Changelog

The garnett package follows semantic versioning.

Unreleased Changes

Fixed

  • Fixed frame ordering for some trajectories read by GetarFileReader. Previously frames were ordered pseudo-arbitrarily depending on a bisection using lexicographic ordering of strings, rather than the key order specified by the gtar library.

Added

  • Added support to GetarFileWriter for writing trajectories containing frames with some missing per-particle quantities.

Version 0.7

Fixed

  • Corrected package dependencies.

[0.7.0] – 2020-03-18

Added

  • Added ability to read _space_group_symop_operation_xyz keys in CIF files.
  • Added to_hoomd_snapshot method to Frame objects. Replaces the deprecated make_snapshot and copyto_snapshot methods.
  • The CIF reader supports a broader range of _atom_site_label values that match component 0 as specified here.
  • Enabled type_shape for SphereUnionShape class.
  • Added ability to read getar files with dynamic properties (such as type_shapes.json) stored at a different period than positions.
  • Added box property to Trajectory objects.
  • Added N property to Frame objects.

Changed

  • Updated GSD reader to use the GSD v2 API.
  • Changed behavior of types, typeid, type_shapes to match HOOMD conventions.
  • Shapes can still be read from GSD via HOOMD-HPMC state but shapes are always written to type_shapes instead of the HPMC state.
  • PosFileWriter requires the number of type_shapes to match the number of types.

Fixed

  • Fixed finding nearest image when applying space group operations to CIF files. The meaning of the tolerance parameter is also adjusted to be absolute (in units of fractional coordinates), rather than relative.

Deprecated

  • The following Frame and Trajectory attributes have been deprecated:
    • positions (now position)
    • orientations (now orientation)
    • velocities (now velocity)
    • shapedef dict has been replaced by type_shapes list. Until this feature is removed, altering shape definitions is only supported if the entire dictionary is set at once.
  • The following Frame methods have been deprecated:
    • make_snapshot (use to_hoomd_snapshot())
    • copyto_snapshot (use to_hoomd_snapshot(snap)
  • The following trajectory module-level functions have been deprecated:
    • make_hoomd_blue_snapshot (use frame.to_hoomd_snapshot())
    • copyfrom_hoomd_blue_snapshot (use Frame.from_hoomd_snapshot(snap))
    • copyto_hoomd_blue_snapshot (use frame.to_hoomd_snapshot(snap))

Removed

  • The Frame.frame_data property and FrameData class have been removed from the public API.

Version 0.6

Fixed

  • Fix installation instructions with pip.
  • Removed unnecessary extra headers from changelog.

[0.6.0] – 2019-11-04

Added

  • Added showEdges to skipped fields when reading POS files.
  • Added to_plato_scene() method to quickly visualize Frame objects.
  • Added support for the GSD shape visualization specification.

Changed

  • GSD and GTAR writers now output shape information that adheres to the GSD shape visualization specification.

Removed

  • Dropped Python 2 support.

Fixed

  • Fix minor bug in PosFileWriter where default shape definition was incorrectly written.

Version 0.5

Added

  • Added rowan as a dependency.
  • Add GETAR file reader/writer.
  • Add shape_dict representation to Shape classes.
  • Add support for particle properties:
    • mass
    • charge
    • diameter
    • image
    • moment of inertia
    • angular momentum
  • Add support for reading/writing shapes in GSD via HOOMD-HPMC state.
  • Add universal reader/writer with format detection.
  • Add orientable attribute to spheres.
  • Extend list of supported shape classes:
    • ellipsoid
    • polygon
    • spheropolygon
    • convex polyhedron
    • convex spheropolyhedron

Changed

  • Raise AttributeError if accessing a frame or trajectory property not defined in the file.
  • Rename several existing shape classes.
  • Improve unit test coverage.
  • Revise documentation.
  • Move shape definitions to separate module.

Deprecated

  • Tests for Python 2 are no longer updated (Python 2 support will be dropped in the next minor release).

Removed

  • Remove acceleration as supported property.
  • Remove the read_gsd_shape_data flag from GSD reader.

Version 0.4

Fixed

  • Fix minor bug related to QR check for 2d boxes.

[0.4.0] – 2017-06-26

Added

  • Add readers/writers:
    • CIF reader
    • GSD writer
  • Support shape definitions:
    • spheropolyhedron
    • polyunion
    • convex polyhedron union
  • Add gf2pos script - convert to pos-file from any supported format.
  • Add shape definitions to GetarFileReader.
  • Interpret the pos-file rotation key word.

Changed

  • GetarFileReader skips records that have a non-empty group field.
  • Improve algorithm for the normalization of frames with non-standard box.
  • Various documentation updates.

Version 0.3

Added

  • The GSDReader now reads velocities.
  • Support PolyV shape definitions.

Changed

  • Update documentation concerning the conversion of rotations from quaternions to euler angles.

Fixed

  • Fix bug related to trajectory arrays when slicing the array.

[0.3.8] – 2016-12-21

Fixed

  • Hot fix: Negative euler angles were not read correctly in skewed boxes using the DCDFileReader.

[0.3.7] – 2016-11-07

Added

  • Add the whence argument to the file format’s seek method.

Fixed

  • Fix bug in DCDfilereader leading to incorrect box dimensions to be read for skewed boxes. Cubic or squared boxes are not affected.

[0.3.6] – 2016-10-20

Fixed

  • Fix quaternion to euler angle conversion example in the DCD file reader documentation.

[0.3.5] – 2016-09-20

Changed

  • GSDHOOMDFileReader uses the native GSD library if installed.
  • Reduced warning verbosity.

Fixed

  • Fix bug that caused the GSDHOOMDFileReader to ignore dimensions specified in the GSD file.

[0.3.4] – 2016-09-08

Added

  • Support velocities in HOOMD-blue XML files.
  • Support SphereUnionShape in PosFileReader.

Changed

  • Support Pos-Files using the keyword ‘box’ instead of ‘boxMatrix’

Fixed

  • Fix bug in PosFileReader which occured with non-standard pos-file in python 3.5
  • Fix bug, which occured when constructing frames from raw frames using box instances instead of a box matrix.

[0.3.3] – 2016-07-19

Fixed

  • Fix bug related to 2-dimensional systems and a box z-dimensions not equal to 1.

[0.3.2] – 2016-07-15

Added

  • Add trajectory.N, trajectory.type and trajectory.type_ids as an alternative mode to access frame length and type information.

Fixed

  • Fix bug in GSDHOOMDFileReader when not providing template frame.

[0.3.1] – 2016-07-08

Changed

  • Update the GSD hoomd module.

[0.3.0] – 2016-07-06

Added

  • Provide a highly optimized cythonized DCDFileReader.
  • Allow trajectory data acess via coherent numpy arrays.
  • Make snapshot creation and copying HOOMD-blue 2.0 compatible.

Changed

  • Update the GSD module.
  • Improve the Box class documentation.
  • Overall improvement of the documentation.

Fixed

  • Fix and optimize the pure-python DCDFileReader.

Version 0.2

Fixed

  • Fix an issue with injavis pos-files causing parser errors.

[0.2.0] – 2016-04-28

Fixed

  • Fix HOOMD-blue snapshot type issue.

Version 0.1

Added

  • Add GSDHoomdFileReader.

Fixed

  • Fix type issue in HoomdBlueXMLFileReader.

[0.1.8] – 2016-04-04

Added

  • Add HoomdBlueXMLFileReader.
  • Add DCDFileReader.
  • Add CifFileWriter.
  • Add GetarFileReader.

Fixed

  • Fix type issue in DCD.

[0.1.6] – 2016-01-28

Changed

  • Extend FileFormat API to increase file-like compatibility.

Fixed

  • Fixed box_matrix calculation.

[0.1.5] – 2016-01-11

Changed

  • Frames only loaded into memory on demand.
  • Improved trajectory iteration logic.

No change logs prior to v0.1.5