Modules

class hoomd_flowws.Init(**kwargs)

Initialize a system

Currently simply places points on a simple cubic lattice.

Parameters:

• number – Number of particles to simulate
• mass_scale – Scaling factor for mass of all particles
• type_ratios – Prevalence (ratio) of each particle type
• type_diameters – Diameter of each particle type (1 by default)
• spacing_scale – Additional scale factor for initial particle placement

run(scope, storage)

Run the contents of this stage

class hoomd_flowws.Interaction(**kwargs)

Specify a new interaction potential to include in future MD stages

Parameters:

• reset – Clear previously-defined interactions beforehand
• type – Interaction class name
• global_params – Global parameters of the interaction
• pair_params – Type pair-based parameters of the interaction

classmethod register_interaction(interaction, *names)

Convenience method to bind one or more names to a force-generation function

run(scope, storage)

Registers this object to provide a force compute in future MD stages

class hoomd_flowws.Damasceno2017Interaction(**kwargs)

Specify a new interaction potential from the paper “Non-close-packed three-dimensional quasicrystals” to include in future MD stages

These interactions are taken directly from the supplemental information of the paper (Journal of Physics: Condensed Matter, Volume 29, Number 23; DOI 10.1088/1361-648X/aa6cc1).

The SI provides 10 potentials with different well depth epsilon; currently this stage will select the reported potential with the nearest well depth to the given value.

Parameters:

• reset – Disable previously-defined interactions
• depth – Well depth epsilon (the nearest reported potential is used)

run(scope, storage)

Registers this object to provide a force compute in future MD stages

class hoomd_flowws.Dshemuchadse2021LJGInteraction(**kwargs)

Specify a new interaction potential from the paper “Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials” to include in future MD stages

These interactions are taken from the methods description in the paper (Proceedings of the National Academy of Sciences May 2021, 118 (21); DOI 10.1073/pnas.2024034118). This module implements the Lennard-Jones Gauss potential, consisting of a Lennard-Jones interaction plus a Gaussian.

The potential is rescaled such that the global minimum is -1 epsilon_0.

Parameters:

• reset – Disable previously-defined interactions
• epsilon – Attractive depth of the Gaussian interaction
• r_0 – Gaussian center location
• sigma_squared_gaussian – Parameter controlling width of the Gaussian
• width – Number of points at which to evaluate the tabulated potential
• r_min – Minimum distance at which to evaluate the tabulated potential
• r_max – Maximum distance at which to evaluate the tabulated potential

run(scope, storage)

Registers this object to provide a force compute in future MD stages

class hoomd_flowws.Dshemuchadse2021OPPInteraction(**kwargs)

Specify a new interaction potential from the paper “Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials” to include in future MD stages

These interactions are taken from the methods description in the paper (Proceedings of the National Academy of Sciences May 2021, 118 (21); DOI 10.1073/pnas.2024034118). This module implements the oscillatory pair potential, consisting of a short-range repulsion and a cosine term that scales with r^-3.

The potential is rescaled such that the global minimum is -1 epsilon_0.

Parameters:

• reset – Disable previously-defined interactions
• k – Interaction parameter k
• phi – Interaction parameter phi
• width – Number of points at which to evaluate the tabulated potential
• r_min – Minimum distance at which to evaluate the tabulated potential

run(scope, storage)

Registers this object to provide a force compute in future MD stages

class hoomd_flowws.ShapeDefinition(**kwargs)

Define per-type shapes for future stages to utilize

Shape information is used for visualization, packing fraction calculations, and pair force/HPMC integrator configuration.

Shapes consist of a base type, any parameters of the shape, and modifications. For example:

# regular polygon with 4 vertices (square)
shape = dict(type='regular_ngon', n=4,
             modifications=[dict(type='scale', factor=2)])
# rounded tetrahedron
shape = dict(type='tetrahedron',
             modifications=[dict(type='round', radius=0.5)])
ShapeDefinition(shape_arguments=[shape])

Parameters:shape_arguments – List of per-shape specifications and modifiers.

run(scope, storage)

Run the contents of this stage

class hoomd_flowws.DEMInteraction(**kwargs)

Specify that DEM interactions should be included in future MD stages

Parameters:

• reset – Clear previously-defined DEM interactions beforehand
• type – Interaction class name

run(scope, storage)

Registers this object to provide a DEM force compute in future MD stages

class hoomd_flowws.Run(**kwargs)

Run for a given number of timesteps using MD

Parameters:

• steps – Number of timesteps to run
• timestep_size – Timestep size
• integrator – Integrator type
• temperature – Temperature for isothermal simulations
• ramp_t_to – Ramp temperature to the given value over time during this stage
• tau_t – Thermostat time constant for isothermal simulations
• pressure – Pressure for isobaric simulations
• tau_p – Barostat time constant for isobaric simulations
• bd_seed – Random number seed for Brownian/Langevin thermostats
• zero_momentum – Period for zeroing the momentum of the system (default: disabled)
• backup_period – Period for dumping a backup file
• dump_period – Period for dumping a trajectory file
• trajectory_quantities – Additional trajectory quantities to dump
• dump_quantities – Dump period and comma-separated list of quantities to record (i.e. temperature,pressure)
• expand_by – Expand each dimension of the box by this ratio during this stage
• compress_to – Compress to the given packing fraction during this stage (overrides expand_by)

run(scope, storage)

Run the contents of this stage

class hoomd_flowws.RunHPMC(**kwargs)

Run for some number of steps using HPMC

Parameters:

• steps – Number of timesteps to run
• integrator – Integrator type
• pressure – Pressure for isobaric simulations
• backup_period – Period for dumping a backup file
• dump_period – Period for dumping a trajectory file
• trajectory_quantities – Additional trajectory quantities to dump
• dump_quantities – Dump period and comma-separated list of quantities to record (i.e. temperature,pressure)
• expand_by – Expand each dimension of the box by this ratio during this stage
• compress_to – Compress to the given packing fraction during this stage (overrides expand_by)
• integrator_seed – Random number seed for integration method
• tune – Tune move distances to achieve the target acceptance ratio after updating a given number of epochs and running the given number of steps at each epoch
• box_move_aspect – Move distance and weight for box aspect ratio moves
• box_move_length – Move distance and weight for box length moves
• box_move_ln_volume – Move distance and weight for box log-volume moves
• box_move_shear – Move distance and weight for box shear moves
• box_move_volume – Move distance and weight for box volume moves