Index

A

action (jaxdem.rl.TrajectoryData attribute) action_space (jaxdem.rl.Model property) (jaxdem.rl.models.Model property) action_space_shape (jaxdem.rl.Environment property) (jaxdem.rl.environments.burrowing_dp.BurrowingDP property) (jaxdem.rl.environments.Environment property) (jaxdem.rl.environments.multi_navigator.MultiNavigator property) (jaxdem.rl.environments.multi_roller.MultiRoller property) (jaxdem.rl.environments.MultiNavigator property) (jaxdem.rl.environments.MultiRoller property) (jaxdem.rl.environments.single_navigator.SingleNavigator property) (jaxdem.rl.environments.single_roller.SingleRoller property) (jaxdem.rl.environments.SingleNavigator property) (jaxdem.rl.environments.SingleRoller property) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator property) (jaxdem.rl.environments.swarm_roller.SwarmRoller property) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D property) (jaxdem.rl.environments.SwarmNavigator property) (jaxdem.rl.environments.SwarmRoller property) (jaxdem.rl.environments.SwarmRoller3D property) (jaxdem.rl.environments.three_gears.ThreeGears property) (jaxdem.rl.environments.ThreeGears property) (jaxdem.rl.environments.two_gears.TwoGears property) (jaxdem.rl.environments.TwoGears property) action_space_size (jaxdem.rl.Environment property) (jaxdem.rl.environments.burrowing_dp.BurrowingDP property) (jaxdem.rl.environments.Environment property) (jaxdem.rl.environments.multi_navigator.MultiNavigator property) (jaxdem.rl.environments.multi_roller.MultiRoller property) (jaxdem.rl.environments.MultiNavigator property) (jaxdem.rl.environments.MultiRoller property) (jaxdem.rl.environments.single_navigator.SingleNavigator property) (jaxdem.rl.environments.single_roller.SingleRoller property) (jaxdem.rl.environments.SingleNavigator property) (jaxdem.rl.environments.SingleRoller property) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator property) (jaxdem.rl.environments.swarm_roller.SwarmRoller property) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D property) (jaxdem.rl.environments.SwarmNavigator property) (jaxdem.rl.environments.SwarmRoller property) (jaxdem.rl.environments.SwarmRoller3D property) (jaxdem.rl.environments.three_gears.ThreeGears property) (jaxdem.rl.environments.ThreeGears property) (jaxdem.rl.environments.two_gears.TwoGears property) (jaxdem.rl.environments.TwoGears property) ActionSpace (class in jaxdem.rl) (class in jaxdem.rl.action_spaces) actor_mu (jaxdem.rl.models.ActorCritic attribute) (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) (jaxdem.rl.models.mlp.ActorCritic attribute) (jaxdem.rl.models.mlp.SharedActorCritic attribute) (jaxdem.rl.models.SharedActorCritic attribute) actor_sigma (jaxdem.rl.models.ActorCritic attribute) (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) (jaxdem.rl.models.mlp.ActorCritic attribute) (jaxdem.rl.models.mlp.SharedActorCritic attribute) (jaxdem.rl.models.SharedActorCritic attribute) actor_torso (jaxdem.rl.models.ActorCritic attribute) (jaxdem.rl.models.mlp.ActorCritic attribute)

ActorCritic (class in jaxdem.rl.models) (class in jaxdem.rl.models.mlp) add() (jaxdem.bonded_forces.BondedForceModel static method) (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel static method) (jaxdem.bonded_forces.DeformableParticleModel static method) (jaxdem.BondedForceModel static method) (jaxdem.State static method) (jaxdem.state.State static method) add_clump() (jaxdem.State static method) (jaxdem.state.State static method) add_connected_facet() (jaxdem.State static method) (jaxdem.state.State static method) add_facet() (jaxdem.State static method) (jaxdem.state.State static method) add_force() (jaxdem.ForceManager static method) (jaxdem.forces.force_manager.ForceManager static method) (jaxdem.forces.ForceManager static method) add_force_at() (jaxdem.ForceManager static method) (jaxdem.forces.force_manager.ForceManager static method) (jaxdem.forces.ForceManager static method) add_mesh() (jaxdem.State static method) (jaxdem.state.State static method) add_torque() (jaxdem.ForceManager static method) (jaxdem.forces.force_manager.ForceManager static method) (jaxdem.forces.ForceManager static method) add_torque_at() (jaxdem.ForceManager static method) (jaxdem.forces.force_manager.ForceManager static method) (jaxdem.forces.ForceManager static method) advantage_c_clip (jaxdem.rl.Trainer attribute) advantage_gamma (jaxdem.rl.Trainer attribute) advantage_lambda (jaxdem.rl.Trainer attribute) advantage_rho_clip (jaxdem.rl.Trainer attribute) allocate_counts() (in module jaxdem.utils.dispersity) alpha (jaxdem.domains.lees_edwards.LeesEdwardsDomain attribute) (jaxdem.domains.LeesEdwardsDomain attribute) (jaxdem.minimizers.optimizers.FIREState attribute), [1] alpha_axis (jaxdem.domains.lees_edwards.LeesEdwardsDomain attribute) (jaxdem.domains.LeesEdwardsDomain attribute) anchor (jaxdem.Domain attribute) (jaxdem.domains.Domain attribute) ang_vel (jaxdem.State attribute) (jaxdem.state.State attribute) angle() (in module jaxdem.utils) (in module jaxdem.utils.angles) angle_between_normals() (in module jaxdem.bonded_forces.deformable_particle) angle_x() (in module jaxdem.utils) (in module jaxdem.utils.angles) anneal_importance_sampling_beta (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) apply() (jaxdem.Domain static method) (jaxdem.domains.Domain static method) (jaxdem.domains.free.FreeDomain static method) (jaxdem.domains.FreeDomain static method) (jaxdem.domains.reflect.ReflectDomain static method) (jaxdem.domains.reflect_sphere.ReflectSphereDomain static method) (jaxdem.domains.ReflectDomain static method) (jaxdem.domains.ReflectSphereDomain static method) (jaxdem.ForceManager static method) (jaxdem.forces.force_manager.ForceManager static method) (jaxdem.forces.ForceManager static method)

B

BaseAsyncWriter (class in jaxdem.writers.async_base) batch_size (jaxdem.State property) (jaxdem.state.State property) beta (jaxdem.domains.lees_edwards.LeesEdwardsDomain attribute) (jaxdem.domains.LeesEdwardsDomain attribute) beta_axis (jaxdem.domains.lees_edwards.LeesEdwardsDomain attribute) (jaxdem.domains.LeesEdwardsDomain attribute) bij (jaxdem.rl.models.ActorCritic attribute) (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) (jaxdem.rl.models.mlp.ActorCritic attribute) (jaxdem.rl.models.mlp.SharedActorCritic attribute) (jaxdem.rl.models.SharedActorCritic attribute) bin_id (jaxdem.analysis.Pairs attribute), [1] (jaxdem.analysis.pairs.Pairs attribute), [1] binary (jaxdem.VTKWriter attribute) (jaxdem.writers.vtk_writer.VTKWriter attribute) (jaxdem.writers.VTKWriter attribute) Binned (class in jaxdem.analysis) (class in jaxdem.analysis.engine) bins() (jaxdem.analysis.bins.BinSpec method) (jaxdem.analysis.BinSpec method)

BinSpec (class in jaxdem.analysis) (class in jaxdem.analysis.bins) bisection_jam() (in module jaxdem.utils) (in module jaxdem.utils.jamming) block_until_ready() (jaxdem.writers.async_base.BaseAsyncWriter method) bond_id (jaxdem.State attribute) (jaxdem.state.State attribute) bonded_force_model (jaxdem.System attribute) (jaxdem.system.System attribute) bonded_hessian() (in module jaxdem.utils) (in module jaxdem.utils.dynamical_matrix) BondedForceModel (class in jaxdem) (class in jaxdem.bonded_forces) box_size (jaxdem.Domain attribute) (jaxdem.domains.Domain attribute) BoxSpace (class in jaxdem.rl.action_spaces) (class in jaxdem.rl.action_spaces.box_space) build_ga_system() (in module jaxdem.utils.particle_creation) build_pairs() (in module jaxdem.analysis) (in module jaxdem.analysis.pairs) build_sphere_system() (in module jaxdem.utils.particle_creation) BurrowingDP (class in jaxdem.rl.environments.burrowing_dp)

C

can_rotate (jaxdem.integrators.velocity_verlet_rescaling.VelocityVerletRescaling attribute) (jaxdem.integrators.VelocityVerletRescaling attribute) carry (jaxdem.rl.Model property) (jaxdem.rl.models.lstm.LSTMActorCritic property) (jaxdem.rl.models.LSTMActorCritic property) (jaxdem.rl.models.mingru.MinGRUActorCritic property) (jaxdem.rl.models.MinGRUActorCritic property) (jaxdem.rl.models.Model property) carry_leading_shape (jaxdem.rl.models.lstm.LSTMActorCritic property) (jaxdem.rl.models.LSTMActorCritic property) (jaxdem.rl.models.mingru.MinGRUActorCritic property) (jaxdem.rl.models.MinGRUActorCritic property) cell (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) cell_size (jaxdem.colliders.cell_list.DynamicCellList attribute) (jaxdem.colliders.DynamicCellList attribute) (jaxdem.colliders.DynamicMultiCellList attribute) (jaxdem.colliders.multi_cell_list.DynamicMultiCellList attribute) CheckpointLoader (class in jaxdem) (class in jaxdem.writers) (class in jaxdem.writers.checkpoints) CheckpointModelLoader (class in jaxdem) (class in jaxdem.writers) (class in jaxdem.writers.checkpoints) CheckpointModelWriter (class in jaxdem) (class in jaxdem.writers) (class in jaxdem.writers.checkpoints) CheckpointWriter (class in jaxdem) (class in jaxdem.writers) (class in jaxdem.writers.checkpoints) clean (jaxdem.CheckpointModelWriter attribute) (jaxdem.CheckpointWriter attribute) (jaxdem.VTKWriter attribute) (jaxdem.writers.async_base.BaseAsyncWriter attribute) (jaxdem.writers.CheckpointModelWriter attribute) (jaxdem.writers.checkpoints.CheckpointModelWriter attribute) (jaxdem.writers.checkpoints.CheckpointWriter attribute) (jaxdem.writers.CheckpointWriter attribute) (jaxdem.writers.vtk_writer.VTKWriter attribute) (jaxdem.writers.VTKWriter attribute) clip_action_env() (in module jaxdem.rl) (in module jaxdem.rl.envWrappers) close() (jaxdem.writers.async_base.BaseAsyncWriter method) clump_id (jaxdem.State attribute) (jaxdem.state.State attribute) clump_non_bonded_hessian() (in module jaxdem.utils) (in module jaxdem.utils.dynamical_matrix) Collider (class in jaxdem) (class in jaxdem.colliders) collider (jaxdem.System attribute) (jaxdem.system.System attribute) compute_advantages() (jaxdem.rl.Trainer static method) compute_clump_pair_friction() (in module jaxdem.utils) (in module jaxdem.utils.contacts) compute_clump_properties() (in module jaxdem.utils) (in module jaxdem.utils.clumps) compute_contact_pressure() (in module jaxdem.utils) (in module jaxdem.utils.contacts) compute_contact_stress_tensor() (in module jaxdem.utils) (in module jaxdem.utils.contacts) compute_element_properties_2D() (in module jaxdem.bonded_forces.deformable_particle) compute_element_properties_3D() (in module jaxdem.bonded_forces.deformable_particle) compute_energy() (in module jaxdem.utils) (in module jaxdem.utils.thermal) compute_force() (jaxdem.Collider static method) (jaxdem.colliders.cell_list.DynamicCellList static method) (jaxdem.colliders.Collider static method) (jaxdem.colliders.DynamicCellList static method) (jaxdem.colliders.DynamicMultiCellList static method) (jaxdem.colliders.multi_cell_list.DynamicMultiCellList static method) (jaxdem.colliders.naive.NaiveSimulator static method) (jaxdem.colliders.NaiveSimulator static method) (jaxdem.colliders.neighbor_list.NeighborList static method) (jaxdem.colliders.NeighborList static method) compute_forces() (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel static method) (jaxdem.bonded_forces.DeformableParticleModel static method) compute_group_pair_friction() (in module jaxdem.utils) (in module jaxdem.utils.contacts) compute_mesh_properties() (in module jaxdem.utils.geometric_asperity_creation) compute_packing_fraction() (in module jaxdem.utils) (in module jaxdem.utils.packing_utils) compute_particle_volume() (in module jaxdem.utils) (in module jaxdem.utils.packing_utils) compute_polygon_properties() (in module jaxdem.utils.geometric_asperity_creation) compute_potential_energy() (in module jaxdem.utils) (in module jaxdem.utils.thermal) (jaxdem.bonded_forces.BondedForceModel method) (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel static method) (jaxdem.bonded_forces.DeformableParticleModel static method) (jaxdem.BondedForceModel method) (jaxdem.Collider static method) (jaxdem.colliders.cell_list.DynamicCellList static method) (jaxdem.colliders.Collider static method) (jaxdem.colliders.DynamicCellList static method) (jaxdem.colliders.DynamicMultiCellList static method) (jaxdem.colliders.multi_cell_list.DynamicMultiCellList static method) (jaxdem.colliders.naive.NaiveSimulator static method) (jaxdem.colliders.NaiveSimulator static method) (jaxdem.colliders.neighbor_list.NeighborList static method) (jaxdem.colliders.NeighborList static method) (jaxdem.ForceManager static method) (jaxdem.forces.force_manager.ForceManager static method) (jaxdem.forces.ForceManager static method) compute_potential_energy_w_aux() (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel static method) (jaxdem.bonded_forces.DeformableParticleModel static method) compute_rotational_kinetic_energy() (in module jaxdem.utils) (in module jaxdem.utils.thermal) compute_rotational_kinetic_energy_per_particle() (in module jaxdem.utils) (in module jaxdem.utils.thermal) compute_surface_properties() (in module jaxdem.utils.surface_properties) compute_temperature() (in module jaxdem.utils) (in module jaxdem.utils.thermal) compute_translational_kinetic_energy() (in module jaxdem.utils) (in module jaxdem.utils.thermal) compute_translational_kinetic_energy_per_particle() (in module jaxdem.utils) (in module jaxdem.utils.thermal)

conj() (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) conjugate_gradient() (in module jaxdem.minimizers) (in module jaxdem.minimizers.optimizers) ConjugateGradientState (class in jaxdem.minimizers.optimizers) count (jaxdem.minimizers.optimizers.ConjugateGradientState attribute), [1] count_clump_contacts() (in module jaxdem.utils) (in module jaxdem.utils.contacts) count_dynamic_dofs() (in module jaxdem.utils.thermal) count_vertex_contacts() (in module jaxdem.utils) (in module jaxdem.utils.contacts) counts (jaxdem.analysis.Binned attribute), [1] (jaxdem.analysis.engine.Binned attribute), [1] counts_per_bin (jaxdem.analysis.Pairs attribute), [1] (jaxdem.analysis.pairs.Pairs attribute), [1] Create() (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel class method) (jaxdem.bonded_forces.DeformableParticleModel class method) (jaxdem.bonded_forces.plastic_bending_deformable_particle.PlasticBendingDeformableParticleModel class method) (jaxdem.bonded_forces.plastic_deformable_particle.PlasticDeformableParticleModel class method) (jaxdem.bonded_forces.plastic_perimeter_deformable_particle.PlasticPerimeterDeformableParticleModel class method) (jaxdem.bonded_forces.PlasticBendingDeformableParticleModel class method) (jaxdem.bonded_forces.PlasticDeformableParticleModel class method) (jaxdem.bonded_forces.PlasticPerimeterDeformableParticleModel class method) (jaxdem.colliders.cell_list.DynamicCellList class method) (jaxdem.colliders.DynamicCellList class method) (jaxdem.colliders.DynamicMultiCellList class method) (jaxdem.colliders.multi_cell_list.DynamicMultiCellList class method) (jaxdem.colliders.neighbor_list.NeighborList class method) (jaxdem.colliders.NeighborList class method) (jaxdem.Domain class method) (jaxdem.domains.Domain class method) (jaxdem.domains.lees_edwards.LeesEdwardsDomain class method) (jaxdem.domains.LeesEdwardsDomain class method) (jaxdem.domains.reflect.ReflectDomain class method) (jaxdem.domains.reflect_sphere.ReflectSphereDomain class method) (jaxdem.domains.ReflectDomain class method) (jaxdem.domains.ReflectSphereDomain class method) create() (jaxdem.Factory class method) (jaxdem.factory.Factory class method) (jaxdem.ForceManager static method) (jaxdem.forces.force_manager.ForceManager static method) (jaxdem.forces.ForceManager static method) Create() (jaxdem.integrators.velocity_verlet_rescaling.VelocityVerletRescaling class method) (jaxdem.integrators.VelocityVerletRescaling class method) (jaxdem.rl.Environment class method) (jaxdem.rl.environments.burrowing_dp.BurrowingDP class method) (jaxdem.rl.environments.Environment class method) (jaxdem.rl.environments.multi_navigator.MultiNavigator class method) (jaxdem.rl.environments.multi_roller.MultiRoller class method) (jaxdem.rl.environments.MultiNavigator class method) (jaxdem.rl.environments.MultiRoller class method) (jaxdem.rl.environments.single_navigator.SingleNavigator class method) (jaxdem.rl.environments.single_roller.SingleRoller class method) (jaxdem.rl.environments.SingleNavigator class method) (jaxdem.rl.environments.SingleRoller class method) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator class method) (jaxdem.rl.environments.swarm_roller.SwarmRoller class method) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D class method) (jaxdem.rl.environments.SwarmNavigator class method) (jaxdem.rl.environments.SwarmRoller class method) (jaxdem.rl.environments.SwarmRoller3D class method) (jaxdem.rl.environments.three_gears.ThreeGears class method) (jaxdem.rl.environments.ThreeGears class method) (jaxdem.rl.environments.two_gears.TwoGears class method) (jaxdem.rl.environments.TwoGears class method) (jaxdem.rl.trainers.ppo_trainer.PPOTrainer class method) (jaxdem.rl.trainers.PPOTrainer class method) create() (jaxdem.State static method) (jaxdem.state.State static method) (jaxdem.System static method) (jaxdem.system.System static method) (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) create_cross_neighbor_list() (jaxdem.Collider static method) (jaxdem.colliders.cell_list.DynamicCellList static method) (jaxdem.colliders.Collider static method) (jaxdem.colliders.DynamicCellList static method) (jaxdem.colliders.DynamicMultiCellList static method) (jaxdem.colliders.multi_cell_list.DynamicMultiCellList static method) (jaxdem.colliders.neighbor_list.NeighborList static method) (jaxdem.colliders.NeighborList static method) create_dp_container() (in module jaxdem.utils.particle_creation) create_ga_state() (in module jaxdem.utils.particle_creation) create_neighbor_list() (jaxdem.Collider static method) (jaxdem.colliders.cell_list.DynamicCellList static method) (jaxdem.colliders.Collider static method) (jaxdem.colliders.DynamicCellList static method) (jaxdem.colliders.DynamicMultiCellList static method) (jaxdem.colliders.multi_cell_list.DynamicMultiCellList static method) (jaxdem.colliders.naive.NaiveSimulator static method) (jaxdem.colliders.NaiveSimulator static method) (jaxdem.colliders.neighbor_list.NeighborList static method) (jaxdem.colliders.NeighborList static method) create_sphere_state() (in module jaxdem.utils.particle_creation) critic (jaxdem.rl.models.ActorCritic attribute) (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) (jaxdem.rl.models.mlp.ActorCritic attribute) (jaxdem.rl.models.mlp.SharedActorCritic attribute) (jaxdem.rl.models.SharedActorCritic attribute) cross() (in module jaxdem.utils) (in module jaxdem.utils.linalg) cross_3X3D_1X2D() (in module jaxdem.utils) (in module jaxdem.utils.linalg) cross_lidar_2d() (in module jaxdem.utils) (in module jaxdem.utils.environment) cross_lidar_3d() (in module jaxdem.utils) (in module jaxdem.utils.environment) CundallStrackForce (class in jaxdem.forces) (class in jaxdem.forces.cundall_strack) current_bending_angles() (in module jaxdem.bonded_forces.deformable_particle) CustomGradientTransformation (class in jaxdem.minimizers.optimizers) cutoff (jaxdem.colliders.neighbor_list.NeighborList attribute) (jaxdem.colliders.NeighborList attribute)

D

damped_newtonian() (in module jaxdem) (in module jaxdem.minimizers) (in module jaxdem.minimizers.optimizers) DampedNewtonianState (class in jaxdem.minimizers.optimizers) decode_callable() (in module jaxdem.utils) (in module jaxdem.utils.serialization) DeformableParticleModel (class in jaxdem.bonded_forces) (class in jaxdem.bonded_forces.deformable_particle) density (jaxdem.Material attribute) (jaxdem.materials.Material attribute) dim (jaxdem.State property) (jaxdem.state.State property) (jaxdem.System attribute) (jaxdem.system.System attribute) dimensionless_overlap_energy() (in module jaxdem.utils.meshes) dir_prev (jaxdem.minimizers.optimizers.ConjugateGradientState attribute), [1] DirectEuler (class in jaxdem.integrators) (class in jaxdem.integrators.direct_euler) directory (jaxdem.VTKWriter attribute) (jaxdem.writers.async_base.BaseAsyncWriter attribute) (jaxdem.writers.vtk_writer.VTKWriter attribute) (jaxdem.writers.VTKWriter attribute) discrete (jaxdem.rl.Model attribute) (jaxdem.rl.models.ActorCritic attribute) (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) (jaxdem.rl.models.mlp.ActorCritic attribute) (jaxdem.rl.models.mlp.SharedActorCritic attribute) (jaxdem.rl.models.Model attribute) (jaxdem.rl.models.SharedActorCritic attribute) displacement() (jaxdem.Domain static method) (jaxdem.domains.Domain static method) (jaxdem.domains.lees_edwards.LeesEdwardsDomain static method) (jaxdem.domains.LeesEdwardsDomain static method) (jaxdem.domains.periodic.PeriodicDomain static method) (jaxdem.domains.PeriodicDomain static method) distribute_bodies() (in module jaxdem.utils.particle_creation) Domain (class in jaxdem) (class in jaxdem.domains)

domain (jaxdem.System attribute) (jaxdem.system.System attribute) done (jaxdem.rl.TrajectoryData attribute) done() (jaxdem.rl.Environment static method) (jaxdem.rl.environments.burrowing_dp.BurrowingDP static method) (jaxdem.rl.environments.Environment static method) (jaxdem.rl.environments.multi_navigator.MultiNavigator static method) (jaxdem.rl.environments.multi_roller.MultiRoller static method) (jaxdem.rl.environments.MultiNavigator static method) (jaxdem.rl.environments.MultiRoller static method) (jaxdem.rl.environments.single_navigator.SingleNavigator static method) (jaxdem.rl.environments.single_roller.SingleRoller static method) (jaxdem.rl.environments.SingleNavigator static method) (jaxdem.rl.environments.SingleRoller static method) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator static method) (jaxdem.rl.environments.swarm_roller.SwarmRoller static method) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D static method) (jaxdem.rl.environments.SwarmNavigator static method) (jaxdem.rl.environments.SwarmRoller static method) (jaxdem.rl.environments.SwarmRoller3D static method) (jaxdem.rl.environments.three_gears.ThreeGears static method) (jaxdem.rl.environments.ThreeGears static method) (jaxdem.rl.environments.two_gears.TwoGears static method) (jaxdem.rl.environments.TwoGears static method) dot() (in module jaxdem.utils) (in module jaxdem.utils.linalg) drip_decay (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) dt (jaxdem.minimizers.optimizers.DampedNewtonianState attribute), [1] (jaxdem.minimizers.optimizers.FIREState attribute), [1] (jaxdem.System attribute) (jaxdem.system.System attribute) duplicate_clump_template() (in module jaxdem.utils.geometric_asperity_creation) DynamicCellList (class in jaxdem.colliders) (class in jaxdem.colliders.cell_list) DynamicMultiCellList (class in jaxdem.colliders) (class in jaxdem.colliders.multi_cell_list)

E

e (jaxdem.materials.elastic_mats.ElasticFriction attribute) (jaxdem.materials.ElasticFriction attribute) eb (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) ec (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) edges (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) edges_id (jaxdem.bonded_forces.plastic_perimeter_deformable_particle.PlasticPerimeterDeformableParticleModel attribute) (jaxdem.bonded_forces.PlasticPerimeterDeformableParticleModel attribute) el (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) Elastic (class in jaxdem.materials) (class in jaxdem.materials.elastic_mats) ElasticFriction (class in jaxdem.materials) (class in jaxdem.materials.elastic_mats) element_adjacency (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) element_adjacency_edges (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) elements (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) elements_id (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) em (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) encode_callable() (in module jaxdem.utils) (in module jaxdem.utils.serialization) encoder (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) energy() (jaxdem.ForceModel static method) (jaxdem.ForceRouter static method) (jaxdem.forces.cundall_strack.CundallStrackForce static method) (jaxdem.forces.CundallStrackForce static method) (jaxdem.forces.FacetFacetSpringForce static method) (jaxdem.forces.ForceModel static method) (jaxdem.forces.ForceRouter static method) (jaxdem.forces.hertz.HertzianForce static method) (jaxdem.forces.HertzianForce static method) (jaxdem.forces.law_combiner.LawCombiner static method) (jaxdem.forces.LawCombiner static method) (jaxdem.forces.LennardJones static method) (jaxdem.forces.lennardjones.LennardJones static method) (jaxdem.forces.router.ForceRouter static method) (jaxdem.forces.SphereFacetSpringForce static method) (jaxdem.forces.spring.FacetFacetSpringForce static method) (jaxdem.forces.spring.SphereFacetSpringForce static method) (jaxdem.forces.spring.SpringForce static method) (jaxdem.forces.SpringForce static method) (jaxdem.forces.WCA static method) (jaxdem.forces.wca.WCA static method) (jaxdem.forces.wca_shifted.WCAShifted static method) (jaxdem.forces.WCAShifted static method) (jaxdem.LawCombiner static method)

energy_functions (jaxdem.ForceManager attribute) (jaxdem.forces.force_manager.ForceManager attribute) (jaxdem.forces.ForceManager attribute) entropy() (jaxdem.rl.action_spaces.Transformed method) env (jaxdem.rl.Trainer attribute) env_params (jaxdem.rl.Environment attribute) (jaxdem.rl.environments.Environment attribute) env_step() (in module jaxdem.utils) (in module jaxdem.utils.environment) env_trajectory_rollout() (in module jaxdem.utils) (in module jaxdem.utils.environment) Environment (class in jaxdem.rl) (class in jaxdem.rl.environments) epoch() (jaxdem.rl.Trainer static method) (jaxdem.rl.trainers.ppo_trainer.PPOTrainer static method) (jaxdem.rl.trainers.PPOTrainer static method) epsilon (jaxdem.materials.lj_mats.LJMaterial attribute) (jaxdem.materials.LJMaterial attribute) eta (jaxdem.integrators.vicsek.VicsekExtrinsic attribute) (jaxdem.integrators.vicsek.VicsekIntrinsic attribute) (jaxdem.integrators.VicsekExtrinsic attribute) (jaxdem.integrators.VicsekIntrinsic attribute) evaluate_binned() (in module jaxdem.analysis) (in module jaxdem.analysis.engine) external_force (jaxdem.ForceManager attribute) (jaxdem.forces.force_manager.ForceManager attribute) (jaxdem.forces.ForceManager attribute) external_force_com (jaxdem.ForceManager attribute) (jaxdem.forces.force_manager.ForceManager attribute) (jaxdem.forces.ForceManager attribute) external_torque (jaxdem.ForceManager attribute) (jaxdem.forces.force_manager.ForceManager attribute) (jaxdem.forces.ForceManager attribute)

F

facet_id (jaxdem.State attribute) (jaxdem.state.State attribute) facet_vertices (jaxdem.State attribute) (jaxdem.state.State attribute) FacetFacetSpringForce (class in jaxdem.forces) (class in jaxdem.forces.spring) Factory (class in jaxdem) (class in jaxdem.factory) fire() (in module jaxdem) (in module jaxdem.minimizers) (in module jaxdem.minimizers.optimizers) FIREState (class in jaxdem.minimizers.optimizers) fixed (jaxdem.State attribute) (jaxdem.state.State attribute) FlatPairs (in module jaxdem.analysis.pairs) flatten_pairs() (in module jaxdem.analysis.pairs) force (jaxdem.State attribute) (jaxdem.state.State attribute) force() (jaxdem.ForceModel static method) (jaxdem.ForceRouter static method) (jaxdem.forces.cundall_strack.CundallStrackForce static method) (jaxdem.forces.CundallStrackForce static method) (jaxdem.forces.FacetFacetSpringForce static method) (jaxdem.forces.ForceModel static method) (jaxdem.forces.ForceRouter static method) (jaxdem.forces.hertz.HertzianForce static method) (jaxdem.forces.HertzianForce static method) (jaxdem.forces.law_combiner.LawCombiner static method) (jaxdem.forces.LawCombiner static method) (jaxdem.forces.LennardJones static method) (jaxdem.forces.lennardjones.LennardJones static method) (jaxdem.forces.router.ForceRouter static method) (jaxdem.forces.SphereFacetSpringForce static method) (jaxdem.forces.spring.FacetFacetSpringForce static method) (jaxdem.forces.spring.SphereFacetSpringForce static method) (jaxdem.forces.spring.SpringForce static method) (jaxdem.forces.SpringForce static method) (jaxdem.forces.WCA static method) (jaxdem.forces.wca.WCA static method) (jaxdem.forces.wca_shifted.WCAShifted static method) (jaxdem.forces.WCAShifted static method) (jaxdem.LawCombiner static method) force_and_energy_fns (jaxdem.bonded_forces.BondedForceModel property) (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel property) (jaxdem.bonded_forces.DeformableParticleModel property) (jaxdem.BondedForceModel property) force_and_history() (jaxdem.ForceModel static method) (jaxdem.ForceRouter static method) (jaxdem.forces.ForceModel static method) (jaxdem.forces.ForceRouter static method) (jaxdem.forces.law_combiner.LawCombiner static method) (jaxdem.forces.LawCombiner static method) (jaxdem.forces.router.ForceRouter static method) (jaxdem.LawCombiner static method)

force_functions (jaxdem.ForceManager attribute) (jaxdem.forces.force_manager.ForceManager attribute) (jaxdem.forces.ForceManager attribute) force_manager (jaxdem.System attribute) (jaxdem.system.System attribute) force_model (jaxdem.System attribute) (jaxdem.system.System attribute) ForceManager (class in jaxdem) (class in jaxdem.forces) (class in jaxdem.forces.force_manager) ForceModel (class in jaxdem) (class in jaxdem.forces) ForceRouter (class in jaxdem) (class in jaxdem.forces) (class in jaxdem.forces.router) forward_and_log_det() (jaxdem.rl.action_spaces.box_space.BoxSpace method) (jaxdem.rl.action_spaces.BoxSpace method) (jaxdem.rl.action_spaces.free_space.FreeSpace method) (jaxdem.rl.action_spaces.FreeSpace method) (jaxdem.rl.action_spaces.max_norm_space.MaxNormSpace method) (jaxdem.rl.action_spaces.MaxNormSpace method) forward_log_det_jacobian() (jaxdem.rl.action_spaces.box_space.BoxSpace method) (jaxdem.rl.action_spaces.BoxSpace method) (jaxdem.rl.action_spaces.max_norm_space.MaxNormSpace method) (jaxdem.rl.action_spaces.MaxNormSpace method) free_mask() (in module jaxdem.integrators) FreeDomain (class in jaxdem.domains) (class in jaxdem.domains.free) FreeSpace (class in jaxdem.rl.action_spaces) (class in jaxdem.rl.action_spaces.free_space) frictional_floor_force() (in module jaxdem.rl.environments.two_gears) from_dict() (jaxdem.ForceRouter static method) (jaxdem.forces.ForceRouter static method) (jaxdem.forces.router.ForceRouter static method) from_materials() (jaxdem.materials.material_table.MaterialTable static method) (jaxdem.materials.MaterialTable static method) (jaxdem.MaterialTable static method) from_rotation_matrix() (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) from_rotvec() (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) from_small_rotvec() (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) from_source() (jaxdem.analysis.bins.LagBinsExact class method) (jaxdem.analysis.bins.LagBinsLinear class method) (jaxdem.analysis.bins.LagBinsLog class method) (jaxdem.analysis.bins.LagBinsPseudoLog class method) (jaxdem.analysis.bins.TimeBins class method) (jaxdem.analysis.LagBinsExact class method) (jaxdem.analysis.LagBinsLinear class method) (jaxdem.analysis.LagBinsLog class method) (jaxdem.analysis.LagBinsPseudoLog class method) (jaxdem.analysis.TimeBins class method)

G

ga_surface_mask() (in module jaxdem.utils.particle_creation) gamma (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) (jaxdem.domains.lees_edwards.LeesEdwardsDomain attribute) (jaxdem.domains.LeesEdwardsDomain attribute) (jaxdem.integrators.Langevin attribute) (jaxdem.integrators.langevin.Langevin attribute) generate_arclength_mesh() (in module jaxdem.utils) (in module jaxdem.utils.meshes) generate_asperities_2d() (in module jaxdem.utils.geometric_asperity_creation) generate_asperities_3d() (in module jaxdem.utils.geometric_asperity_creation) generate_faceted_mesh() (in module jaxdem.utils) (in module jaxdem.utils.meshes) generate_fibonacci_sphere_mesh() (in module jaxdem.utils) (in module jaxdem.utils.meshes) generate_ga_clump_state() (in module jaxdem.utils.geometric_asperity_creation) generate_ga_deformable_state() (in module jaxdem.utils.geometric_asperity_creation) generate_helix_mesh() (in module jaxdem.utils) (in module jaxdem.utils.meshes) generate_icosphere_mesh() (in module jaxdem.utils) (in module jaxdem.utils.meshes) generate_mesh() (in module jaxdem.utils.geometric_asperity_creation) generate_thomson_mesh() (in module jaxdem.utils) (in module jaxdem.utils.meshes)

generate_torus_mesh() (in module jaxdem.utils) (in module jaxdem.utils.meshes) get_clump_rattler_ids() (in module jaxdem.utils) (in module jaxdem.utils.contacts) get_effective_property() (jaxdem.material_matchmakers.harmonic.HarmonicMaterialMatchmaker static method) (jaxdem.material_matchmakers.HarmonicMaterialMatchmaker static method) (jaxdem.material_matchmakers.linear.LinearMaterialMatchmaker static method) (jaxdem.material_matchmakers.LinearMaterialMatchmaker static method) (jaxdem.material_matchmakers.MaterialMatchmaker static method) (jaxdem.MaterialMatchmaker static method) get_facet_indices() (in module jaxdem.forces.facet_contact) get_pair_forces_and_ids() (in module jaxdem.utils) (in module jaxdem.utils.contacts) get_polydisperse_radii() (in module jaxdem.utils) (in module jaxdem.utils.dispersity) get_sphere_rattler_ids() (in module jaxdem.utils) (in module jaxdem.utils.contacts) grad_prev (jaxdem.minimizers.optimizers.ConjugateGradientState attribute), [1] graphdef (jaxdem.rl.Trainer attribute) graphstate (jaxdem.rl.Trainer attribute) gravity (jaxdem.ForceManager attribute) (jaxdem.forces.force_manager.ForceManager attribute) (jaxdem.forces.ForceManager attribute) grid_state() (in module jaxdem.utils), [1]

H

HarmonicMaterialMatchmaker (class in jaxdem.material_matchmakers) (class in jaxdem.material_matchmakers.harmonic) HertzianForce (class in jaxdem.forces) (class in jaxdem.forces.hertz)

history (jaxdem.colliders.neighbor_list.NeighborList attribute) (jaxdem.colliders.NeighborList attribute)

I

importance_sampling_alpha (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) importance_sampling_beta (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) inertia (jaxdem.State attribute) (jaxdem.state.State attribute) INERTIA_REGULARIZATION (in module jaxdem.state) info() (jaxdem.rl.Environment static method) (jaxdem.rl.environments.Environment static method) init_history() (jaxdem.ForceModel method) (jaxdem.ForceRouter method) (jaxdem.forces.ForceModel method) (jaxdem.forces.ForceRouter method) (jaxdem.forces.law_combiner.LawCombiner method) (jaxdem.forces.LawCombiner method) (jaxdem.forces.router.ForceRouter method) (jaxdem.LawCombiner method) initial_bendings (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) initial_body_contents (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) initial_edge_lengths (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) initial_element_measures (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) initialize() (jaxdem.Integrator static method) Integrator (class in jaxdem) interact_same_bond_id (jaxdem.System attribute) (jaxdem.system.System attribute) inv() (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) inv_box_size (jaxdem.Domain attribute) (jaxdem.domains.Domain attribute) inverse_and_log_det() (jaxdem.rl.action_spaces.box_space.BoxSpace method) (jaxdem.rl.action_spaces.BoxSpace method) (jaxdem.rl.action_spaces.free_space.FreeSpace method) (jaxdem.rl.action_spaces.FreeSpace method) (jaxdem.rl.action_spaces.max_norm_space.MaxNormSpace method) (jaxdem.rl.action_spaces.MaxNormSpace method)

is_active() (jaxdem.VTKBaseWriter class method) (jaxdem.writers.vtk_deformable_particle_writer.VTKDeformableEdgeAdjacenciesWriter class method) (jaxdem.writers.vtk_deformable_particle_writer.VTKDeformableEdgesWriter class method) (jaxdem.writers.vtk_deformable_particle_writer.VTKDeformableElementsWriter class method) (jaxdem.writers.vtk_facets_writer.VTKFacetsWriter class method) (jaxdem.writers.vtk_spheres_writer.VTKFacetSpheresWriter class method) (jaxdem.writers.vtk_spheres_writer.VTKSpheresWriter class method) (jaxdem.writers.VTKBaseWriter class method) (jaxdem.writers.VTKDeformableEdgeAdjacenciesWriter class method) (jaxdem.writers.VTKDeformableEdgesWriter class method) (jaxdem.writers.VTKDeformableElementsWriter class method) (jaxdem.writers.VTKFacetSpheresWriter class method) (jaxdem.writers.VTKFacetsWriter class method) (jaxdem.writers.VTKSpheresWriter class method) is_com_force (jaxdem.ForceManager attribute) (jaxdem.forces.force_manager.ForceManager attribute) (jaxdem.forces.ForceManager attribute) is_valid (jaxdem.State property) (jaxdem.state.State property) is_wrapped() (in module jaxdem.rl) (in module jaxdem.rl.envWrappers) isf_angular_kernel_2d() (in module jaxdem.analysis) (in module jaxdem.analysis.kernels) isf_self_isotropic_kernel() (in module jaxdem.analysis) (in module jaxdem.analysis.kernels) isf_self_kvecs_kernel() (in module jaxdem.analysis.kernels) iter_tuples() (jaxdem.analysis.bins.BinSpec method) (jaxdem.analysis.bins.LagBinsExact method) (jaxdem.analysis.bins.TimeBins method) (jaxdem.analysis.BinSpec method) (jaxdem.analysis.LagBinsExact method) (jaxdem.analysis.TimeBins method)

J

j0() (in module jaxdem.analysis.bessel) j1() (in module jaxdem.analysis.bessel) jammed_state (jaxdem.utils.jamming.JamResult attribute) jammed_system (jaxdem.utils.jamming.JamResult attribute) JamResult (class in jaxdem.utils.jamming) jaxdem module jaxdem.analysis module jaxdem.analysis.bessel module jaxdem.analysis.bins module jaxdem.analysis.engine module jaxdem.analysis.kernels module jaxdem.analysis.pairs module jaxdem.bonded_forces module jaxdem.bonded_forces.deformable_particle module jaxdem.bonded_forces.plastic_bending_deformable_particle module jaxdem.bonded_forces.plastic_deformable_particle module jaxdem.bonded_forces.plastic_perimeter_deformable_particle module jaxdem.colliders module jaxdem.colliders.cell_list module jaxdem.colliders.multi_cell_list module jaxdem.colliders.naive module jaxdem.colliders.neighbor_list module jaxdem.domains module jaxdem.domains.free module jaxdem.domains.lees_edwards module jaxdem.domains.periodic module jaxdem.domains.reflect module jaxdem.domains.reflect_sphere module jaxdem.factory module jaxdem.forces module jaxdem.forces.cundall_strack module jaxdem.forces.facet_contact module jaxdem.forces.force_manager module jaxdem.forces.hertz module jaxdem.forces.law_combiner module jaxdem.forces.lennardjones module jaxdem.forces.router module jaxdem.forces.spring module jaxdem.forces.wca module jaxdem.forces.wca_shifted module jaxdem.integrators module jaxdem.integrators.direct_euler module jaxdem.integrators.langevin module jaxdem.integrators.spiral module jaxdem.integrators.velocity_verlet module jaxdem.integrators.velocity_verlet_rescaling module jaxdem.integrators.velocity_verlet_spiral module jaxdem.integrators.vicsek module jaxdem.material_matchmakers module jaxdem.material_matchmakers.harmonic module jaxdem.material_matchmakers.linear module jaxdem.materials module jaxdem.materials.elastic_mats module jaxdem.materials.lj_mats module jaxdem.materials.material_table module jaxdem.minimizers module jaxdem.minimizers.optimizers module jaxdem.minimizers.routines module

jaxdem.rl module jaxdem.rl.action_spaces module jaxdem.rl.action_spaces.box_space module jaxdem.rl.action_spaces.free_space module jaxdem.rl.action_spaces.max_norm_space module jaxdem.rl.environments module jaxdem.rl.environments.burrowing_dp module jaxdem.rl.environments.hardcoded_bed module jaxdem.rl.environments.multi_navigator module jaxdem.rl.environments.multi_roller module jaxdem.rl.environments.single_navigator module jaxdem.rl.environments.single_roller module jaxdem.rl.environments.swarm_navigator module jaxdem.rl.environments.swarm_roller module jaxdem.rl.environments.swarm_roller_3d module jaxdem.rl.environments.three_gears module jaxdem.rl.environments.two_gears module jaxdem.rl.envWrappers module jaxdem.rl.models module jaxdem.rl.models.lstm module jaxdem.rl.models.mingru module jaxdem.rl.models.mlp module jaxdem.rl.trainers module jaxdem.rl.trainers.ppo_trainer module jaxdem.state module jaxdem.system module jaxdem.utils module jaxdem.utils.angles module jaxdem.utils.clumps module jaxdem.utils.contacts module jaxdem.utils.dispersity module jaxdem.utils.dynamical_matrix module jaxdem.utils.dynamics_routines module jaxdem.utils.environment module jaxdem.utils.geometric_asperity_creation module jaxdem.utils.h5 module jaxdem.utils.jamming module jaxdem.utils.linalg module jaxdem.utils.load_legacy module jaxdem.utils.meshes module jaxdem.utils.packing_utils module jaxdem.utils.particle_creation module jaxdem.utils.quaternion module jaxdem.utils.random_sphere_configuration module jaxdem.utils.rollout_schedules module jaxdem.utils.serialization module jaxdem.utils.surface_properties module jaxdem.utils.thermal module jaxdem.writers module jaxdem.writers.async_base module jaxdem.writers.checkpoints module jaxdem.writers.vtk_deformable_particle_writer module jaxdem.writers.vtk_domain_writer module jaxdem.writers.vtk_facets_writer module jaxdem.writers.vtk_spheres_writer module jaxdem.writers.vtk_writer module

K

k_B (jaxdem.integrators.Langevin attribute) (jaxdem.integrators.langevin.Langevin attribute) (jaxdem.integrators.velocity_verlet_rescaling.VelocityVerletRescaling attribute) (jaxdem.integrators.VelocityVerletRescaling attribute) KernelFn (class in jaxdem.analysis) (class in jaxdem.analysis.kernels)

key (jaxdem.rl.Trainer attribute) (jaxdem.System attribute) (jaxdem.system.System attribute) kw (jaxdem.minimizers.optimizers.CustomGradientTransformation attribute) kws (jaxdem.rl.action_spaces.ActionSpace property) (jaxdem.rl.ActionSpace property)

L

LagBinsExact (class in jaxdem.analysis) (class in jaxdem.analysis.bins) LagBinsLinear (class in jaxdem.analysis) (class in jaxdem.analysis.bins) LagBinsLog (class in jaxdem.analysis) (class in jaxdem.analysis.bins) LagBinsPseudoLog (class in jaxdem.analysis) (class in jaxdem.analysis.bins) Langevin (class in jaxdem.integrators) (class in jaxdem.integrators.langevin) latest_step() (jaxdem.CheckpointLoader method) (jaxdem.CheckpointModelLoader method) (jaxdem.writers.CheckpointLoader method) (jaxdem.writers.CheckpointModelLoader method) (jaxdem.writers.checkpoints.CheckpointLoader method) (jaxdem.writers.checkpoints.CheckpointModelLoader method) LawCombiner (class in jaxdem) (class in jaxdem.forces) (class in jaxdem.forces.law_combiner) laws (jaxdem.ForceModel attribute) (jaxdem.forces.ForceModel attribute) LeesEdwardsDomain (class in jaxdem.domains) (class in jaxdem.domains.lees_edwards) LennardJones (class in jaxdem.forces) (class in jaxdem.forces.lennardjones) lidar_2d() (in module jaxdem.utils) (in module jaxdem.utils.environment) lidar_3d() (in module jaxdem.utils) (in module jaxdem.utils.environment) linear_integrator (jaxdem.System attribute) (jaxdem.system.System attribute) LinearIntegrator (class in jaxdem) (class in jaxdem.integrators) LinearMaterialMatchmaker (class in jaxdem.material_matchmakers) (class in jaxdem.material_matchmakers.linear)

LJMaterial (class in jaxdem.materials) (class in jaxdem.materials.lj_mats) load() (in module jaxdem.utils) (in module jaxdem.utils.h5) (jaxdem.CheckpointLoader method) (jaxdem.CheckpointModelLoader method) (jaxdem.writers.CheckpointLoader method) (jaxdem.writers.CheckpointModelLoader method) (jaxdem.writers.checkpoints.CheckpointLoader method) (jaxdem.writers.checkpoints.CheckpointModelLoader method) load_legacy_dp() (in module jaxdem.utils) (in module jaxdem.utils.load_legacy) load_legacy_simulation() (in module jaxdem.utils) (in module jaxdem.utils.load_legacy) load_legacy_state() (in module jaxdem.utils) (in module jaxdem.utils.load_legacy) load_legacy_system() (in module jaxdem.utils) (in module jaxdem.utils.load_legacy) log_det_expectation() (jaxdem.rl.action_spaces.ActionSpace method) (jaxdem.rl.action_spaces.box_space.BoxSpace method) (jaxdem.rl.action_spaces.BoxSpace method) (jaxdem.rl.action_spaces.free_space.FreeSpace method) (jaxdem.rl.action_spaces.FreeSpace method) (jaxdem.rl.action_spaces.max_norm_space.MaxNormSpace method) (jaxdem.rl.action_spaces.MaxNormSpace method) (jaxdem.rl.ActionSpace method) log_prob (jaxdem.rl.TrajectoryData attribute) loss_fn() (jaxdem.rl.trainers.ppo_trainer.PPOTrainer static method) (jaxdem.rl.trainers.PPOTrainer static method) lstm_features (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) LSTMActorCritic (class in jaxdem.rl.models) (class in jaxdem.rl.models.lstm)

M

make_save_steps_linear() (in module jaxdem.utils) (in module jaxdem.utils.rollout_schedules) make_save_steps_pseudolog() (in module jaxdem.utils) (in module jaxdem.utils.rollout_schedules) make_single_deformable_ga_particle_2d() (in module jaxdem.utils.geometric_asperity_creation) make_single_deformable_ga_particle_3d() (in module jaxdem.utils.geometric_asperity_creation) make_single_particle_2d() (in module jaxdem.utils.geometric_asperity_creation) make_single_particle_3d() (in module jaxdem.utils.geometric_asperity_creation) mass (jaxdem.State attribute) (jaxdem.state.State attribute) mat_id (jaxdem.State attribute) (jaxdem.state.State attribute) mat_table (jaxdem.System attribute) (jaxdem.system.System attribute) matcher (jaxdem.materials.material_table.MaterialTable attribute) (jaxdem.materials.MaterialTable attribute) (jaxdem.MaterialTable attribute) Material (class in jaxdem) (class in jaxdem.materials) MaterialMatchmaker (class in jaxdem) (class in jaxdem.material_matchmakers) MaterialTable (class in jaxdem) (class in jaxdem.materials) (class in jaxdem.materials.material_table) max_neighbors (jaxdem.colliders.neighbor_list.NeighborList attribute) (jaxdem.colliders.NeighborList attribute) (jaxdem.integrators.vicsek.VicsekExtrinsic attribute) (jaxdem.integrators.vicsek.VicsekIntrinsic attribute) (jaxdem.integrators.VicsekExtrinsic attribute) (jaxdem.integrators.VicsekIntrinsic attribute) max_num_agents (jaxdem.rl.Environment property) (jaxdem.rl.environments.burrowing_dp.BurrowingDP property) (jaxdem.rl.environments.Environment property) (jaxdem.rl.environments.three_gears.ThreeGears property) (jaxdem.rl.environments.ThreeGears property) (jaxdem.rl.environments.two_gears.TwoGears property) (jaxdem.rl.environments.TwoGears property) max_queue_size (jaxdem.VTKWriter attribute) (jaxdem.writers.async_base.BaseAsyncWriter attribute) (jaxdem.writers.vtk_writer.VTKWriter attribute) (jaxdem.writers.VTKWriter attribute) max_to_keep (jaxdem.CheckpointModelWriter attribute) (jaxdem.CheckpointWriter attribute) (jaxdem.writers.CheckpointModelWriter attribute) (jaxdem.writers.checkpoints.CheckpointModelWriter attribute) (jaxdem.writers.checkpoints.CheckpointWriter attribute) (jaxdem.writers.CheckpointWriter attribute) max_workers (jaxdem.VTKWriter attribute) (jaxdem.writers.async_base.BaseAsyncWriter attribute) (jaxdem.writers.vtk_writer.VTKWriter attribute) (jaxdem.writers.VTKWriter attribute) MaxNormSpace (class in jaxdem.rl.action_spaces) (class in jaxdem.rl.action_spaces.max_norm_space) mean (jaxdem.analysis.Binned attribute), [1] (jaxdem.analysis.engine.Binned attribute), [1] merge() (jaxdem.bonded_forces.BondedForceModel static method) (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel static method) (jaxdem.bonded_forces.DeformableParticleModel static method) (jaxdem.BondedForceModel static method) (jaxdem.State static method) (jaxdem.state.State static method) metadata (jaxdem.Factory property) (jaxdem.factory.Factory property) (jaxdem.materials.material_table.MaterialTable property) (jaxdem.materials.MaterialTable property) (jaxdem.MaterialTable property) (jaxdem.minimizers.optimizers.CustomGradientTransformation property) (jaxdem.System property) (jaxdem.system.System property) MinGRUActorCritic (class in jaxdem.rl.models) (class in jaxdem.rl.models.mingru) minibatch_size (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) minimize() (in module jaxdem) (in module jaxdem.minimizers) (in module jaxdem.minimizers.routines) (jaxdem.System static method) (jaxdem.system.System static method) minimize_on_hyper_ellipsoid() (in module jaxdem.utils.meshes) minimize_sphere_configuration() (in module jaxdem.utils.random_sphere_configuration) minimizer (jaxdem.System attribute) (jaxdem.system.System attribute) Model (class in jaxdem.rl) (class in jaxdem.rl.models) model (jaxdem.rl.Trainer property) module jaxdem jaxdem.analysis jaxdem.analysis.bessel jaxdem.analysis.bins jaxdem.analysis.engine jaxdem.analysis.kernels jaxdem.analysis.pairs jaxdem.bonded_forces jaxdem.bonded_forces.deformable_particle jaxdem.bonded_forces.plastic_bending_deformable_particle jaxdem.bonded_forces.plastic_deformable_particle jaxdem.bonded_forces.plastic_perimeter_deformable_particle jaxdem.colliders jaxdem.colliders.cell_list jaxdem.colliders.multi_cell_list jaxdem.colliders.naive jaxdem.colliders.neighbor_list jaxdem.domains jaxdem.domains.free jaxdem.domains.lees_edwards jaxdem.domains.periodic jaxdem.domains.reflect jaxdem.domains.reflect_sphere jaxdem.factory jaxdem.forces jaxdem.forces.cundall_strack jaxdem.forces.facet_contact jaxdem.forces.force_manager jaxdem.forces.hertz jaxdem.forces.law_combiner jaxdem.forces.lennardjones jaxdem.forces.router jaxdem.forces.spring jaxdem.forces.wca jaxdem.forces.wca_shifted jaxdem.integrators jaxdem.integrators.direct_euler jaxdem.integrators.langevin jaxdem.integrators.spiral jaxdem.integrators.velocity_verlet jaxdem.integrators.velocity_verlet_rescaling jaxdem.integrators.velocity_verlet_spiral jaxdem.integrators.vicsek jaxdem.material_matchmakers jaxdem.material_matchmakers.harmonic jaxdem.material_matchmakers.linear jaxdem.materials jaxdem.materials.elastic_mats jaxdem.materials.lj_mats jaxdem.materials.material_table jaxdem.minimizers jaxdem.minimizers.optimizers jaxdem.minimizers.routines jaxdem.rl jaxdem.rl.action_spaces jaxdem.rl.action_spaces.box_space jaxdem.rl.action_spaces.free_space jaxdem.rl.action_spaces.max_norm_space jaxdem.rl.environments jaxdem.rl.environments.burrowing_dp jaxdem.rl.environments.hardcoded_bed jaxdem.rl.environments.multi_navigator jaxdem.rl.environments.multi_roller jaxdem.rl.environments.single_navigator jaxdem.rl.environments.single_roller jaxdem.rl.environments.swarm_navigator jaxdem.rl.environments.swarm_roller jaxdem.rl.environments.swarm_roller_3d jaxdem.rl.environments.three_gears jaxdem.rl.environments.two_gears jaxdem.rl.envWrappers jaxdem.rl.models jaxdem.rl.models.lstm jaxdem.rl.models.mingru jaxdem.rl.models.mlp jaxdem.rl.trainers jaxdem.rl.trainers.ppo_trainer jaxdem.state jaxdem.system jaxdem.utils jaxdem.utils.angles jaxdem.utils.clumps jaxdem.utils.contacts jaxdem.utils.dispersity jaxdem.utils.dynamical_matrix jaxdem.utils.dynamics_routines jaxdem.utils.environment jaxdem.utils.geometric_asperity_creation jaxdem.utils.h5 jaxdem.utils.jamming jaxdem.utils.linalg jaxdem.utils.load_legacy jaxdem.utils.meshes jaxdem.utils.packing_utils jaxdem.utils.particle_creation jaxdem.utils.quaternion jaxdem.utils.random_sphere_configuration jaxdem.utils.rollout_schedules jaxdem.utils.serialization jaxdem.utils.surface_properties jaxdem.utils.thermal jaxdem.writers jaxdem.writers.async_base jaxdem.writers.checkpoints jaxdem.writers.vtk_deformable_particle_writer jaxdem.writers.vtk_domain_writer jaxdem.writers.vtk_facets_writer jaxdem.writers.vtk_spheres_writer jaxdem.writers.vtk_writer

msad_kernel_2d() (in module jaxdem.analysis) (in module jaxdem.analysis.kernels) msd_kernel() (in module jaxdem.analysis) (in module jaxdem.analysis.kernels) mu (jaxdem.materials.elastic_mats.ElasticFriction attribute) (jaxdem.materials.ElasticFriction attribute) mu_r (jaxdem.materials.elastic_mats.ElasticFriction attribute) (jaxdem.materials.ElasticFriction attribute) MultiNavigator (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.multi_navigator) MultiRoller (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.multi_roller)

N

N (jaxdem.State property) (jaxdem.state.State property) N_bad (jaxdem.minimizers.optimizers.FIREState attribute), [1] n_build_times (jaxdem.colliders.neighbor_list.NeighborList attribute) (jaxdem.colliders.NeighborList attribute) N_good (jaxdem.minimizers.optimizers.FIREState attribute), [1] n_lidar_elevation (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D attribute) (jaxdem.rl.environments.SwarmRoller3D attribute) n_lidar_rays (jaxdem.rl.environments.multi_navigator.MultiNavigator attribute) (jaxdem.rl.environments.multi_roller.MultiRoller attribute) (jaxdem.rl.environments.MultiNavigator attribute) (jaxdem.rl.environments.MultiRoller attribute) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator attribute) (jaxdem.rl.environments.swarm_roller.SwarmRoller attribute) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D attribute) (jaxdem.rl.environments.SwarmNavigator attribute) (jaxdem.rl.environments.SwarmRoller attribute) (jaxdem.rl.environments.SwarmRoller3D attribute) NaiveSimulator (class in jaxdem.colliders) (class in jaxdem.colliders.naive) neighbor_list (jaxdem.colliders.neighbor_list.NeighborList attribute) (jaxdem.colliders.NeighborList attribute) neighbor_mask (jaxdem.colliders.cell_list.DynamicCellList attribute) (jaxdem.colliders.DynamicCellList attribute) (jaxdem.colliders.DynamicMultiCellList attribute) (jaxdem.colliders.multi_cell_list.DynamicMultiCellList attribute) neighbor_radius (jaxdem.integrators.vicsek.VicsekExtrinsic attribute) (jaxdem.integrators.vicsek.VicsekIntrinsic attribute) (jaxdem.integrators.VicsekExtrinsic attribute) (jaxdem.integrators.VicsekIntrinsic attribute) NeighborList (class in jaxdem.colliders) (class in jaxdem.colliders.neighbor_list)

network (jaxdem.rl.models.mlp.SharedActorCritic attribute) (jaxdem.rl.models.SharedActorCritic attribute) non_bonded_hessian() (in module jaxdem.utils) (in module jaxdem.utils.dynamical_matrix) norm() (in module jaxdem.utils) (in module jaxdem.utils.linalg) norm2() (in module jaxdem.utils) (in module jaxdem.utils.linalg) num_bins() (jaxdem.analysis.bins.BinSpec method) (jaxdem.analysis.bins.LagBinsExact method) (jaxdem.analysis.bins.TimeBins method) (jaxdem.analysis.BinSpec method) (jaxdem.analysis.LagBinsExact method) (jaxdem.analysis.TimeBins method) num_envs (jaxdem.rl.Environment property) (jaxdem.rl.environments.Environment property) num_epochs (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) num_gears (jaxdem.rl.environments.three_gears.ThreeGears attribute) (jaxdem.rl.environments.ThreeGears attribute) (jaxdem.rl.environments.two_gears.TwoGears attribute) (jaxdem.rl.environments.TwoGears attribute) num_minibatches (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) num_objectives (jaxdem.rl.environments.swarm_navigator.SwarmNavigator attribute) (jaxdem.rl.environments.swarm_roller.SwarmRoller attribute) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D attribute) (jaxdem.rl.environments.SwarmNavigator attribute) (jaxdem.rl.environments.SwarmRoller attribute) (jaxdem.rl.environments.SwarmRoller3D attribute) num_steps_epoch (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute)

O

obs (jaxdem.rl.TrajectoryData attribute) obs_dim (jaxdem.rl.models.lstm.LSTMActorCritic attribute) (jaxdem.rl.models.LSTMActorCritic attribute) observation() (jaxdem.rl.Environment static method) (jaxdem.rl.environments.burrowing_dp.BurrowingDP static method) (jaxdem.rl.environments.Environment static method) (jaxdem.rl.environments.multi_navigator.MultiNavigator static method) (jaxdem.rl.environments.multi_roller.MultiRoller static method) (jaxdem.rl.environments.MultiNavigator static method) (jaxdem.rl.environments.MultiRoller static method) (jaxdem.rl.environments.single_navigator.SingleNavigator static method) (jaxdem.rl.environments.single_roller.SingleRoller static method) (jaxdem.rl.environments.SingleNavigator static method) (jaxdem.rl.environments.SingleRoller static method) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator static method) (jaxdem.rl.environments.swarm_roller.SwarmRoller static method) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D static method) (jaxdem.rl.environments.SwarmNavigator static method) (jaxdem.rl.environments.SwarmRoller static method) (jaxdem.rl.environments.SwarmRoller3D static method) (jaxdem.rl.environments.three_gears.ThreeGears static method) (jaxdem.rl.environments.ThreeGears static method) (jaxdem.rl.environments.two_gears.TwoGears static method) (jaxdem.rl.environments.TwoGears static method) observation_space_size (jaxdem.rl.Environment property) (jaxdem.rl.environments.burrowing_dp.BurrowingDP property) (jaxdem.rl.environments.Environment property) (jaxdem.rl.environments.multi_navigator.MultiNavigator property) (jaxdem.rl.environments.multi_roller.MultiRoller property) (jaxdem.rl.environments.MultiNavigator property) (jaxdem.rl.environments.MultiRoller property) (jaxdem.rl.environments.single_navigator.SingleNavigator property) (jaxdem.rl.environments.single_roller.SingleRoller property) (jaxdem.rl.environments.SingleNavigator property) (jaxdem.rl.environments.SingleRoller property) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator property) (jaxdem.rl.environments.swarm_roller.SwarmRoller property) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D property) (jaxdem.rl.environments.SwarmNavigator property) (jaxdem.rl.environments.SwarmRoller property) (jaxdem.rl.environments.SwarmRoller3D property) (jaxdem.rl.environments.three_gears.ThreeGears property) (jaxdem.rl.environments.ThreeGears property) (jaxdem.rl.environments.two_gears.TwoGears property) (jaxdem.rl.environments.TwoGears property) (jaxdem.rl.models.lstm.LSTMActorCritic property) (jaxdem.rl.models.LSTMActorCritic property) (jaxdem.rl.models.mingru.MinGRUActorCritic property) (jaxdem.rl.models.MinGRUActorCritic property)

old_pos (jaxdem.colliders.neighbor_list.NeighborList attribute) (jaxdem.colliders.NeighborList attribute) overflow (jaxdem.Collider attribute) (jaxdem.colliders.Collider attribute)

P

packing_fraction (jaxdem.utils.jamming.JamResult attribute) pair (jaxdem.materials.material_table.MaterialTable attribute) (jaxdem.materials.MaterialTable attribute) (jaxdem.MaterialTable attribute) pair_i (jaxdem.analysis.Pairs attribute), [1] (jaxdem.analysis.pairs.Pairs attribute), [1] pair_j (jaxdem.analysis.Pairs attribute), [1] (jaxdem.analysis.pairs.Pairs attribute), [1] pair_non_bonded_hessian() (in module jaxdem.utils) (in module jaxdem.utils.dynamical_matrix) PAIR_UNROLL (in module jaxdem.colliders.cell_list) Pairs (class in jaxdem.analysis) (class in jaxdem.analysis.pairs) pairs (jaxdem.analysis.Binned attribute), [1] (jaxdem.analysis.engine.Binned attribute), [1] pe_band_jam() (in module jaxdem.utils) (in module jaxdem.utils.jamming) periodic (jaxdem.Domain property) (jaxdem.domains.Domain property) (jaxdem.domains.lees_edwards.LeesEdwardsDomain property) (jaxdem.domains.LeesEdwardsDomain property) (jaxdem.domains.periodic.PeriodicDomain property) (jaxdem.domains.PeriodicDomain property) PeriodicDomain (class in jaxdem.domains) (class in jaxdem.domains.periodic) PlasticBendingDeformableParticleModel (class in jaxdem.bonded_forces) (class in jaxdem.bonded_forces.plastic_bending_deformable_particle) PlasticDeformableParticleModel (class in jaxdem.bonded_forces) (class in jaxdem.bonded_forces.plastic_deformable_particle)

PlasticPerimeterDeformableParticleModel (class in jaxdem.bonded_forces) (class in jaxdem.bonded_forces.plastic_perimeter_deformable_particle) point_segment_distance() (in module jaxdem.forces.facet_contact) point_triangle_distance() (in module jaxdem.forces.facet_contact) poisson (jaxdem.materials.Elastic attribute) (jaxdem.materials.elastic_mats.Elastic attribute) (jaxdem.materials.elastic_mats.ElasticFriction attribute) (jaxdem.materials.ElasticFriction attribute) pos (jaxdem.State property) (jaxdem.state.State property) pos_c (jaxdem.State attribute) (jaxdem.state.State attribute) pos_p (jaxdem.State attribute) (jaxdem.state.State attribute) potential_energy (jaxdem.utils.jamming.JamResult attribute) ppo_clip_eps (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) ppo_entropy_coeff (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) ppo_value_coeff (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) PPOTrainer (class in jaxdem.rl.trainers) (class in jaxdem.rl.trainers.ppo_trainer) pressure_bisection_jam() (in module jaxdem.utils) (in module jaxdem.utils.jamming) project_to_tangent() (in module jaxdem.utils.meshes) props (jaxdem.materials.material_table.MaterialTable attribute) (jaxdem.materials.MaterialTable attribute) (jaxdem.MaterialTable attribute)

Q

q (jaxdem.State attribute) (jaxdem.state.State attribute) quasistatic_compress_to_packing_fraction() (in module jaxdem.utils) (in module jaxdem.utils.packing_utils)

Quaternion (class in jaxdem.utils) (class in jaxdem.utils.quaternion)

R

rad (jaxdem.State attribute) (jaxdem.state.State attribute) random_points_on_hyper_ellipsoid() (in module jaxdem.utils.meshes) random_sphere_configuration() (in module jaxdem.utils.random_sphere_configuration) random_state() (in module jaxdem.utils), [1] randomize_orientations() (in module jaxdem.utils), [1] ratio (jaxdem.rl.TrajectoryData attribute) RC_FACTOR (jaxdem.forces.LennardJones attribute) (jaxdem.forces.lennardjones.LennardJones attribute) ReflectDomain (class in jaxdem.domains) (class in jaxdem.domains.reflect) ReflectSphereDomain (class in jaxdem.domains) (class in jaxdem.domains.reflect_sphere) refresh_collider() (in module jaxdem.colliders) register() (jaxdem.Factory class method) (jaxdem.factory.Factory class method) registry_name() (jaxdem.Factory class method) (jaxdem.factory.Factory class method) remove_rattlers() (in module jaxdem.utils) (in module jaxdem.utils.contacts) required_material_properties (jaxdem.ForceModel property) (jaxdem.ForceRouter property) (jaxdem.forces.cundall_strack.CundallStrackForce property) (jaxdem.forces.CundallStrackForce property) (jaxdem.forces.ForceModel property) (jaxdem.forces.ForceRouter property) (jaxdem.forces.hertz.HertzianForce property) (jaxdem.forces.HertzianForce property) (jaxdem.forces.law_combiner.LawCombiner property) (jaxdem.forces.LawCombiner property) (jaxdem.forces.LennardJones property) (jaxdem.forces.lennardjones.LennardJones property) (jaxdem.forces.router.ForceRouter property) (jaxdem.forces.spring.SpringForce property) (jaxdem.forces.SpringForce property) (jaxdem.forces.WCA property) (jaxdem.forces.wca.WCA property) (jaxdem.forces.wca_shifted.WCAShifted property) (jaxdem.forces.WCAShifted property) (jaxdem.LawCombiner property) requires_history (jaxdem.ForceModel property) (jaxdem.ForceRouter property) (jaxdem.forces.ForceModel property) (jaxdem.forces.ForceRouter property) (jaxdem.forces.law_combiner.LawCombiner property) (jaxdem.forces.LawCombiner property) (jaxdem.forces.router.ForceRouter property) (jaxdem.LawCombiner property) rescale_every (jaxdem.integrators.velocity_verlet_rescaling.VelocityVerletRescaling attribute) (jaxdem.integrators.VelocityVerletRescaling attribute) reset() (jaxdem.rl.Environment static method) (jaxdem.rl.environments.burrowing_dp.BurrowingDP static method) (jaxdem.rl.environments.Environment static method) (jaxdem.rl.environments.multi_navigator.MultiNavigator static method) (jaxdem.rl.environments.multi_roller.MultiRoller static method) (jaxdem.rl.environments.MultiNavigator static method) (jaxdem.rl.environments.MultiRoller static method) (jaxdem.rl.environments.single_navigator.SingleNavigator static method) (jaxdem.rl.environments.single_roller.SingleRoller static method) (jaxdem.rl.environments.SingleNavigator static method) (jaxdem.rl.environments.SingleRoller static method) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator static method) (jaxdem.rl.environments.swarm_roller.SwarmRoller static method) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D static method) (jaxdem.rl.environments.SwarmNavigator static method) (jaxdem.rl.environments.SwarmRoller static method) (jaxdem.rl.environments.SwarmRoller3D static method) (jaxdem.rl.environments.three_gears.ThreeGears static method) (jaxdem.rl.environments.ThreeGears static method) (jaxdem.rl.environments.two_gears.TwoGears static method) (jaxdem.rl.environments.TwoGears static method) (jaxdem.rl.Model method) (jaxdem.rl.models.lstm.LSTMActorCritic method) (jaxdem.rl.models.LSTMActorCritic method) (jaxdem.rl.models.mingru.MinGRUActorCritic method) (jaxdem.rl.models.MinGRUActorCritic method) (jaxdem.rl.models.Model method)

reset_if_done() (jaxdem.rl.Environment static method) (jaxdem.rl.environments.Environment static method) restitution_coefficient (jaxdem.domains.reflect.ReflectDomain attribute) (jaxdem.domains.reflect_sphere.ReflectSphereDomain attribute) (jaxdem.domains.ReflectDomain attribute) (jaxdem.domains.ReflectSphereDomain attribute) retract_to_surface() (in module jaxdem.utils.meshes) reward (jaxdem.rl.TrajectoryData attribute) reward() (jaxdem.rl.Environment static method) (jaxdem.rl.environments.burrowing_dp.BurrowingDP static method) (jaxdem.rl.environments.Environment static method) (jaxdem.rl.environments.multi_navigator.MultiNavigator static method) (jaxdem.rl.environments.multi_roller.MultiRoller static method) (jaxdem.rl.environments.MultiNavigator static method) (jaxdem.rl.environments.MultiRoller static method) (jaxdem.rl.environments.single_navigator.SingleNavigator static method) (jaxdem.rl.environments.single_roller.SingleRoller static method) (jaxdem.rl.environments.SingleNavigator static method) (jaxdem.rl.environments.SingleRoller static method) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator static method) (jaxdem.rl.environments.swarm_roller.SwarmRoller static method) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D static method) (jaxdem.rl.environments.SwarmNavigator static method) (jaxdem.rl.environments.SwarmRoller static method) (jaxdem.rl.environments.SwarmRoller3D static method) (jaxdem.rl.environments.three_gears.ThreeGears static method) (jaxdem.rl.environments.ThreeGears static method) (jaxdem.rl.environments.two_gears.TwoGears static method) (jaxdem.rl.environments.TwoGears static method) riesz_energy() (in module jaxdem.utils.meshes) rotate() (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) rotate_back() (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) rotation_integrator (jaxdem.System attribute) (jaxdem.system.System attribute) RotationIntegrator (class in jaxdem) (class in jaxdem.integrators) run_packing_fraction_protocol() (in module jaxdem.utils) (in module jaxdem.utils.dynamics_routines)

S

same_as() (jaxdem.rl.action_spaces.box_space.BoxSpace method) (jaxdem.rl.action_spaces.BoxSpace method) (jaxdem.rl.action_spaces.free_space.FreeSpace method) (jaxdem.rl.action_spaces.FreeSpace method) (jaxdem.rl.action_spaces.max_norm_space.MaxNormSpace method) (jaxdem.rl.action_spaces.MaxNormSpace method) save() (in module jaxdem.utils) (in module jaxdem.utils.h5) (jaxdem.CheckpointModelWriter method) (jaxdem.CheckpointWriter method) (jaxdem.VTKWriter method) (jaxdem.writers.CheckpointModelWriter method) (jaxdem.writers.checkpoints.CheckpointModelWriter method) (jaxdem.writers.checkpoints.CheckpointWriter method) (jaxdem.writers.CheckpointWriter method) (jaxdem.writers.vtk_writer.VTKWriter method) (jaxdem.writers.VTKWriter method) save_every (jaxdem.CheckpointModelWriter attribute) (jaxdem.CheckpointWriter attribute) (jaxdem.VTKWriter attribute) (jaxdem.writers.async_base.BaseAsyncWriter attribute) (jaxdem.writers.CheckpointModelWriter attribute) (jaxdem.writers.checkpoints.CheckpointModelWriter attribute) (jaxdem.writers.checkpoints.CheckpointWriter attribute) (jaxdem.writers.CheckpointWriter attribute) (jaxdem.writers.vtk_writer.VTKWriter attribute) (jaxdem.writers.VTKWriter attribute) scale_to_packing_fraction() (in module jaxdem.utils) (in module jaxdem.utils.packing_utils) scale_to_temperature() (in module jaxdem.utils) (in module jaxdem.utils.thermal) sec2_log() (jaxdem.rl.action_spaces.box_space.BoxSpace static method) (jaxdem.rl.action_spaces.BoxSpace static method) (jaxdem.rl.action_spaces.max_norm_space.MaxNormSpace static method) (jaxdem.rl.action_spaces.MaxNormSpace static method) secondary_collider (jaxdem.colliders.neighbor_list.NeighborList attribute) (jaxdem.colliders.NeighborList attribute) segment_segment_distance() (in module jaxdem.forces.facet_contact) set_temperature() (in module jaxdem.utils) (in module jaxdem.utils.thermal) shape (jaxdem.State property) (jaxdem.state.State property) SharedActorCritic (class in jaxdem.rl.models) (class in jaxdem.rl.models.mlp) shift() (jaxdem.Domain static method) (jaxdem.domains.Domain static method) (jaxdem.domains.lees_edwards.LeesEdwardsDomain static method) (jaxdem.domains.LeesEdwardsDomain static method) (jaxdem.domains.periodic.PeriodicDomain static method) (jaxdem.domains.PeriodicDomain static method) signed_angle() (in module jaxdem.utils) (in module jaxdem.utils.angles) signed_angle_x() (in module jaxdem.utils) (in module jaxdem.utils.angles) signed_bending_angles() (in module jaxdem.bonded_forces.deformable_particle) SingleNavigator (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.single_navigator) SingleRoller (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.single_roller) skin (jaxdem.colliders.neighbor_list.NeighborList attribute) (jaxdem.colliders.NeighborList attribute) skip_frames (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) species_id (jaxdem.State attribute) (jaxdem.state.State attribute) SphereFacetSpringForce (class in jaxdem.forces) (class in jaxdem.forces.spring) Spiral (class in jaxdem.integrators) (class in jaxdem.integrators.spiral) SpringForce (class in jaxdem.forces) (class in jaxdem.forces.spring) stack() (jaxdem.bonded_forces.BondedForceModel class method) (jaxdem.BondedForceModel class method) (jaxdem.State static method) (jaxdem.state.State static method) (jaxdem.System static method) (jaxdem.system.System static method)

State (class in jaxdem) (class in jaxdem.state) state (jaxdem.rl.Environment attribute) (jaxdem.rl.environments.Environment attribute) step() (jaxdem.rl.Environment static method) (jaxdem.rl.environments.burrowing_dp.BurrowingDP static method) (jaxdem.rl.environments.Environment static method) (jaxdem.rl.environments.multi_navigator.MultiNavigator static method) (jaxdem.rl.environments.multi_roller.MultiRoller static method) (jaxdem.rl.environments.MultiNavigator static method) (jaxdem.rl.environments.MultiRoller static method) (jaxdem.rl.environments.single_navigator.SingleNavigator static method) (jaxdem.rl.environments.single_roller.SingleRoller static method) (jaxdem.rl.environments.SingleNavigator static method) (jaxdem.rl.environments.SingleRoller static method) (jaxdem.rl.environments.swarm_navigator.SwarmNavigator static method) (jaxdem.rl.environments.swarm_roller.SwarmRoller static method) (jaxdem.rl.environments.swarm_roller_3d.SwarmRoller3D static method) (jaxdem.rl.environments.SwarmNavigator static method) (jaxdem.rl.environments.SwarmRoller static method) (jaxdem.rl.environments.SwarmRoller3D static method) (jaxdem.rl.environments.three_gears.ThreeGears static method) (jaxdem.rl.environments.ThreeGears static method) (jaxdem.rl.environments.two_gears.TwoGears static method) (jaxdem.rl.environments.TwoGears static method) (jaxdem.rl.Trainer static method) (jaxdem.System static method) (jaxdem.system.System static method) step_after_force() (jaxdem.Integrator static method) (jaxdem.integrators.direct_euler.DirectEuler static method) (jaxdem.integrators.DirectEuler static method) (jaxdem.integrators.Langevin static method) (jaxdem.integrators.langevin.Langevin static method) (jaxdem.integrators.Spiral static method) (jaxdem.integrators.spiral.Spiral static method) (jaxdem.integrators.velocity_verlet.VelocityVerlet static method) (jaxdem.integrators.velocity_verlet_rescaling.VelocityVerletRescaling static method) (jaxdem.integrators.velocity_verlet_spiral.VelocityVerletSpiral static method) (jaxdem.integrators.VelocityVerlet static method) (jaxdem.integrators.VelocityVerletRescaling static method) (jaxdem.integrators.VelocityVerletSpiral static method) (jaxdem.integrators.vicsek.VicsekExtrinsic static method) (jaxdem.integrators.vicsek.VicsekIntrinsic static method) (jaxdem.integrators.VicsekExtrinsic static method) (jaxdem.integrators.VicsekIntrinsic static method) step_before_force() (jaxdem.Integrator static method) (jaxdem.integrators.Langevin static method) (jaxdem.integrators.langevin.Langevin static method) (jaxdem.integrators.velocity_verlet.VelocityVerlet static method) (jaxdem.integrators.velocity_verlet_spiral.VelocityVerletSpiral static method) (jaxdem.integrators.VelocityVerlet static method) (jaxdem.integrators.VelocityVerletSpiral static method) step_count (jaxdem.System attribute) (jaxdem.system.System attribute) stop_at_epoch (jaxdem.rl.trainers.ppo_trainer.PPOTrainer attribute) (jaxdem.rl.trainers.PPOTrainer attribute) submit() (jaxdem.writers.async_base.BaseAsyncWriter method) subtract_drift (jaxdem.integrators.velocity_verlet_rescaling.VelocityVerletRescaling attribute) (jaxdem.integrators.VelocityVerletRescaling attribute) sums (jaxdem.analysis.Binned attribute), [1] (jaxdem.analysis.engine.Binned attribute), [1] SwarmNavigator (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.swarm_navigator) SwarmRoller (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.swarm_roller) SwarmRoller3D (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.swarm_roller_3d) System (class in jaxdem) (class in jaxdem.system) system (jaxdem.rl.Environment attribute) (jaxdem.rl.environments.Environment attribute)

T

table (jaxdem.ForceRouter attribute) (jaxdem.forces.ForceRouter attribute) (jaxdem.forces.router.ForceRouter attribute) target_fn (jaxdem.System attribute) (jaxdem.system.System attribute) tau_s (jaxdem.bonded_forces.plastic_bending_deformable_particle.PlasticBendingDeformableParticleModel attribute) (jaxdem.bonded_forces.plastic_deformable_particle.PlasticDeformableParticleModel attribute) (jaxdem.bonded_forces.plastic_perimeter_deformable_particle.PlasticPerimeterDeformableParticleModel attribute) (jaxdem.bonded_forces.PlasticBendingDeformableParticleModel attribute) (jaxdem.bonded_forces.PlasticDeformableParticleModel attribute) (jaxdem.bonded_forces.PlasticPerimeterDeformableParticleModel attribute) temperature (jaxdem.integrators.Langevin attribute) (jaxdem.integrators.langevin.Langevin attribute) (jaxdem.integrators.velocity_verlet_rescaling.VelocityVerletRescaling attribute) (jaxdem.integrators.VelocityVerletRescaling attribute) ThreeGears (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.three_gears) time (jaxdem.System attribute) (jaxdem.system.System attribute)

TimeBins (class in jaxdem.analysis) (class in jaxdem.analysis.bins) torque (jaxdem.State attribute) (jaxdem.state.State attribute) train() (jaxdem.rl.Trainer static method) (jaxdem.rl.trainers.ppo_trainer.PPOTrainer static method) (jaxdem.rl.trainers.PPOTrainer static method) Trainer (class in jaxdem.rl) trajectory_rollout() (jaxdem.rl.Trainer static method) (jaxdem.System static method) (jaxdem.system.System static method) TrajectoryData (class in jaxdem.rl) Transformed (class in jaxdem.rl.action_spaces) triangle_triangle_distance() (in module jaxdem.forces.facet_contact) TwoGears (class in jaxdem.rl.environments) (class in jaxdem.rl.environments.two_gears) type_name (jaxdem.Factory property) (jaxdem.factory.Factory property) (jaxdem.minimizers.optimizers.CustomGradientTransformation attribute)

U

unit() (in module jaxdem.utils) (in module jaxdem.utils.linalg) (jaxdem.utils.Quaternion static method) (jaxdem.utils.quaternion.Quaternion static method) unit_and_norm() (in module jaxdem.utils) (in module jaxdem.utils.linalg) unjammed_state (jaxdem.utils.jamming.JamResult attribute) unjammed_system (jaxdem.utils.jamming.JamResult attribute) unstack() (jaxdem.bonded_forces.BondedForceModel class method) (jaxdem.BondedForceModel class method) (jaxdem.State static method) (jaxdem.state.State static method) (jaxdem.System static method) (jaxdem.system.System static method) unwrap() (in module jaxdem.rl) (in module jaxdem.rl.envWrappers)

unwrap_angles_2d() (in module jaxdem.analysis) (in module jaxdem.analysis.kernels) update_reference_state() (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel method) (jaxdem.bonded_forces.DeformableParticleModel method) (jaxdem.bonded_forces.plastic_bending_deformable_particle.PlasticBendingDeformableParticleModel method) (jaxdem.bonded_forces.plastic_deformable_particle.PlasticDeformableParticleModel method) (jaxdem.bonded_forces.plastic_perimeter_deformable_particle.PlasticPerimeterDeformableParticleModel method) (jaxdem.bonded_forces.PlasticBendingDeformableParticleModel method) (jaxdem.bonded_forces.PlasticDeformableParticleModel method) (jaxdem.bonded_forces.PlasticPerimeterDeformableParticleModel method) user_post_step_actions() (jaxdem.System method) (jaxdem.system.System method) user_pre_step_actions() (jaxdem.System method) (jaxdem.system.System method)

V

v0 (jaxdem.integrators.vicsek.VicsekExtrinsic attribute) (jaxdem.integrators.vicsek.VicsekIntrinsic attribute) (jaxdem.integrators.VicsekExtrinsic attribute) (jaxdem.integrators.VicsekIntrinsic attribute) valid_interaction_mask() (in module jaxdem.colliders) value (jaxdem.rl.TrajectoryData attribute) value_of_bin() (jaxdem.analysis.bins.BinSpec method) (jaxdem.analysis.bins.LagBinsExact method) (jaxdem.analysis.bins.TimeBins method) (jaxdem.analysis.BinSpec method) (jaxdem.analysis.LagBinsExact method) (jaxdem.analysis.TimeBins method) values() (jaxdem.analysis.bins.BinSpec method) (jaxdem.analysis.BinSpec method) vectorise_env() (in module jaxdem.rl) (in module jaxdem.rl.envWrappers) vel (jaxdem.minimizers.optimizers.DampedNewtonianState attribute), [1] (jaxdem.minimizers.optimizers.FIREState attribute), [1] (jaxdem.State attribute) (jaxdem.state.State attribute) VelocityVerlet (class in jaxdem.integrators) (class in jaxdem.integrators.velocity_verlet) VelocityVerletRescaling (class in jaxdem.integrators) (class in jaxdem.integrators.velocity_verlet_rescaling) VelocityVerletSpiral (class in jaxdem.integrators) (class in jaxdem.integrators.velocity_verlet_spiral)

VicsekExtrinsic (class in jaxdem.integrators) (class in jaxdem.integrators.vicsek) VicsekIntrinsic (class in jaxdem.integrators) (class in jaxdem.integrators.vicsek) volume (jaxdem.State attribute) (jaxdem.state.State attribute) VTKBaseWriter (class in jaxdem) (class in jaxdem.writers) VTKDeformableEdgeAdjacenciesWriter (class in jaxdem.writers) (class in jaxdem.writers.vtk_deformable_particle_writer) VTKDeformableEdgesWriter (class in jaxdem.writers) (class in jaxdem.writers.vtk_deformable_particle_writer) VTKDeformableElementsWriter (class in jaxdem.writers) (class in jaxdem.writers.vtk_deformable_particle_writer) VTKDomainWriter (class in jaxdem.writers) (class in jaxdem.writers.vtk_domain_writer) VTKFacetSpheresWriter (class in jaxdem.writers) (class in jaxdem.writers.vtk_spheres_writer) VTKFacetsWriter (class in jaxdem.writers) (class in jaxdem.writers.vtk_facets_writer) VTKSpheresWriter (class in jaxdem.writers) (class in jaxdem.writers.vtk_spheres_writer) VTKWriter (class in jaxdem) (class in jaxdem.writers) (class in jaxdem.writers.vtk_writer)

W

w (jaxdem.utils.Quaternion attribute), [1] (jaxdem.utils.quaternion.Quaternion attribute), [1] w_b (jaxdem.bonded_forces.deformable_particle.DeformableParticleModel attribute) (jaxdem.bonded_forces.DeformableParticleModel attribute) WCA (class in jaxdem.forces) (class in jaxdem.forces.wca) WCAShifted (class in jaxdem.forces) (class in jaxdem.forces.wca_shifted) weight() (jaxdem.analysis.bins.BinSpec method) (jaxdem.analysis.bins.LagBinsExact method) (jaxdem.analysis.bins.TimeBins method) (jaxdem.analysis.BinSpec method) (jaxdem.analysis.LagBinsExact method) (jaxdem.analysis.TimeBins method) write() (jaxdem.VTKBaseWriter class method) (jaxdem.writers.vtk_deformable_particle_writer.VTKDeformableEdgeAdjacenciesWriter class method) (jaxdem.writers.vtk_deformable_particle_writer.VTKDeformableEdgesWriter class method) (jaxdem.writers.vtk_deformable_particle_writer.VTKDeformableElementsWriter class method) (jaxdem.writers.vtk_domain_writer.VTKDomainWriter class method) (jaxdem.writers.vtk_facets_writer.VTKFacetsWriter class method) (jaxdem.writers.vtk_spheres_writer.VTKFacetSpheresWriter class method) (jaxdem.writers.vtk_spheres_writer.VTKSpheresWriter class method) (jaxdem.writers.VTKBaseWriter class method) (jaxdem.writers.VTKDeformableEdgeAdjacenciesWriter class method) (jaxdem.writers.VTKDeformableEdgesWriter class method) (jaxdem.writers.VTKDeformableElementsWriter class method) (jaxdem.writers.VTKDomainWriter class method) (jaxdem.writers.VTKFacetSpheresWriter class method) (jaxdem.writers.VTKFacetsWriter class method) (jaxdem.writers.VTKSpheresWriter class method)

writers (jaxdem.VTKWriter attribute) (jaxdem.writers.vtk_writer.VTKWriter attribute) (jaxdem.writers.VTKWriter attribute)

X

xyz (jaxdem.utils.Quaternion attribute), [1] (jaxdem.utils.quaternion.Quaternion attribute), [1]

Y

young (jaxdem.materials.Elastic attribute) (jaxdem.materials.elastic_mats.Elastic attribute) (jaxdem.materials.elastic_mats.ElasticFriction attribute) (jaxdem.materials.ElasticFriction attribute)

Z

zero_mode_mask() (in module jaxdem.utils) (in module jaxdem.utils.dynamical_matrix)