GSD/HOOMD file reader — OVITO User Manual 3.16.0 documentation

# GSD/HOOMD file reader

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 dynamics 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:

> - Configuration: Simulation cell definition

> - Particle data: Particle properties

> - Bond data: Bonded interactions

> - Angle data: Angular interactions

> - Dihedral data: Dihedral interactions

> - Improper data: Improper interactions

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.