Source code for gmso.formats.gsd

"""Write GSD files from GMSO topologies."""

from __future__ import division

from gmso.external.convert_hoomd import to_gsd_snapshot
from gmso.formats.formats_registry import saves_as
from import has_gsd

__all__ = ["write_gsd"]

if has_gsd:
    import gsd.hoomd

[docs] @saves_as(".gsd") def write_gsd( top, filename, base_units=None, rigid_bodies=None, shift_coords=True, write_special_pairs=True, ): """Output a GSD file (HOOMD v3 default data format). The `GSD` binary file format is the native format of HOOMD-Blue. This file can be used as a starting point for a HOOMD-Blue simulation, for analysis, and for visualization in various tools. Parameters ---------- top : gmso.Topology gmso.Topology object filename : str Path of the output file. rigid_bodies : list of int, optional, default=None List of rigid body information. An integer value is required for each atom corresponding to the index of the rigid body the particle is to be associated with. A value of None indicates the atom is not part of a rigid body. shift_coords : bool, optional, default=True Shift coordinates from (0, L) to (-L/2, L/2) if necessary. write_special_pairs : bool, optional, default=True Writes out special pair information necessary to correctly use the OPLS fudged 1,4 interactions in HOOMD. Notes ----- Force field parameters are not written to the GSD file and must be included manually in a HOOMD input script. Work on a HOOMD plugin is underway to read force field parameters from a Foyer XML file. """ gsd_snapshot = to_gsd_snapshot( top=top, base_units=base_units, rigid_bodies=rigid_bodies, shift_coords=shift_coords, parse_special_pairs=write_special_pairs, )[0] with, mode="w") as gsd_file: gsd_file.append(gsd_snapshot)