jax_dna.simulators.jax_md

jax_md sampler implementation for jax_dna.

Submodules

Classes

`JaxMDSimulator`	A sampler based on running a jax_md simulation routine.
`NeighborList`	Neighbor list for managing unbonded neighbors.
`NoNeighborList`	A dummy neighbor list that does nothing.
`SimulationState`	This is a protocol to help with typing.
`StaticSimulatorParams`	Static parameters for the simulator.

Package Contents

class jax_dna.simulators.jax_md.JaxMDSimulator[source]

Bases: jax_dna.simulators.base.BaseSimulation

A sampler based on running a jax_md simulation routine.

energy_configs: list[jax_dna.energy.configuration.BaseConfiguration]

energy_fns: list[jax_dna.energy.base.BaseEnergyFunction]

simulator_params: jax_dna.simulators.jax_md.utils.StaticSimulatorParams

space: jax_md.space.Space

transform_fn: collections.abc.Callable

simulator_init: collections.abc.Callable[[collections.abc.Callable, collections.abc.Callable], jax_md.simulate.Simulator]

neighbors: jax_dna.simulators.jax_md.utils.NeighborHelper

topology: jax_dna.input.topology.Topology

__post_init__() → None[source]: Builds the run function using the provided parameters.

class jax_dna.simulators.jax_md.NeighborList[source]

Bases: NeighborHelper

Neighbor list for managing unbonded neighbors.

displacement_fn: collections.abc.Callable

topology: jax_dna.input.topology.Topology

r_cutoff: float

dr_threshold: float

box_size: jax.numpy.ndarray

init_positions: jax_md.rigid_body.RigidBody

__post_init__() → None[source]: Initialize the neighbor list.

property idx: jax.numpy.ndarray: Return the indices of the unbonded neighbors.

allocate(locs: jax_md.rigid_body.RigidBody) → NeighborList[source]: Allocate memory for the neighbor list.

update(locs: jax_md.rigid_body.RigidBody) → NeighborList[source]: Update the neighbor list.

class jax_dna.simulators.jax_md.NoNeighborList[source]

Bases: NeighborHelper

A dummy neighbor list that does nothing.

unbonded_nbrs: jax.numpy.ndarray

property idx: jax.numpy.ndarray: Return the indices of the unbonded neighbors.

allocate(locs: jax_md.rigid_body.RigidBody) → NoNeighborList[source]: Allocate memory for the neighbor list.

update(locs: jax_md.rigid_body.RigidBody) → NoNeighborList[source]: Update the neighbor list.

class jax_dna.simulators.jax_md.SimulationState[source]

Bases: Protocol

This is a protocol to help with typing.

Every state implements at least position and mass. More info about the specific states can be found here:

https://github.com/jax-md/jax-md/blob/main/jax_md/simulate.py

position: jax_md.rigid_body.RigidBody

mass: jax_md.rigid_body.RigidBody

class jax_dna.simulators.jax_md.StaticSimulatorParams[source]

Static parameters for the simulator.

seq: jax_dna.utils.types.Arr_Nucleotide

mass: jax_md.rigid_body.RigidBody

gamma: jax_md.rigid_body.RigidBody

bonded_neighbors: jax.numpy.ndarray

checkpoint_every: int

dt: float

kT: float

property sim_init_fn: collections.abc.Callable: Return the simulator init function.

property init_fn: dict[str, jax_md.rigid_body.RigidBody | jax.numpy.ndarray]: Return the kwargs for initial state of the simulator.

property step_fn: dict[str, jax_md.rigid_body.RigidBody | jax.numpy.ndarray]: Return the kwargs for the step_fn of the simulator.