ChangeLog.md

Change Log

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

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Added

• freud.diffraction.StaticStructureFactorDebye class (unstable) can be used to compute the static structure factor S(k) using the Debye formula.

Fixed

• Updated lambda functions to capture this by reference, to ensure compatibility with C++20 and above.

v2.6.2 -- 2021-06-26

Fixed

• Upgrade to auditwheel 4.0.0 in cibuildwheel to ensure RPATH is patched properly for libfreud.so in Linux wheels.

v2.6.1 -- 2021-06-23

Fixed

• Added missing git submodules to source distribution.

v2.6.0 - 2021-06-22

Added

• Added out option for the wrap, unwrap, make_absolute, and make_fractional methods of Box.
• The Steinhardt and SolidLiquid classes expose the raw qlmi arrays.
• The Steinhardt class supports computing order parameters for multiple l.

Changed

• Improvements to plotting for the DiffractionPattern.
• Wheels are now built with cibuildwheel.

Fixed

• Fixed/Improved the k values and vectors in the DiffractionPattern (more improvement needed).
• Fixed incorrect computation of Steinhardt averaged quantities. Affects all previous versions of freud 2.
• Fixed documented formulas for Steinhardt class.
• Fixed broken arXiv links in bibliography.

v2.5.1 - 2021-04-06

Added

• The compute method of DiffractionPattern class has a reset argument.

Fixed

• Documentation on ReadTheDocs builds and renders.

v2.5.0 - 2021-03-16

Changed

• NeighborList filter method has been optimized.
• TBB 2021 is now supported (removed use of deprecated TBB features).
• Added new pre-commit hooks for black, isort, and pyupgrade.
• Testing framework now uses pytest.

v2.4.1 - 2020-11-16

Fixed

• Python 3.8 builds with Windows MSVC were broken due to an unrecognized CMake compiler option.
• Fixed broken documentation by overriding scikit-build options.
• RPATH on Linux is now set correctly to find TBB libraries not on the global search path.
• 2D box image calculations now return zero for the image z value.
• Fixed wrong attribute name in EnvironmentCluster.plot.

v2.4.0 - 2020-11-09

Added

• The Box class has a method contains to determine particle membership in a box.
• NeighborList class exposes num_points and num_query_points attributes.
• compute method of GaussianDensity class has a values argument.
• Support for pre-commit hooks.
• Python 3.9 is supported.

Changed

• NeighborList raises a ValueError instead of a RuntimeError if provided invalid constructor arguments.
• freud now builds using scikit-build (requires CMake).

Deprecated

• freud.order.Translational

Fixed

• Source distributions now include Cython source files.
• Hexatic order parameter (unweighted) normalizes by number of neighbors instead of the symmetry order k.
• Particles with an i-j normal vector of [0, 0, 0] are excluded from 2D Voronoi NeighborList computations for numerical stability reasons.
• Memory leak in makeDefaultNlist function where a NeighborList was being allocated and not freed.

v2.3.0 - 2020-08-03

Added

• Support for garnett 0.7.
• Custom NeighborLists can be created from a set of points using from_points. Distances will be calculated automatically.
• The Box class has methods compute_distances and compute_all_distances to calculate distances between arrays of points and query points.
• Hexatic can now compute 2D Minkowski Structure Metrics, using weighted=True along with a Voronoi NeighborList.
• Examples have been added to the Cluster, Density, Environment, and Order Modules.
• Module examples have been integrated with doctests to ensure they are up to date with API.
• SphereVoxelization class in the density module computes a grid of voxels occupied by spheres.
• freud.diffraction.DiffractionPattern class (unstable) can be used to compute 2D diffraction patterns.

Changed

• Cython is now a required dependency (not optional). Cythonized .cpp files have been removed.
• An instance of GaussianDensity cannot compute 3D systems if it has been previously computed 2D systems.

Fixed

• Histogram bin locations are computed in a more numerically stable way.
• Improved error handling of Cubatic input parameters.
• PMFTs are now properly normalized such that the pair correlation function tends to unity for an ideal gas.
• PMFTXYT uses the correct orientations when points and query_points differ.
• GaussianDensity Gaussian normalization in 2D systems has been corrected.

Removed

• Python 3.5 is no longer supported. Python 3.6+ is required.

v2.2.0 - 2020-02-24

Added

• NeighborQuery objects can now create NeighborLists with neighbors sorted by bond distance.
• LocalDescriptors compute takes an optional maximum number of neighbors to compute for each particle.

Fixed

• Corrected calculation of neighbor distances in the Voronoi NeighborList.
• Added finite tolerance to ensure stability of 2D Voronoi NeighborList computations.

v2.1.0 - 2019-12-19

Added

• The Box class has methods center_of_mass and center for periodic-aware center of mass and shifting points to center on the origin.

Changed

• The make_random_box system method no longer overwrites the NumPy global random number generator state.
• The face_orientations argument of PMFTXYZ has been renamed to equiv_orientations and must be provided as an Mx4 array, where M is the number of symmetrically equivalent particle orientations.
• Improved documentation about query modes.
• The Voronoi class uses smarter heuristics for its voro++ block sizes, resulting in significant performance gains for large systems.

Fixed

• The from_box method correctly passes user provided dimensions to from_matrix it if is called.
• Correctly recognize Ovito DataCollection objects in from_system.
• Corrected ClusterProperties calculation of centers of mass in specific systems.
• Set z positions to 0 for 2D GSD systems in from_system.
• PMFTXY and PMFTXYZ index into query orientations using the query point index instead of the point index.

v2.0.1 - 2019-11-08

Added

• Rewrote development documentation to match the conventions and logic in version 2.0 of the code.

Fixed

• Automatic conversion of 2D systems from various data sources.
• Mybinder deployment works with freud v2.0.
• Minor errors in freud-examples have been corrected.

v2.0.0 - 2019-10-31

Added

• Ability to specify "system-like" objects that contain a box and set of points for most computes.
• NeighborLists and query arguments are now accepted on equal footing by compute methods that involve neighbor finding via the neighbors=... argument.
• Extensive new documentation including tutorial for new users and reference sections on crucial topics.
• Standard method for preprocessing arguments of pair computations.
• New internal ManagedArray object that allows data persistence and improves indexing in C++.
• Internal threaded storage uses the standard ManagedArray object.
• C++ Histogram class to standardize n-dimensional binning and simplify writing new methods.
• Upper bound r_max option for number of neighbors queries.
• Lower bound r_min option for all queries.
• Steinhardt now supports l = 0, 1.
• C++ BondHistogramCompute class encapsulates logic of histogram-based methods.
• 2D PMFTs accept quaternions as well as angles for their orientations.
• ClusterProperties computes radius of gyration from the gyration tensor for each cluster.
• freud.data module for generating example particle systems.
• Optional normalization for RDF, useful for small systems.
• plot() methods for NeighborQuery and Box objects.
• Added support for reading system data directly from MDAnalysis, garnett, gsd, HOOMD-blue, and OVITO.
• Various validation tests.

Changed

• All compute objects that perform neighbor computations now use NeighborQuery internally.
• Neighbor-based compute methods now accept NeighborQuery (or "system-like") objects as the first argument.
• All compute objects that perform neighbor computations now loop over NeighborBond objects.
• Renamed (ref_points, points) to (points, query_points) to clarify their usage.
• Bond vector directionality is standardized for all computes that use it (always from query_point to point).
• Standardized naming of various common parameters across freud such as the search distance r_max.
• Accumulation is now performed with compute(..., reset=False).
• Arrays returned to Python persist even after the compute object is destroyed or resizes its arrays.
• All class attributes are stored in the C++ members and accessed via getters wrapped as Python properties.
• Code in the freud.common has been moved to freud.util.
• NeighborQuery objects require z == 0 for all points if the box is 2D.
• Renamed several Box methods, box.ParticleBuffer is now locality.PeriodicBuffer.
• Cluster now finds connected components of the neighbor graph (the cluster cutoff distance is given through query arguments).
• Refactored and renamed attributes of Cluster and ClusterProperties modules.
• CorrelationFunction of complex inputs performs the necessary conjugation of the values before computing.
• Updated GaussianDensity constructor to accept tuples as width instead of having 2 distinct signatures.
• RDF bin centers are now strictly at the center of bins.
• RDF no longer performs parallel accumulation of cumulative counts (provided no performance gains and was substantially more complex code).
• MatchEnv has been split into separate classes for the different types of computations it is capable of performing, and these classes all use v2.0-style APIs.
• The Voronoi class was rewritten to use voro++ for vastly improved performance and correctness in edge cases.
• Improved Voronoi plotting code.
• Cubatic uses standard library random functions instead of Saru (which has been removed from the repo).
• APIs for several order parameters have been standardized.
• SolidLiquid order parameter has been completely rewritten, fixing several bugs and simplifying its C++ code.
• Steinhardt uses query arguments.
• PMFTXY2D has been renamed to PMFTXY.
• Removed unused orientations from PMFTXYZ and PMFTXY.
• PMFTXY and PMFTXYZ include the phase space volume of coordinates that are implicitly integrated out (one angle in PMFTXY, and three angles in PMFTXYZ).
• Documentation uses automodule instead of autoclass.
• Citations are now included using bibtex and sphinxcontrib-bibtex.

Fixed

• Removed all neighbor exclusion logic from all classes, depends entirely on locality module now.
• Compute classes requiring 2D systems check the dimensionality of their input boxes.
• LinkCell nearest neighbor queries properly check the largest distance found before proceeding to next shell.
• LocalDensity uses the correct number of points/query points.
• RDF no longer forces the first bin of the PCF and first two bins of the cumulative counts to be 0.
• Steinhardt uses the ThreadStorage class and properly resets memory where needed.

Removed

• The freud.util module.
• Python 2 is no longer supported. Python 3.5+ is required.
• LinkCell no longer exposes the internals of the cell list data structure.
• Cubatic no longer returns the per-particle tensor or the constant r4 tensor.

v1.2.2 - 2019-08-15

Changed

• LocalWl return values are real instead of complex.

Fixed

• Fixed missing Condon-Shortley phase affecting LocalWl and Steinhardt Wl computations. This missing factor of -1 caused results for third-order (Wl) Steinhardt order parameters to be incorrect, shown by their lack of rotational invariance. This problem was introduced in v0.5.0.
• Reduced various compiler warnings.
• Possible out of bounds LinkCell access.
• RDF plots now use the provided ax object.

v1.2.1 - 2019-07-26

Changed

• Optimized performance for RotationalAutocorrelation.
• Added new tests for cases with two different sets of points.

Fixed

• Fixed bug resulting in the LocalQlNear and LocalWlNear class wrongly using a hard instead of a soft cut-off, which may have resulted in an incorrect number of neighbors. This would cause incorrect results especially for systems with an average n-th nearest-neighbor distance smaller than rmax. This problem was introduced in v0.6.4.
• Fixed duplicate neighbors found by LinkCell NeighborQuery methods
• Corrected data in LocalQl, LocalWl documentation example
• Repeated Cubatic Order Parameter computations use the correct number of replicates.
• Repeated calls to LocalQl.computeNorm properly reset the underlying data.
• Clarified documentation for LocalBondProjection and MSD

v1.2.0 - 2019-06-27

Added

• Added .plot() method and IPython/Jupyter PNG representations for many classes.
• AttributeError is raised when one tries to access an attribute that has not yet been computed.
• Added freud.parallel.getNumThreads() method.
• New examples for integration with simulation and visualization workflows.

Changed

• Removed extra C++ includes to speed up builds.
• The C++ style is now based on clang-format.
• Refactored C++ handling of thread-local storage.
• SolLiq order parameter computations are parallelized with TBB.
• Optimized performance of Voronoi.
• Several Box properties are now given as NumPy arrays instead of tuples.
• Box methods handling multiple vectors are parallelized with TBB.
• Eigen is now used for all matrix diagonalizations.

Fixed

• Calling setNumThreads works correctly even if a parallel compute method has already been called.
• Fixed segfault with chained calls to NeighborQuery API.
• Correct exclude_ii logic.

Removed

• Removed outdated computeNList function from LocalDescriptors.

v1.1.0 - 2019-05-23

Added

• New neighbor querying API to enable reuse of query data structures (see NeighborQuery class).
• AABBQuery (AABB tree-based neighbor finding) added to public API.
• Ability to dynamically select query method based on struct of arguments.
• All compute objects have __repr__ and __str__ methods defined.
• NeighborLists can be accessed as arrays of particle indices via __getitem__.
• ParticleBuffer supports different buffer sizes in x, y, z.
• Box makeCoordinates, makeFraction, getImage now support 2D arrays with multiple points.

Changed

• Use constant memoryviews to prevent errors with read-only inputs.
• LocalQl is now parallelized with TBB.
• Optimized performance of RotationalAutocorrelation.
• NematicOrderParameter uses SelfAdjointEigenSolver for improved stability.
• Added build flags for Cython debugging.
• LinkCell computes cell neighbors on-demand and caches the results for significant speedup.

Fixed

• Corrected type of y_max argument to PMFTXY2D from int to float.
• Reduce logging verbosity about array conversion.
• Fixed number of threads set upon exiting the NumThreads context manager.
• Corrected quaternion array sizes and added missing defaults in the documentation.
• Empty ParticleBuffers return valid array shapes for concatenation.
• Wheels are built against NumPy 1.10 for improved backwards compatibility.

v1.0.0 - 2019-02-08

Added

• Freshly updated README and documentation homepage.
• Moved to GitHub.
• New msd.MSD class for computing mean-squared displacements.
• New order.RotationalAutocorrelation class.
• Cython memoryviews are now used to convert between C++ and Cython.
• New and improved freud logo.
• Internal-only AABB tree (faster for many large systems, but API is unstable).

Changed

• Improved module documentation, especially for PMFT.
• Refactored internals of LocalQl and related classes.
• Upgraded ReadTheDocs configuration.

Fixed

• Improved CubaticOrderParameter handling of unusable seeds.
• Fixed box error in NearestNeighbors.

Removed

• All long-deprecated methods and classes were removed.
• Bond module removed.

v0.11.4 - 2018-11-09

Added

• Builds are now tested on Windows via Appveyor, though officially unsupported.

Fixed

• Multiple user-reported issues in setup.py were resolved.
• C++ errors are handled more cleanly as Python exceptions.
• Fixed bug in SolLiq box parameters.
• Documentation corrected for NeighborList.
• Various minor compiler errors on Windows were resolved.

v0.11.3 - 2018-10-18

Fixed

• Linux wheels are now pushed to the real PyPI server instead of the test server.
• macOS deployment pyenv requires patch versions to be specified.

v0.11.2 - 2018-10-18

Fixed

• Error in Python versions in macOS automatic deployment.

v0.11.1 - 2018-10-18

Added

• PyPI builds automatically deploy for Mac and Linux.

Changed

• macOS deployment target is now 10.12 instead of 10.9 to ensure TBB compatibility.
• Unwrapping positions with images is now vectorized.
• Minor documentation fixes.

Fixed

• TBB includes were not always detected correctly by setup.py.

v0.11.0 - 2018-09-27

Added

• Example notebooks are now shown in the documentation.
• Many unit tests were added.
• New class: freud.environment.LocalBondProjection.
• freud is now available on the Python Package Index (PyPI) as freud-analysis.

Changed

• Documentation was revised for several modules.
• New class freud.box.ParticleBuffer was adapted from the previous VoronoiBuffer to include support for triclinic boxes.
• The bond and pmft modules verify system dimensionality matches the coordinate system used.
• Minor optimization: arrays are reduced across threads only when necessary.

Fixed

• NumPy arrays of lengths 2, 3, 6 are now correctly ducktyped into boxes.
• Removed internal use of deprecated code.
• C++ code using uint has been changed to unsigned int, to improve compiler compatibility.

Deprecated

• In freud.locality.LinkCell, computeCellList() has been replaced by compute().

Removed

• The kspace module has been removed.

v0.10.0 - 2018-08-27

Added

• Codecov to track test coverage.
• Properties were added to MatchEnv, AngularSeparation, Cubatic/Nematic order parameters, Voronoi.

Changed

• freud uses Cython and setup.py instead of CMake for installation.
• Properties (not get functions) are the official way to access computed results.
• Interface module has been improved significantly.
• density.FloatCF, density.ComplexCF, order parameter documentation is improved.
• Many compute methods now use points, orientations from ref_points, ref_orientations if not provided.
• Reset methods have been renamed to reset.

Fixed

• kspace module had a missing factor of pi in the volume calculation of FTsphere.

Deprecated

• Get functions have been deprecated.
• Setter methods have been deprecated.
• Reduce methods are called internally, so the user-facing methods have been deprecated.

Removed

• GaussianDensity.resetDensity() is called internally.

v0.9.0 - 2018-07-30

Added

• Allow specification of rmin for LocalWl (previously was only possible for LocalQl).
• New environment module. Contains classes split from the order module.
• Box duck-typing: methods accepting a box argument will convert box-like objects into freud.box.Box objects.
• All Python/Cython code is now validated with flake8 during continuous integration.

Changed

• Refactoring of LocalQl and LocalWl Steinhardt order parameters.
• MatchEnv uses BiMap instead of boost::bimap.
• All boost shared_arrays have been replaced with std::shared_ptr.
• Replaced boost geometry with standard containers in brute force registration code.
• NearestNeighbors automatically uses ref_points as the points if points are not provided.
• Box::unwrap and Box::wrap return the vectors after updating.
• Everything other than true order parameters moved from Order module to Environment module.
• Use lambda function in parallel_for in CorrelationFunction.
• Tests no longer depend on nose. Python's unittest is used instead.
• Vastly improved documentation clarity and correctness across all modules.
• Docstrings are now in Google format. The developer guide offers guidance for module authors.

Fixed

• Fixed LocalDescriptors producing NaN's in some cases.
• Fixed cython passing C++ the default argument force_resize to NeighborList::resize.
• Standardize freud.common.convert_array error message.

Removed

• Boost is no longer needed to build or run freud.
• Removed undocumented shapesplit module.
• Removed extra argument from TransOrderParam in C++.

v0.8.2 - 2018-06-07

Added

• Allow specification of maximum number of neighbors to use when computing LocalDescriptors

Changed

• Using the default neighbor list with LocalDescriptors requires specifying the precompute argument
• Updated and improved tests
• Cleaned AngularSeparation module and documentation

v0.8.1 - 2018-05-09

Fixed

• Memory issue in nlist resolved

v0.8.0 - 2018-04-06

Added

• Voronoi neighborlist now includes periodic neighbors
• Voronoi neighborlist computes weight according to the facet area in 3D
• Box module exposes getImage(vec)
• Voronoi module can compute and return cell volumes/areas

Changed

• Cluster module supports box argument in compute methods.
• Refactored C++ code to reduce extraneous #includes
• Refactored PMFT code
• Refactored box module to remove unused methods
• Resolved bug in kspace.AnalyzeSFactor3D

Deprecated

• Box module getCoordinates() in favor of duplicate box.makeCoordinates()

Removed

• Removed deprecated API for ComplexWRDF and FloatWRDF

v0.7.0 - 2018-03-02

Added

• Added nematic order parameter
• Added optional rmin argument to density.RDF
• Added credits file
• Wrote development guide
• Added Python interface for box periodicity

Changed

• Various bug fixes and code cleaning
• Fixed all compile-time warnings
• Ensured PEP 8 compliance everywhere
• Minimized boost dependence
• Many documentation rewrites
• Wrote development guide
• Made tests deterministic (seeded RNGs)
• Removed deprecated Box API warnings
• Standardized numpy usage

v0.6.4 - 2018-02-05

• Added a generic neighbor list interface
• Set up CircleCI for continuous integration
• Set up documentation on ReadTheDocs
• Added bumpversion support
• Various bug fixes
• Added python-style properties for accessing data
• Fixed issues with voronoi neighbor list

v0.6.0

• trajectory module removed
• box constructor API updated
• PMFTXYZ API updated to take in more quaternions for face_orientations, or have a sensible default value
• NearestNeighbors:
  • over-expanding box fixed
  • strict rmax mode added
  • ability to get wrapped vectors added
  • minor updates to C-API to return full lists from C
• Addition of Bonding modules
• Addition of local environment matching

v0.5.0

• Replace boost::shared_array with std::shared_ptr (C++ 11)
• Moved all tbb template classes to lambda expressions
• Moved trajectory.Box to box.Box
• trajectory is deprecated
• Fixed Bond Order Diagram and allow for global, local, or orientation correlation
• Added python-level voronoi calculation
• Fixed issues with compiling on OS X, including against conda python installs
• Added code to compute bonds between particles in various coordinate systems

v0.4.1

• PMFT: Fixed issue involving binning of angles correctly
• PMFT: Fixed issue in R12 which prevented compute/accumulate from being called with non-flattened arrays
• PMFT: Updated xyz api to allow simpler symmetric orientations to be supplied
• PMFT: Updated pmftXY2D api
• PMFT: Histograms are properly normalized, allowing for comparison between systems without needing to "zero" the system
• fsph: Added library to calculate spherical harmonics via cython
• Local Descriptors: Uses fsph, updates to API
• Parallel: Added default behavior to setNumThreads and added context manager

v0.4.0

• Add compiler flags for C++11 features
• Added Saru RNG (specifically for Cubatic Order Parameter, available to all)
• Cubatic Order Parameter
• Rank 4 tensor struct
• Environment Matching/Cluster Environment
• Shape aware fourier transform for structure factor calculation
• Added deprecation warnings; use python -W once to check warnings
• Added Change Log
• Moved all documentation in Sphinx; documentation improvements
• C++ wrapping moved from Boost to Cython
• Itercell only available in python 3.x
• PMFT:
  • XY
  • XYZ with symmetry, API updated
  • R, T1, T2
  • X, Y, T2
• viz removed (is not compatible with cython)

No change logs prior to v0.4.0