Changelog

The garnett package follows semantic versioning.

Version 0.5

[0.5.0] – 2019-08-20

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• Tests for Python 2 are no longer updated (Python 2 support will be dropped in the next minor release).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

[0.4.1] – 2017-08-23

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

[0.3.9] – 2017-01-30

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

[0.2.1] – 2016-07-10

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

[0.1.9] – 2016-04-09

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