Netket

[GitHub commits](https://github.com/netket/netket/compare/v3.1...v3.2).

New features
* `GraphOperator` (and `Heisenberg`) now support passing a custom mapping of graph nodes to Hilbert space sites via the new `acting_on_subspace` argument. This makes it possible to create `GraphOperator`s that act on a subset of sites, which is useful in composite Hilbert spaces. [924](https://github.com/netket/netket/pull/924)
* `PauliString` now supports any Hilbert space with local size 2. The Hilbert space is now the optional first argument of the constructor. [960](https://github.com/netket/netket/pull/960)
* `PauliString` now can be multiplied and summed together, performing some simple algebraic simplifications on the strings they contain. They also lazily initialize their internal data structures, making them faster to construct but slightly slower the first time that their matrix elements are accessed. [955](https://github.com/netket/netket/pull/955)
* `PauliString`s can now be constructed starting from an `OpenFermion` operator. [956](https://github.com/netket/netket/pull/956)
* In addition to nearest-neighbor edges, `Lattice` can now generate edges between next-nearest and, more generally, k-nearest neighbors via the constructor argument `max_neighbor_order`. The edges can be distinguished by their `color` property (which is used, e.g., by `GraphOperator` to apply different bond operators). [970](https://github.com/netket/netket/pull/970)
* Two continuous-space operators (`KineticEnergy` and `PotentialEnergy`) have been implemented. [971](https://github.com/netket/netket/pull/971)
* `Heisenberg` Hamiltonians support different coupling strengths on `Graph` edges with different colors. [972](https://github.com/netket/netket/pull/972).
* The `little_group` and `space_group_irreps` methods of `SpaceGroupBuilder` take the wave vector as either varargs or iterables. [975](https://github.com/netket/netket/pull/975)
* A new `netket.experimental` submodule has been created and all experimental features have been moved there. Note that in contrast to the other `netket` submodules, `netket.experimental` is not imported by default. [976](https://github.com/netket/netket/pull/976)

Breaking Changes
* Moved `nk.vqs.variables_from_***` to `nk.experimental.vqs` module. Also moved the experimental samplers to `nk.sampler.MetropolisPt` and `nk.sampler.MetropolisPmap` to `nk.experimental.sampler`. [976](https://github.com/netket/netket/pull/976)
* `operator.size`, has been deprecated. If you were using this function, please transition to `operator.hilbert.size`. [985](https://github.com/netket/netket/pull/985)

Bug Fixes
* A bug where `LocalOperator.get_conn_flattened` would read out-of-bounds memory has been fixed. It is unlikely that the bug was causing problems, but it triggered warnings when running Numba with boundscheck activated. [966](https://github.com/netket/netket/pull/966)
* The dependency `python-igraph` has been updated to `igraph` following the rename of the upstream project in order to work on conda. [986](https://github.com/netket/netket/pull/986)
* {attr}`~netket.vqs.MCState.n_samples_per_rank` was returning wrong values and has now been fixed. [987](https://github.com/netket/netket/pull/987)
* The `DenseSymm` layer now also accepts objects of type `HashableArray` as `symmetries` argument. [989](https://github.com/netket/netket/pull/989)
* A bug where `VMC.info()` was erroring has been fixed. [984](https://github.com/netket/netket/pull/984)

[GitHub commits](https://github.com/netket/netket/compare/v3.0...v3.1).

New features
* Added Conversion methods `to_qobj()` to operators and variational states, that produce QuTiP's qobjects.
* A function `nk.nn.activation.reim` has been added that transforms a nonlinearity to act seperately on the real and imaginary parts
* Nonlinearities `reim_selu` and `reim_relu` have been added
* Autoregressive Neural Networks (ARNN) now have a `machine_pow` field (defaults to 2) used to change the exponent used for the normalization of the wavefunction. [940](https://github.com/netket/netket/pull/940).

Breaking Changes
* The default initializer for `netket.models.GCNN` has been changed to from `jax.nn.selu` to `netket.nn.reim_selu` [892](https://github.com/netket/netket/pull/892)
* `netket.nn.initializers` has been deprecated in favor of `jax.nn.initializers` [935](https://github.com/netket/netket/pull/935).
* Subclasses of {class}`netket.models.AbstractARNN` must define the field `machine_pow` [940](https://github.com/netket/netket/pull/940)
* `nk.hilbert.HilbertIndex` and `nk.operator.spin.DType` are now unexported (they where never intended to be visible). [904](https://github.com/netket/netket/pull/904)
* `AbstractOperator`s have been renamed `DiscreteOperator`s. `AbstractOperator`s still exist, but have almost no functionality and they are intended as the base class for more arbitrary (eg. continuous space) operators. If you have defined a custom operator inheriting from `AbstractOperator` you should change it to derive from `DiscreteOperator`. [929](https://github.com/netket/netket/pull/929)


Internal Changes
* `PermutationGroup.product_table` now consumes less memory and is more performant. This is helpfull when working with large symmetry groups. [884](https://github.com/netket/netket/pull/884) [#891](https://github.com/netket/netket/pull/891)
* Added size check to `DiscreteOperator.get_conn` and throw helpful error messages if those do not match. [927](https://github.com/netket/netket/pull/927)
* The internal `numba4jax` module has been factored out into a standalone library, named (how original) [`numba4jax`](http://github.com/PhilipVinc/numba4jax). This library was never intended to be used by external users, but if for any reason you were using it, you should switch to the external library. [#934](https://github.com/netket/netket/pull/934)
* `netket.jax` now includes several _batching_ utilities like `batched_vmap` and `batched_vjp`. Those can be used to build memory efficient batched code, but are considered internal, experimental and might change without warning. [925](https://github.com/netket/netket/pull/925).


Bug Fixes
* Autoregressive networks now work with `Qubit` hilbert spaces. [937](https://github.com/netket/netket/pull/937)

[GitHub commits](https://github.com/netket/netket/compare/v3.0b4...v3.0).

New features


Breaking Changes
* The default initializer for `netket.nn.Dense` layers now matches the same default as `flax.linen`, and it is `lecun_normal` instead of `normal(0.01)` [869](https://github.com/netket/netket/pull/869)
* The default initializer for `netket.nn.DenseSymm` layers is now chosen in order to give variance 1 to every output channel, therefore defaulting to `lecun_normal` [870](https://github.com/netket/netket/pull/870)

Internal Changes


Bug Fixes

[GitHub commits](https://github.com/netket/netket/compare/v3.0b3...v3.0b4).

New features
* DenseSymm now accepts a mode argument to specify whever the symmetries should be computed with a full dense matrix or FFT. The latter method is much faster for sufficiently large systems. Other kwargs have been added to satisfy the interface. The api changes are also reflected in RBMSymm and GCNN. [792](https://github.com/netket/netket/pull/792)

Breaking Changes
* The so-called legacy netket in `netket.legacy` has been removed. [773](https://github.com/netket/netket/pull/773)

Internal Changes
* The methods `expect` and `expect_and_grad` of `MCState` now use dispatch to select the relevant implementation of the algorithm. They can therefore be expanded and overridden without editing NetKet's source code. [804](https://github.com/netket/netket/pull/804)
* `netket.utils.mpi_available` has been moved to `netket.utils.mpi.available` to have a more consistent api interface (all mpi-related properties in the same submodule). [827](https://github.com/netket/netket/pull/827)
* `netket.logging.TBLog` has been renamed to `netket.logging.TensorBoardLog` for better readability. A deprecation warning is now issued if the older name is used [827](https://github.com/netket/netket/pull/827)
* When `MCState` initializes a model by calling `model.init`, the call is now jitted. This should speed it up for non-trivial models but might break non-jit invariant models. [832](https://github.com/netket/netket/pull/832)
* `operator.get_conn_padded` now supports arbitrarily-dimensioned bitstrings as input and reshapes the output accordingly. [834](https://github.com/netket/netket/pull/834)
* NetKet's implementation of dataclasses now support `pytree_node=True/False` on cached properties. [835](https://github.com/netket/netket/pull/835)
* Plum version has been bumped to 1.5.1 to avoid broken versions (1.4, 1.5). [856](https://github.com/netket/netket/pull/856).
* Numba version 0.54 is now allowed [857](https://github.com/netket/netket/pull/857).


Bug Fixes
* Fix Progress bar bug. [810](https://github.com/netket/netket/pull/810)
* Make the repr/printing of history objects nicer in the REPL. [819](https://github.com/netket/netket/pull/819)
* The field `MCState.model` is now read-only, to prevent user errors. [822](https://github.com/netket/netket/pull/822)
* The order of the operators in `PauliString` does no longer influences the estimate of the number of non-zero connected elements. [836](https://github.com/netket/netket/pull/836)

[GitHub commits](https://github.com/netket/netket/compare/v3.0b2...v3.0b3).

New features

* The {py:mod}`netket.utils.group` submodule provides utilities for geometrical and permutation groups. `Lattice` (and its specialisations like `Grid`) use these to automatically construct the space groups of lattices, as well as their character tables for generating wave functions with broken symmetry. [724](https://github.com/netket/netket/pull/724)
* Autoregressive neural networks, sampler, and masked linear layers have been added to `models`, `sampler` and `nn` [705](https://github.com/netket/netket/pull/705).


Breaking Changes

* The `netket.graph.Grid` class has been removed. {ref}`netket.graph.Grid` will now return an instance of {class}`graph.Lattice` supporting the same API but with new functionalities related to spatial symmetries. The `color_edges` optional keyword argument has been removed without deprecation. [724](https://github.com/netket/netket/pull/724)
* `MCState.n_discard` has been renamed `MCState.n_discard_per_chain` and the old binding has been deprecated [739](https://github.com/netket/netket/pull/739).
* `nk.optimizer.qgt.QGTOnTheFly` option `centered=True` has been removed because we are now convinced the two options yielded equivalent results. `QGTOnTheFly` now always behaves as if `centered=False` [706](https://github.com/netket/netket/pull/706).

Internal Changes

* `networkX` has been replaced by `igraph`, yielding a considerable speedup for some graph-related operations [729](https://github.com/netket/netket/pull/729).
* `netket.hilbert.random` module now uses `plum-dispatch` (through `netket.utils.dispatch`) to select the correct implementation of `random_state` and `flip_state`. This makes it easy to define new hilbert states and extend their functionality easily. [734](https://github.com/netket/netket/pull/734).
* The AbstractHilbert interface is now much smaller in order to also support continuous Hilbert spaces. Any functionality specific to discrete hilbert spaces (what was previously supported) has been moved to a new abstract type `netket.hilbert.DiscreteHilbert`. Any Hilbert space previously subclassing {ref}`netket.hilbert.AbstractHilbert` should be modified to subclass {ref}`netket.hilbert.DiscreteHilbert` [800](https://github.com/netket/netket/pull/800).

Bug Fixes

* `nn.to_array` and `MCState.to_array`, if `normalize=False`, do not subtract the logarithm of the maximum value from the state [705](https://github.com/netket/netket/pull/705).
* Autoregressive networks now work with Fock space and give correct errors if the hilbert space is not supported [806](https://github.com/netket/netket/pull/806).
* Autoregressive networks are now much (x10-x100) faster [705](https://github.com/netket/netket/pull/705).
* Do not throw errors when calling `operator.get_conn_flattened(states)` with a jax array [764](https://github.com/netket/netket/pull/764).
* Fix bug with the driver progress bar when `step_size != 1` [747](https://github.com/netket/netket/pull/747).

[GitHub commits](https://github.com/netket/netket/compare/v3.0b1...v3.0b2).

New features

* Group Equivariant Neural Networks have been added to `models` [620](https://github.com/netket/netket/pull/620)
* Permutation invariant RBM and Permutation invariant dense layer have been added to `models`
and `nn.linear` [573](https://github.com/netket/netket/pull/573)
* Add the property `acceptance` to `MetropolisSampler`'s `SamplerState`, computing the
MPI-enabled acceptance ratio. [592](https://github.com/netket/netket/pull/592).
* Add `StateLog`, a new logger that stores the parameters of the model during the
optimization in a folder or in a tar file. [645](https://github.com/netket/netket/pull/645)
* A warning is now issued if NetKet detects to be running under `mpirun` but MPI dependencies
are not installed [631](https://github.com/netket/netket/pull/631)
* `operator.LocalOperator`s now do not return a zero matrix element on the diagonal if the whole
diagonal is zero. [623](https://github.com/netket/netket/pull/623).
* `logger.JSONLog` now automatically flushes at every iteration if it does not consume significant
CPU cycles. [599](https://github.com/netket/netket/pull/599)
* The interface of Stochastic Reconfiguration has been overhauled and made more modular. You can now
specify the solver you wish to use, NetKet provides some dense solvers out of the box, and there are
3 different ways to compute the Quantum Geometric Tensor. Read the documentation to learn more about
it. [674](https://github.com/netket/netket/pull/674)
* Unless you specify the QGT implementation you wish to use with SR, we use an automatic heuristic based
on your model and the solver to pick one.
This might affect SR performance. [674](https://github.com/netket/netket/pull/674)


Breaking Changes

* For all samplers, `n_chains` now sets the _total_ number of chains across all MPI ranks. This is a breaking change
compared to the old API, where `n_chains` would set the number of chains on a single MPI rank. It is still possible to
set the number of chains per MPI rank by specifying `n_chains_per_rank` instead of `n_chains`. This change, while breaking
allows us to be consistent with the interface of {class}`variational.MCState`, where `n_samples` is the total number of samples
across MPI nodes.
* `MetropolisSampler.reset_chain` has been renamed to `MetropolisSampler.reset_chains`.
Likewise in the constructor of all samplers.
* Briefly during development releases `MetropolisSamplerState.acceptance_ratio` returned
the percentage (not ratio) of acceptance. `acceptance_ratio` is now deprecated in
favour of the correct `acceptance`.
* `models.Jastrow` now internally symmetrizes the matrix before computing its value [644](https://github.com/netket/netket/pull/644)
* `MCState.evaluate` has been renamed to `MCState.log_value` [632](https://github.com/netket/netket/pull/632)
* `nk.optimizer.SR` no longer accepts keyword argument relative to the sparse solver. Those should be passed
inside the closure or `functools.partial` passed as `solver` argument.
* `nk.optimizer.sr.SRLazyCG` and `nk.optimizer.sr.SRLazyGMRES` have been deprecated and will soon be removed.
* Parts of the `Lattice` API have been overhauled, with deprecations of several methods in favor of a consistent usage of `Lattice.position` for real-space location of sites and `Lattice.basis_coords` for location of sites in terms of basis vectors. `Lattice.sites` has been added, which provides a sequence of `LatticeSite` objects combining all site properties. Furthermore, `Lattice` now provides lookup of sites from their position via `id_from_position` using a hashing scheme that works across periodic boundaries. [703](https://github.com/netket/netket/pull/703) [#715](https://github.com/netket/netket/pull/715)
* `nk.variational` has been renamed to `nk.vqs` and will be removed in a future release.

Bug Fixes

* Fix `operator.BoseHubbard` usage under jax Hamiltonian Sampling [662](https://github.com/netket/netket/pull/662)
* Fix `SROnTheFly` for `R->C` models with non homogeneous parameters [661](https://github.com/netket/netket/pull/661)
* Fix MPI Compilation deadlock when computing expectation values [655](https://github.com/netket/netket/pull/655)
* Fix bug preventing the creation of a `hilbert.Spin` Hilbert space with odd sites and even `S`. [641](https://github.com/netket/netket/pull/641)
* Fix bug [635](https://github.com/netket/netket/pull/635) preventing the usage of `NumpyMetropolisSampler` with `MCState.expect` [#635](https://github.com/netket/netket/pull/635)
* Fix bug [635](https://github.com/netket/netket/pull/635) where the {class}`graph.Lattice` was not correctly computing neighbours because of floating point issues. [#633](https://github.com/netket/netket/pull/633)
* Fix bug the Y Pauli matrix, which was stored as its conjugate. [618](https://github.com/netket/netket/pull/618) [#617](https://github.com/netket/netket/pull/617) [#615](https://github.com/netket/netket/pull/615)