Changelog¶
The garnett package follows semantic versioning.
Version 0.7¶
[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 toFrame
objects. Replaces the deprecatedmake_snapshot
andcopyto_snapshot
methods. - The CIF reader supports a broader range of
_atom_site_label
values that match component 0 as specified here. - Enabled
type_shape
forSphereUnionShape
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 toTrajectory
objects. - Added
N
property toFrame
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 oftype_shapes
to match the number oftypes
.
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
andTrajectory
attributes have been deprecated:positions
(nowposition
)orientations
(noworientation
)velocities
(nowvelocity
)shapedef
dict has been replaced bytype_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
(useto_hoomd_snapshot()
)copyto_snapshot
(useto_hoomd_snapshot(snap)
- The following
trajectory
module-level functions have been deprecated:make_hoomd_blue_snapshot
(useframe.to_hoomd_snapshot()
)copyfrom_hoomd_blue_snapshot
(useFrame.from_hoomd_snapshot(snap)
)copyto_hoomd_blue_snapshot
(useframe.to_hoomd_snapshot(snap)
)
Removed¶
- The
Frame.frame_data
property andFrameData
class have been removed from the public API.
Version 0.6¶
[0.6.1] – 2019-11-05¶
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 visualizeFrame
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¶
[0.5.0] – 2019-08-20¶
Added¶
- Added rowan as a dependency.
- Add GETAR file reader/writer.
- Add
shape_dict
representation toShape
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¶
[0.4.0] – 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
inPosFileReader
.
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
andtrajectory.type_ids
as an alternative mode to access frame length and type information.
Fixed¶
- Fix bug in
GSDHOOMDFileReader
when not providing template frame.
[0.3.0] – 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¶
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.