HOOMD-blue File Writers

Write GSD (General Simulation Data)

Default data file format for HOOMD-blue

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)[source]

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-blue force field (>= 3.0)

HOOMD v3 forcefield format.

mbuild.formats.hoomd_forcefield.create_hoomd_forcefield(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)[source]

Convert a parametrized pmd.Structure to a HOOMD snapshot and forces.

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

Keyword arguments to pass to to_hoomdsnapshot

pppm_kwargsdict

Keyword arguments to pass to hoomd.md.long_range.pppm.make_pppm_coulomb_forces

init_snaphoomd.Snapshot, optional, default=None

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

Returns
hoomd_snapshothoomd.Snapshot

HOOMD snapshot object to initialize the simulation

hoomd_forcefieldlist[hoomd.md.force.Force]

List of hoomd force computes created during conversion

ReferenceValuesnamedtuple

Values used in scaling

Create HOOMD-blue Simulation (v2.x)

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='140394318943808'>)[source]

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

HOOMD-blue Snapshot

HOOMD snapshot format.

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

Convert a Snapshot to a Compound.

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

Parameters
snapshothoomd.Snapshot 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)[source]

Convert a Compound or parmed.Structure to hoomd.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.Snapshot, 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.Snapshot
ReferenceValuesnamedtuple

Values used in scaling

Notes

Force field parameters are not written to the hoomd_snapshot