This is the API documentation for all readers and writers provided by garnett.

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Automatic reader/writer¶

garnett.read(filename_or_fileobj, template=None, fmt=None)[source]¶

This function reads a file and returns a trajectory, autodetecting the file format unless fmt is specified.

Return type:
Parameters:	filename_or_fileobj (string or file object) – Filename to read. template (string) – Optional template for the GSDHOOMDFileReader. fmt (string) – File format, one of ‘gsd’, ‘gtar’, ‘pos’, ‘cif’, ‘dcd’, ‘xml’(default: None, autodetected from filename_or_fileobj)
Returns:	Trajectory read from the file.

garnett.write(traj, filename_or_fileobj, fmt=None)[source]¶

This function writes a trajectory to a file, autodetecting the file format unless fmt is specified.

Parameters:	traj (`Trajectory`) – Trajectory to write. filename_or_fileobj (string or file object) – Filename to write. fmt (string) – File format, one of ‘gsd’, ‘gtar’, ‘pos’, ‘cif’(default: None, autodetected from filename_or_fileobj)

General API¶

Readers and writers are defined in the reader and writer modules.All readers and writers work with file-like objects and use the following API:

Important

Some readers and writers work with binary files, which means that when opening those files for reading or writing you need to use the rb or wb mode.This applies for example to DCD-files:

File Formats¶

This table outlines the supported properties of each format reader and writer.

Format	Position	Box	Orientation	Velocity	Shape	Additional Properties (See below)
POS	RW	RW	RW	N/A+	RW	N/A
GSD	RW	RW	RW	RW	RW	RW
GTAR	RW	RW	RW	RW	RW	RW
CIF	RW	RW	N/A	N/A	N/A	N/A
DCD	R	R	R	R	N/A	N/A
XML	R	R	R	R	N/A	N/A

RW indicates garnett can read and write on this format.
R indicates garnett can only read.
N/A indicates the format does not support storing this property.
Additional Properties:
- Mass
- Charge
- Diameter
- Angular momentum
- Moment of inertia
- Image

The following collection of readers and writers is ordered by different file formats.

POS Files¶

The POS format is a non-standardized text-based format which is human-readable, but very inefficient for storing of trajectory data.The format is used as primary input/output format for the injavis visualization tool.HOOMD-blue provides a writer for this format, which is classified as deprecated since version 2.0.

class garnett.reader.PosFileReader(precision=None)[source]¶

POS-file reader for the Glotzer Group, University of Michigan.

Authors: Carl Simon Adorf, Richmond Newmann

Parameters:	precision (int) – The number of digits toround floating-point values to.

read(stream, default_type='A')[source]¶

Read text stream and return a trajectory instance.

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Parameters:	stream (A file-like textstream.) – The stream, which contains the posfile. default_type (str) – The default particle type forposfile dialects without type definition.

class garnett.writer.PosFileWriter(rotate=False)[source]¶

POS-file writer for the Glotzer Group, University of Michigan.

Author: Carl Simon Adorf

Parameters:	rotate (bool) – Rotate the system into the view rotation instead of addingit to the metadata with the ‘rotation’ keyword.

dump(trajectory)[source]¶

Serialize trajectory into pos-format.

Parameters:	trajectory (`Trajectory`) – The trajectory to serialize.
Return type:	str

write(trajectory, file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)[source]¶

Serialize a trajectory into pos-format and write it to file.

Parameters:	trajectory (`Trajectory`) – The trajectory to serialize file – A file-like object.

GSD (HOOMD-blue schema)¶

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The GSD format is a highly efficient and versatile binary format for storing and reading trajectory data.HOOMD-blue provides a writer for this format.

See also: http://gsd.readthedocs.io

class garnett.reader.GSDHOOMDFileReader[source]¶

HOOMD-blue GSD file reader for the Glotzer Group, University of Michigan.

Author: Carl Simon Adorf

This class provides a wrapper for the trajectory readerimplementation as part of the gsd package.

A gsd file may not contain all shape information.To provide additional information it is possibleto pass a frame object, whose propertiesare copied into each frame of the gsd trajectory.

The example is given for a HOOMD-blue XML frame:

About the read_gsd_shape_data parameter: This parameter was removed. By default,: shape information is read from a passed frame object, if oneprovided. Otherwise, shape information is read from the gsd file.

read(stream, frame=None)[source]¶

Read binary stream and return a trajectory instance.

Parameters:	stream (A file-like binary stream) – The stream, which contains the gsd-file. frame (`trajectory.Frame`) – A frame containing shape informationthat is not encoded in the GSD-format. By default,shape information is read from the passed frame object,if one provided. Otherwise, shape informationis read from the gsd file.