of the + solver is to be used as an arguments: + ``args={"state": MESolver.StateFeedback(default=rho0)}`` + +Integrators: + +- The SciPy zvode integrator is available with the BDF and + Adams methods as ``bdf`` and ``adams``. +- The SciPy dop853 integrator (an eighth order Runge-Kutta method by + Dormand & Prince) is available as ``dop853``. +- The SciPy lsoda integrator is available as ``lsoda``. +- QuTiP's own implementation of Verner's "most efficient" Runge-Kutta methods + of order 7 and 9 are available as ``vern7`` and ``vern9``. See + http://people.math.sfu.ca/~jverner/ for a description of the methods. +- QuTiP's own implementation of a solver that directly diagonalizes the + the system to be integrated is available as ``diag``. It only works on + time-independent systems and is slow to setup, but once the diagonalization + is complete, it generates solutions very quickly. +- QuTiP's own implementatoin of an approximate Krylov subspace integrator is + available as ``krylov``. This integrator is only usable with ``sesolve``. + +Result class: + +- A new ``.e_data`` attribute provides expectation values as a dictionary. + Unlike ``.expect``, the values are provided in a Python list rather than + a numpy array, which better supports non-numeric types. +- The contents of the ``.stats`` attribute changed significantly and is + now more consistent across solvers. + +Monte-Carlo Solver (mcsolve): + +- The system, H, may now be a super-operator. +- The ``seed`` parameter now supports supplying numpy ``SeedSequence`` or + ``Generator`` types. +- The new ``timeout`` and ``target_tol`` parameters allow the solver to exit + early if a timeout or target tolerance is reached. +- The ntraj option no longer supports a list of numbers of trajectories. + Instead, just run the solver multiple times and use the class ``MCSolver`` + if setting up the solver uses a significant amount of time. +- The ``map_func`` parameter has been replaced by the ``map`` option. +- A loky based parallel map as been added. +- A mpi based parallel map as been added. +- The result returned by ``mcsolve`` now supports calculating photocurrents + and calculating the steady state over N trajectories. +- The old ``parfor`` parallel execution function has been removed from + ``qutip.parallel``. Use ``parallel_map``, ``loky_map`` or ``mpi_pmap`` instead. +- Added improved sampling options which converge much faster when the + probability of collapse is small. + +Non Markovian Monte-Carlo Solver (nm_mcsolve): + +- New Monte-Carlo Solver supporting negative decay rates. +- Enjoy of most of the improvement made to the original Monte-Carlo Solver. +- ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????/ +- Paul, anything to add? +- ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????/ + +Stochastic Equation Solvers (ssesolve, smesolve) + +- Function call greatly changed: many keyword arguments are now options. +- m_ops and dW_factors are now changed from the default from the new class interface only. +- Use the same parallel maps as mcsolve: support for loky and mpi map added. +- End conditions ``timeout`` and ``target_tol`` added. +- The ``seed`` parameter now supports supplying numpy ``SeedSequence``. +- Wiener function is now available as a feedback. + +Bloch-Redfield Master Equation Solver (brmesolve): + +- The ``a_ops`` and ``spectra`` support implementations been heavily reworked to + reuse the techniques from the new Coefficient and QobjEvo classes. +- The ``use_secular`` parameter has been removed. Use ``sec_cutoff=-1`` instead. +- The required tolerance is now read from ``qutip.settings``. + +Krylov Subspace Solver (krylovsolve): + +- The Krylov solver is now implemented using ``SESolver`` and the ``krylov`` + ODE integrator. The function ``krylovsolve`` is maintained for convenience + and now supports many more options. +- The ``sparse`` parameter has been removed. Supply a sparse ``Qobj`` for the + Hamiltonian instead. + +Floquet Solver (fsesolve and fmmesolve): + +- The Floquet solver has been rewritten to use a new ``FloquetBasis`` class + which manages the transformations from lab to Floquet basis and back. +- Many of the internal methods used by the old Floquet solvers have + been removed. The Floquet tensor may still be retried using + the function ``floquet_tensor``. +- The Floquet Markov Master Equation solver has had many changes and + new options added. The environment temperature may be specified using + ``w_th``, and the result states are stored in the lab basis and optionally + in the Floquet basis using ``store_floquet_state``. +- The spectra functions supplied to ``fmmesolve`` must now be vectorized + (i.e. accept and return numpy arrays for frequencies and densities) and + must accept negative frequence (i.e. usually include a ``w > 0`` factor + so that the returned densities are zero for negative frequencies). +- The number of sidebands to keep, ``kmax`` may only be supplied when using + the ``FMESolver`` +- The ``Tsteps`` parameter has been removed from both ``fsesolve`` and + ``fmmesolve``. The ``precompute`` option to ``FloquetBasis`` may be used + instead. + +Evolution of State Solver (essovle): + +- The function ``essolve`` has been removed. Use the ``diag`` integration + method with ``sesolve`` or ``mesolve`` instead. + +Steady-state solvers (steadystate module): + +- The ``method`` parameter and ``solver`` parameters have been separated. Previously + they were mixed together in the ``method`` parameter. +- The previous options are now passed as parameters to the steady state + solver and mostly passed through to the underlying SciPy functions. +- The logging and statistics have been removed. + +Correlation functions (correlation module): + +- A new ``correlation_3op`` function has been added. It supports ``MESolver`` + or ``BRMESolver``. +- The ``correlation``, ``correlation_4op``, and ``correlation_ss`` functions have been + removed. +- Support for calculating correlation with ``mcsolve`` has been removed. + +Propagators (propagator module): + +- A class interface, ``qutip.Propagator``, has been added for propagators. +- Propagation of time-dependent systems is now supported using ``QobjEvo``. +- The ``unitary_mode`` and ``parallel`` options have been removed. + +Correlation spectra (spectrum module): + +- The functions ``spectrum_ss`` and ``spectrum_pi`` have been removed and + are now internal functions. +- The ``use_pinv`` parameter for ``spectrum`` has been removed and the + functionality merged into the ``solver`` parameter. Use ``solver="pi"`` + instead. + +Hierarchical Equation of Motion Solver (HEOM) + +- Added support for combining bosonic and fermionic baths. +- ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? +- Simon, there is a lot more than you and other have done for HEOM, please brag a little +- ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? + + +QuTiP core +---------- + +There have been numerous other small changes to core QuTiP features: + +- ``qft(...)`` the function that returns the quantum Fourier + transform operator was moved from ``qutip.qip.algorithm`` into ``qutip``. +- The Bloch-Redfield solver tensor, ``brtensor``, has been moved into + ``qutip.core``. See the section above on the Bloch-Redfield solver + for details. +- The functions ``mat2vec`` and ``vec2mat`` for transforming states to and + from super-operator states have been renamed to ``stack_columns`` and + ``unstack_columns``. +- The function ``liouvillian_ref`` has been removed. Used ``liouvillian`` + instead. +- The superoperator transforms ``super_to_choi``, ``choi_to_super``, + ``choi_to_kraus``, ``choi_to_chi`` and ``chi_to_choi`` have been removed. + Used ``to_choi``, ``to_super``, ``to_kraus`` and ``to_chi`` instead. +- All of the random object creation functions now accepted a + numpy ``Generator`` as a seed. +- The ``dims`` parameter of all random object creation functions has + been removed. Supply the dimensions as the first parameter if + explicit dimensions are required. +- The function ``rand_unitary_haar`` has been removed. Use + ``rand_unitary(distribution="haar")`` instead. +- The functions ``rand_dm_hs`` and ``rand_dm_ginibre`` have been removed. + Use ``rand_dm(distribution="hs")`` and ``rand_dm(distribution="ginibre")`` + instead. +- The function ``rand_ket_haar`` has been removed. Use + ``rand_ket(distribution="haar")`` instead. +- The measurement functions have had the ``target`` parameter for + expanding the measurement operator removed. Used ``expand_operator`` + to expand the operator instead. +- ``qutip.Bloch`` now supports applying colours per-point, state or vector in + ``add_point``, ``add_states``, and ``add_vectors``. +- Dimensions use a class instead of layered lists. +- Allow measurement functions to support degenerate operators. +- Add ``qeye_like`` and ``qzero_like``. +- Added fermionic annihilation and creation operators. + +QuTiP settings +-------------- + +Previously ``qutip.settings`` was an ordinary module. Now ``qutip.settings`` is +an instance of a settings class. All the runtime modifiable settings for +core operations are in ``qutip.settings.core``. The other settings are not +modifiable at runtime. + +- Removed ``load``. ``reset`` and ``save`` functions. +- Removed ``.debug``, ``.fortran``, ``.openmp_thresh``. +- New ``.compile`` stores the compilation options for compiled coefficients. +- New ``.core["rtol"]`` core option gives the default relative tolerance used by QuTiP. +- The absolute tolerance setting ``.atol`` has been moved to ``.core["atol"]``. + +Visualization +------------- + +- Add arguments of plot_wigner() and plot_wigner_fock_distribution() to specify parameters for wigner(). +- Removed Bloch3D: redundant to Bloch. +- Improved the function calls, all visualization functions take ``fig``, ``ax`` and ``cmap`` keyword arguments. +- Most visualization functions respect the ``colorblind_safe`` setting. +- Added new functions to create animations from a list of Qobj or directly from solver results (if states are saved.) +- + + +Package reorganization +---------------------- + +- ``qutip.qip`` has been moved into its own package, qutip-qip. Once installed, qutip-qip is available as either ``qutip.qip`` or ``qutip_qip``. Some widely useful gates have been retained in ``qutip.gates``. +- ``qutip.lattice`` has been moved into its own package, qutip-lattice. It is available from ``. +- ``qutip.sparse`` has been removed. It contained the old sparse matrix representation and is replaced by the new implementation in ``qutip.data``. +- ``qutip.piqs`` functions are no longer available from the ``qutip`` namespace. They are accessible from ``qutip.piqs`` instead. + +Miscellaneous +------------- + +- Support has been added for 64-bit integer sparse matrix indices, allowing + sparse matrices with up to 2**63 rows and columns. This support needs to + be enabled at compilation time by calling ``setup.py`` and passing + ``--with-idxint-64``. + +Feature removals +---------------- + +- Support for OpenMP has been removed. If there is enough demand and a good plan for how to organize it, OpenMP support may return in a future QuTiP release. +- The ``qutip.parfor`` function has been removed. Use ``qutip.parallel_map`` instead. +- ``qutip.graph`` has been removed and replaced by SciPy's graph functions. +- ``qutip.topology`` has been removed. It contained only one function ``berry_curvature``. +- The ``~/.qutip/qutiprc`` config file is no longer supported. It contained settings for the OpenMP support. + + +Changes from QuTiP 5.0.0b1: +-------------------------- + +Features +-------- + +- Add dtype to printed ouput of qobj (#2352 by Rochisha Agarwal) + + +Miscellaneous +------------- + +- Allow scipy 1.12 to be used with qutip. (#2354 by Pieter Eendebak) + + QuTiP 5.0.0b1 (2024-03-04) ========================== @@ -58,7 +513,7 @@ Features - Change the order of parameters in expand_operator (#1991) - Add `svn` and `solve` to dispatched (#2002) - Added nm_mcsolve to provide support for Monte-Carlo simulations of master equations with possibly negative rates. The method implemented here is described in arXiv:2209.08958 [quant-ph]. (#2070 by pmenczel) -- Add support for combining bosinic and fermionic HEOM baths (#2089) +- Add support for combining bosonic and fermionic HEOM baths (#2089) - Added __repr__ to QobjEvo (#2111 by lklivingstone) - Improve print(qutip.settings) by make it shorter (#2113 by tamakoshi2001) - Create the `trace_oper_ket` operation (#2126) diff --git a/doc/changes/2352.feature b/doc/changes/2352.feature deleted file mode 100644 index 96b9a87c15..0000000000 --- a/doc/changes/2352.feature +++ /dev/null @@ -1 +0,0 @@ -Add dtype to printed ouput of qobj \ No newline at end of file diff --git a/doc/changes/2354.misc b/doc/changes/2354.misc deleted file mode 100644 index e3cfa9de56..0000000000 --- a/doc/changes/2354.misc +++ /dev/null @@ -1 +0,0 @@ -Allow scipy 1.12 to be used with qutip. \ No newline at end of file From 9c61cd55415f9f24bd7123f4487d6e5321bc7b0f Mon Sep 17 00:00:00 2001 From: Eric Giguere Date: Wed, 27 Mar 2024 07:38:25 +0900 Subject: [PATCH 2/5] Add last minute PR --- doc/changelog.rst | 2 +- doc/changes/2363.doc | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) delete mode 100644 doc/changes/2363.doc diff --git a/doc/changelog.rst b/doc/changelog.rst index 18f0a93a33..41e916a3d0 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -111,7 +111,7 @@ detailed below: - Rushiraj Gadhvi (qutip.ipynbtools.version_table() can now be called without Cython installed, `#2110 `) - Harsh Khilawala (Moved HTMLProgressBar from qutip/ipynbtools.py to qutip/ui/progressbar.py, `#2112 `) - Avatar Srinidhi P V (Added new argument bc_type to take boundary conditions when creating QobjEvo, `#2114 `) -- NAME (DESCRIPTION, `#0000 `) +- Andrey Rakhubovsky (Fix types in docstring of projection(), `#2363 `) Qobj changes diff --git a/doc/changes/2363.doc b/doc/changes/2363.doc deleted file mode 100644 index 981f95c320..0000000000 --- a/doc/changes/2363.doc +++ /dev/null @@ -1 +0,0 @@ -Fix types in docstring of projection() From 020162ed9f2782600cc2b926aecb648b7603ba56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eric=20Gigu=C3=A8re?= Date: Tue, 26 Mar 2024 21:31:25 -0400 Subject: [PATCH 3/5] Update doc/changelog.rst Co-authored-by: Paul --- doc/changelog.rst | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/doc/changelog.rst b/doc/changelog.rst index 41e916a3d0..eaa2c9896b 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -262,10 +262,9 @@ Monte-Carlo Solver (mcsolve): Non Markovian Monte-Carlo Solver (nm_mcsolve): - New Monte-Carlo Solver supporting negative decay rates. -- Enjoy of most of the improvement made to the original Monte-Carlo Solver. -- ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????/ -- Paul, anything to add? -- ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????/ +- Based on the influence martingale approach, Donvil et al., Nat Commun 13, 4140 (2022). +- Most of the improvements made to the regular Monte-Carlo solver are also available here. +- The value of the influence martingale is available through the ``.trace`` attribute of the result. Stochastic Equation Solvers (ssesolve, smesolve) From 0eb1861aafa799f27f7603f697924a2e19d2859a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eric=20Gigu=C3=A8re?= Date: Tue, 26 Mar 2024 22:25:22 -0400 Subject: [PATCH 4/5] Apply suggestions from code review Co-authored-by: Simon Cross --- doc/changelog.rst | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/doc/changelog.rst b/doc/changelog.rst index eaa2c9896b..ea1488a993 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -29,7 +29,7 @@ Much of the user-facing API of QuTiP remains familiar, but there have had to be many small breaking changes. If we can make changes to easy migrating code from QuTiP 4 to QuTiP 5, please let us know. -Any extensive list of changes follows. +An extensive list of changes follows. Contributors ------------ @@ -59,13 +59,13 @@ QuTiP 5: - Christian Staufenbiel updated many of the tutorials (``). - Xavier Sproken update the benchmarks (``). -During an internship at RIKEN, Patrick Hopf created new quantum control method and +During an internship at RIKEN, Patrick Hopf created a new quantum control method and improved the existing methods interface: - Patrick Hopf created new quantum control package (``). Four experimental data layers backends were written either as part of Google Summer -of Code or as separate projects. While these are still alpha quality, the helped +of Code or as separate projects. While these are still alpha quality, they helped significantly to test the data layer API: - ``qutip-tensorflow``: a TensorFlow backend by Asier Galicia (``) @@ -348,10 +348,11 @@ Correlation spectra (spectrum module): Hierarchical Equation of Motion Solver (HEOM) +- Updated the solver to use the new QuTiP integrators and data layer. +- Updated all the HEOM tutorials to QuTiP 5. - Added support for combining bosonic and fermionic baths. -- ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? -- Simon, there is a lot more than you and other have done for HEOM, please brag a little -- ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? +- Sped up the construction of the RHS of the HEOM solver by a factor of 4x. +- As in QuTiP 4, the HEOM supports arbitrary spectral densities, bosonic and fermionic baths, Páde and Matsubara expansions of the correlation functions, calculating the Matsubara terminator and inspection of the ADOs (auxiliary density operators). QuTiP core @@ -411,18 +412,18 @@ modifiable at runtime. Visualization ------------- -- Add arguments of plot_wigner() and plot_wigner_fock_distribution() to specify parameters for wigner(). -- Removed Bloch3D: redundant to Bloch. -- Improved the function calls, all visualization functions take ``fig``, ``ax`` and ``cmap`` keyword arguments. -- Most visualization functions respect the ``colorblind_safe`` setting. -- Added new functions to create animations from a list of Qobj or directly from solver results (if states are saved.) -- +- Added arguments to ``plot_wigner`` and ``plot_wigner_fock_distribution`` to specify parameters for ``wigner``. +- Removed ``Bloch3D``. The same functionality is provided by ``Bloch``. +- Added ``fig``, ``ax`` and ``cmap`` keyword arguments to all visualization functions. +- Most visualization functions now respect the ``colorblind_safe`` setting. +- Added new functions to create animations from a list of ``Qobj`` or directly from solver results with saved states. Package reorganization ---------------------- - ``qutip.qip`` has been moved into its own package, qutip-qip. Once installed, qutip-qip is available as either ``qutip.qip`` or ``qutip_qip``. Some widely useful gates have been retained in ``qutip.gates``. +- ``qutip.control`` has been moved to qutip-qtrl and once installed qutip-qtrl is available as either ``qutip.control`` or ``qutip_qtrl``. Note that ``quitp_qtrl`` is provided primarily for backwards compatibility. Improvements to optimal control will take place in the new ``qutip_qoc`` package. - ``qutip.lattice`` has been moved into its own package, qutip-lattice. It is available from ``. - ``qutip.sparse`` has been removed. It contained the old sparse matrix representation and is replaced by the new implementation in ``qutip.data``. - ``qutip.piqs`` functions are no longer available from the ``qutip`` namespace. They are accessible from ``qutip.piqs`` instead. From f05f4a247abf8bd52a3e114a9ec315dbc94573c7 Mon Sep 17 00:00:00 2001 From: Eric Giguere Date: Wed, 27 Mar 2024 11:27:43 +0900 Subject: [PATCH 5/5] Add removal entries --- doc/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/changelog.rst b/doc/changelog.rst index ea1488a993..c4125aeb41 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -444,6 +444,8 @@ Feature removals - ``qutip.graph`` has been removed and replaced by SciPy's graph functions. - ``qutip.topology`` has been removed. It contained only one function ``berry_curvature``. - The ``~/.qutip/qutiprc`` config file is no longer supported. It contained settings for the OpenMP support. +- Deprecate ``three_level_atom`` +- Deprecate ``orbital`` Changes from QuTiP 5.0.0b1: