GSD/HOOMD file reader

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User interface of the GSD file reader, which appears as part of a pipeline’s file source.

Binary file format written by the HOOMD-blue molecular dynamic simulation code. For a specification of the file format, see the GSD (General Simulation Data) website.

OVITO loads all data chunks from the following categories of a GSD file:

In addition, OVITO loads logged data from the GSD file, either as global attributes, user-defined particle properties, or user-defined bond properties. See Log data for more details.

Particle shapes

The file reader supports shape definitions in a GSD file and automatically generates a user-defined shape for each particle type. Currently, the following GSD shape types are supported:

  • Sphere

  • Ellipsoid

  • Polygon

  • ConvexPolyhedron (with 1, 2, 4, or more vertices)

  • Mesh

  • SphereUnion

For shape types with a positive rounding radius, OVITO generates a tessellated mesh representation of the shape. The Shape rounding resolution parameter controls the quality of the generated mesh (an integer value in the range 1 to 6).

Log data

OVITO loads logged data from the GSD file found in data chunks under the log/ directory:

  • log/*: Loaded as global attributes

  • log/particles/*: Loaded as user-defined particle properties

  • log/bonds/*: Loaded as user-defined bond properties

  • log/angles/*: Loaded as user-defined angle properties

  • log/dihedrals/*: Loaded as user-defined dihedral properties

  • log/impropers/*: Loaded as user-defined improper properties

This includes data chunks located in nested sub-folders of the listed root directories.

User-defined particle properties with three vector components of type float are automatically given a Vectors visual element to allow easy visualization.

Python parameters

The file reader accepts the following optional keyword parameters in a call to the import_file() or load() Python functions.

import_file(location, resolution=4)
Parameters:

resolution (int) – Controls the resolution of shape meshes generated by the file reader if the GSD file contains particle shape definitions of type Polygon or ConvexPolyhedron with a non-zero rounding radius. The resolution value must be in the range 1 to 6 – with higher values yielding smoother corners but also resulting in a more detailed mesh, which will lead to longer rendering times.