Universe

class tissue_forge.UniverseInterface

property angles

All angles in the universe

property bonds

All bonds in the universe

property boundary_conditions

Boundary conditions

property center: fVector3

Universe center point

property cutoff: float

Global interaction cutoff distance

property dihedrals

All dihedrals in the universe

property dim: fVector3

Universe dimensions

property dt

Time step

property flux_steps: int

Number of flux steps per simulation step

grid(shape)

Gets a three-dimesional array of particle lists, of all the particles in the system.

Parameters:

shape – shape of grid

Returns:

three-dimension array of particle lists according to discretization and location

property kinetic_energy

Universe kinetic energy

property name: str

name of the model / script

property num_types: int

Number of particle types

property particles

Gets all particles in the universe

Return type:

ParticleList

reset_species()

Reset all species in all particles

start()

Starts the universe time evolution, and advanced the universe forward by timesteps in dt. All methods to build and manipulate universe objects are valid whether the universe time evolution is running or stopped.

step(until: float = 0)

Performs a single time step of the universe if no arguments are given. Optionally runs until until.

Parameters:

until – period to execute, in units of simulation time (default executes one time step).

stop()

Stops the universe time evolution. This essentially freezes the universe, everything remains the same, except time no longer moves forward.

property temperature

Universe temperature

property time

Current time

virial(origin=None, radius: float | None = None, types=None) → fMatrix3

Computes the virial tensor for the either the entire simulation domain, or a specific local virial tensor at a location and radius. Optionally can accept a list of particle types to restrict the virial calculation for specify types.

Parameters:

• origin – An optional length-3 array for the origin. Defaults to the center of the simulation domain if not given.

• radius – An optional number specifying the size of the region to compute the virial tensor for. Defaults to the entire simulation domain.

• types – An optional list of Particle types to include in the calculation. Defaults to every particle type.

Returns:

virial tensor

property volume: float

Universe volume

tissue_forge.Universe

Type:

UniverseInterface

Universe runtime interface