HOOMD-blue File Writers

Write GSD (General Simulation Data)

Default data file format for HOOMD v2

GSD format.

https://gsd.readthedocs.io/en/stable/

mbuild.formats.gsdwriter.write_gsd(structure, filename, ref_distance=1.0, ref_mass=1.0, ref_energy=1.0, rigid_bodies=None, shift_coords=True, write_special_pairs=True, **kwargs)

Output a GSD file (HOOMD v2 default data format).

Parameters

structureparmed.Structure

ParmEd Structure object

filenamestr

Path of the output file.

ref_distancefloat, optional, default=1.0

Reference distance for conversion to reduced units

ref_massfloat, optional, default=1.0

Reference mass for conversion to reduced units

ref_energyfloat, optional, default=1.0

Reference energy for conversion to reduced units

rigid_bodieslist 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_coordsbool, optional, default=True

Shift coordinates from (0, L) to (-L/2, L/2) if necessary.

write_special_pairsbool, 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 into a HOOMD input script.

Create Hoomd Simulation

HOOMD simulation format.

mbuild.formats.hoomd_simulation.create_hoomd_simulation(structure, ref_distance=1.0, ref_mass=1.0, ref_energy=1.0, r_cut=1.2, auto_scale=False, snapshot_kwargs={}, pppm_kwargs={'Nx': 8, 'Ny': 8, 'Nz': 8, 'order': 4}, init_snap=None, restart=None, nlist=<Mock name='mock.md.nlist.cell' id='140447003187808'>)

Convert a parametrized pmd.Structure to hoomd.SimulationContext.

Parameters

structureparmed.Structure

ParmEd Structure object

ref_distancefloat, optional, default=1.0

Reference distance for conversion to reduced units

ref_massfloat, optional, default=1.0

Reference mass for conversion to reduced units

ref_energyfloat, optional, default=1.0

Reference energy for conversion to reduced units

r_cutfloat, optional, default 1.2

Cutoff radius, in reduced units

auto_scalebool, optional, default=False

Automatically use largest sigma value as ref_distance, largest mass value as ref_mass, and largest epsilon value as ref_energy

snapshot_kwargsdict

Kwargs to pass to to_hoomdsnapshot

pppm_kwargsdict

Kwargs to pass to hoomd’s pppm function

init_snaphoomd.data.SnapshotParticleData, optional, default=None

Initial snapshot to which to add the ParmEd structure object (useful for rigid bodies)

restartstr, optional, default=None

Path to the gsd file from which to restart the simulation. https://hoomd-blue.readthedocs.io/en/v2.9.4/restartable-jobs.html Note: It is assumed that the ParmEd structure and the system in restart.gsd contain the same types. The ParmEd structure is still used to initialize the forces, but restart.gsd is used to initialize the system state (e.g., particle positions, momenta, etc).

nlisthoomd.md.nlist, default=hoomd.md.nlist.cell

Type of neighborlist to use, see https://hoomd-blue.readthedocs.io/en/stable/module-md-nlist.html for more information.

Returns

hoomd_objectslist

List of hoomd objects created during conversion

ReferenceValuesnamedtuple

Values used in scaling

Notes

While the hoomd objects are returned, the hoomd.SimulationContext is accessible via hoomd.context.current. If you pass a non-parametrized pmd.Structure, you will not have angle, dihedral, or force field information. You may be better off creating a hoomd.Snapshot. Reference units should be expected to convert parmed Structure units:

— angstroms, kcal/mol, and daltons

Hoomdsnapshot

HOOMD snapshot format.

mbuild.formats.hoomd_snapshot.from_snapshot(snapshot, scale=1.0)

Convert a Snapshot to a Compound.

Snapshot can be a hoomd.data.Snapshot or a gsd.hoomd.Snapshot.

Parameters

snapshothoomd._hoomd.SnapshotSystemData_float or gsd.hoomd.Snapshot

Snapshot from which to build the mbuild Compound.

scalefloat, optional, default 1.0

Value by which to scale the length values

Returns

compCompound

mbuild.formats.hoomd_snapshot.to_hoomdsnapshot(structure, ref_distance=1.0, ref_mass=1.0, ref_energy=1.0, rigid_bodies=None, shift_coords=True, write_special_pairs=True, auto_scale=False, parmed_kwargs={}, hoomd_snapshot=None)

Convert a Compound or parmed.Structure to hoomd.data.Snapshot.

Parameters

structureparmed.Structure

ParmEd Structure object

ref_distancefloat, optional, default=1.0

Reference distance for conversion to reduced units

ref_massfloat, optional, default=1.0

Reference mass for conversion to reduced units

ref_energyfloat, optional, default=1.0

Reference energy for conversion to reduced units

rigid_bodieslist 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_coordsbool, optional, default=True

Shift coordinates from (0, L) to (-L/2, L/2) if necessary.

auto_scalebool, optional, default=False

Automatically use largest sigma value as ref_distance, largest mass value as ref_mass and largest epsilon value as ref_energy

write_special_pairsbool, optional, default=True

Writes out special pair information necessary to correctly use the OPLS fudged 1,4 interactions in HOOMD.

hoomd_snapshothoomd.data.SnapshotParticleData, optional, default=None

Initial snapshot to which to add the ParmEd structure object. The box information of the initial snapshot will be overwritten. (useful for rigid bodies)

Returns

hoomd_snapshothoomd.data.Snapshot

ReferenceValuesnamedtuple

Values used in scaling

Notes

Force field parameters are not written to the hoomd_snapshot