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Change Log

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

v3.1.0 -- 2024-06-17

Added

  • New continuous coordination number compute freud.order.ContinuousCoordination.
  • New methods for conversion of box lengths and angles to/from freud.box.Box.
  • Add copy button to documentation code snippets.
  • Support Numpy 2.0.

Fixed

  • Default value for terminate_after_blocked in FilterRAD.

Removed

  • freud.order.Translational.
  • Support for Python 3.8.

v3.0.0 -- 2024-02-22

Added

  • Coloring plots by polytope area in freud.locality.Voronoi.
  • Neighbor vectors to freud.locality.NeighborLists.

Changed

  • The normalize argument to freud.density.RDF is now normalization_mode.
  • The neighbors argument to env_neighbors for EnvironmentMotifMatch class.
  • The neighbors argument to cluster_neighbors for EnvironmentCluster class.
  • freud.order.Nematic uses orientation vectors instead of quaternions and a nematic director.
  • freud.order.Nematic raises a warning when the zero is vector passed.
  • Remove zero-padding from arrays in freud.environment.EnvironmentCluster and freud.environment.EnvironmentMotifMatch and replace with ragged lists of NumPy arrays.
  • Provide support via GitHub discussions.

Removed

  • The global_search flag in freud.environment.EnvironmentCluster.

v2.13.2 -- 2023-11-27

Added

  • Support for python 3.12

Removed

  • Support for python 3.7

v2.13.1 -- 2023-09-14

Added

  • The gsd.hoomd.Frame class is supported as a system-like input.

Changed

  • Require building with cython>=3.0.2

v2.13.0 -- 2023-05-09

Added

  • Filter neighborlists with freud.locality.FilterSANN and freud.locality.FilterRAD.

Fixed

  • Neighborlists generated by certain compute objects now exist after the compute object is garbage collected.
  • All source files have the freud license header at the top.
  • The compute() method of each compute object returns self.

Changed

  • Documentation renders with the furo theme.

Removed

  • Support for Python 3.6

v2.12.1 -- 2022-12-05

Added

  • Support for Python 3.11.

Fixed

  • n(r) property in freud.density.RDF is now properly normalized by the number of query points.

v2.12.0 -- 2022-11-09

Added

  • Mass dependence in freud.cluster.ClusterProperties.
  • Inertia tensor calculation in freud.cluster.ClusterProperties.

Fixed

  • Compatibility with new namespace for MDAnalysis.coordinates.timestep.Timestep.

v2.11.0 -- 2022-08-09

Added

  • Support for 2D systems in freud.diffraction.StaticStructureFactorDebye.
  • Compilation uses the C++17 standard.

Fixed

  • EnvironmentMotifMatch correctly handles NeighborLists with more neighbors per particle than the motif.

v2.10.0 -- 2022-05-18

Added

  • include_input_points argument to freud.locality.PeriodicBuffer.
  • macos-arm64 binary builds on conda-forge and PyPI.

Changed

  • freud.data.UnitCell.generate_system now generates positions in the same order as the basis positions.

v2.9.0 -- 2022-04-19

Added

  • (breaking) Some freud.diffraction.StaticStructureFactorDebye property names changed to be more descriptive.
  • freud.diffraction.DiffractionPattern now raises an exception when used with non-cubic boxes.

Fixed

  • freud.diffraction.StaticStructureFactorDebye implementation now gives S_k[0] = N.
  • Cython is no longer listed as an install requirement in setup.py.

Removed

  • Custom CMake build type ReleaseWithDocs.

v2.8.0 -- 2022-01-25

Added

  • freud.diffraction.StaticStructureFactorDirect class (unstable) can be used to compute the static structure factor S(k) by sampling reciprocal space vectors.
  • Python 3.10 is supported.
  • Documentation examples are tested with pytest.
  • Use clang-format as pre-commit hook.
  • Add related tools section to the documentation.

Fixed

  • freud.diffraction.DiffractionPattern normalization changed such that S(k=0) = N.
  • Added error checking for r_min, r_max arguments in freud.density.RDF, freud.locality.NeighborList, freud.locality.NeighborQuery, and freud.density.LocalDensity classes.
  • CMake build system only uses references to TBB target.

Changed

  • Re-organized tests for the static structure factor classes.
  • Move util::Histogram<T>::Axes to util::Axes.
  • Use new flake8 plugin flake8-force for linting Cython code.

v2.7.0 -- 2021-10-01

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.
  • Fixed Box.contains to run in linear time, O(num_points).
  • Fixed compilation to pass compiler optimization flags when build type is ReleaseWithDocs (major perf regression since 2.4.1).

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