Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V A allocate (jax_md.partition.NeighborListFns attribute) alpha (jax_md.minimize.FireDescentState attribute) angular_momentum_to_conjugate_momentum() (in module jax_md.rigid_body) angular_symmetry_functions() (in module jax_md._nn.behler_parrinello) angular_symmetry_functions_neighbor_list() (in module jax_md._nn.behler_parrinello) athermal_moduli() (in module jax_md.elasticity) B barostat (jax_md.simulate.NPTNoseHooverState attribute) behler_parrinello() (in module jax_md.energy) behler_parrinello_neighbor_list() (in module jax_md.energy) bks() (in module jax_md.energy) bks_neighbor_list() (in module jax_md.energy) bks_pair() (in module jax_md.energy) bks_silica_neighbor_list() (in module jax_md.energy) bks_silica_pair() (in module jax_md.energy) bond() (in module jax_md.smap) box_mass (jax_md.simulate.NPTNoseHooverState attribute) box_position (jax_md.simulate.NPTNoseHooverState attribute) box_velocity (jax_md.simulate.NPTNoseHooverState attribute) brownian() (in module jax_md.simulate) BrownianState (class in jax_md.simulate) C canonicalize_displacement_or_metric() (in module jax_md.space) canonicalize_force() (in module jax_md.quantity) cell_capacity (jax_md.partition.CellList attribute) cell_list() (in module jax_md.partition) cell_list_capacity (jax_md.partition.NeighborList attribute) cell_list_fn (jax_md.partition.NeighborList attribute) cell_size (jax_md.partition.NeighborList attribute) CellList (class in jax_md.partition) center (jax_md.rigid_body.RigidBody attribute) chain (jax_md.simulate.NVTNoseHooverState attribute) chain_length (in module jax_md.simulate) chain_steps (in module jax_md.simulate) concatenate_shapes() (in module jax_md.rigid_body) conjugate_momentum_to_angular_momentum() (in module jax_md.rigid_body) cosine_angles() (in module jax_md.quantity) D degrees_of_freedom (jax_md.simulate.NoseHooverChain attribute) Dense (jax_md.partition.NeighborListFormat attribute) did_buffer_overflow (jax_md.partition.CellList attribute) distance() (in module jax_md.space) dt (in module jax_md.simulate) (jax_md.minimize.FireDescentState attribute) E eam() (in module jax_md.energy) eam_from_lammps_parameters() (in module jax_md.energy) eam_from_lammps_parameters_neighbor_list() (in module jax_md.energy) eam_neighbor_list() (in module jax_md.energy) edge_idx (jax_md.nn.GraphsTuple attribute) edges (jax_md.nn.GraphsTuple attribute) error (jax_md.partition.NeighborList attribute) extract_elements() (in module jax_md.elasticity) extract_isotropic_moduli() (in module jax_md.elasticity) F fire_descent() (in module jax_md.minimize) FireDescentState (class in jax_md.minimize) force (jax_md.minimize.FireDescentState attribute) (jax_md.simulate.NPTNoseHooverState attribute) (jax_md.simulate.NVEState attribute) (jax_md.simulate.NVTLangevinState attribute) (jax_md.simulate.NVTNoseHooverState attribute) force() (in module jax_md.quantity) format (jax_md.partition.NeighborList attribute) free() (in module jax_md.space) G Global (jax_md.smap.ParameterTreeMapping attribute) globals (jax_md.nn.GraphsTuple attribute) gradient_descent() (in module jax_md.minimize) graph_network() (in module jax_md.energy) graph_network_neighbor_list() (in module jax_md.energy) GraphMapFeatures (class in jax_md.nn) GraphNetwork (class in jax_md.nn) GraphsTuple (class in jax_md.nn) gupta_gold55() (in module jax_md.energy) gupta_potential() (in module jax_md.energy) H hybrid_swap_mc() (in module jax_md.simulate) I id_buffer (jax_md.partition.CellList attribute) idx (jax_md.partition.NeighborList attribute) J jax_md.elasticity module jax_md.energy module jax_md.minimize module jax_md.nn module jax_md.partition module jax_md.quantity module jax_md.rigid_body module jax_md.simulate module jax_md.smap module jax_md.space module K kinetic_energy (jax_md.simulate.NoseHooverChain attribute) kinetic_energy() (in module jax_md.quantity) (in module jax_md.rigid_body) L lennard_jones() (in module jax_md.energy) lennard_jones_neighbor_list() (in module jax_md.energy) lennard_jones_pair() (in module jax_md.energy) load_lammps_eam_parameters() (in module jax_md.energy), [1] load_lammps_tersoff_parameters() (in module jax_md.energy) M mandel_to_tensor() (in module jax_md.elasticity) map_bond() (in module jax_md.space) map_neighbor() (in module jax_md.space) map_product() (in module jax_md.space) mapping (jax_md.smap.ParameterTree attribute) mass (jax_md.simulate.BrownianState attribute) (jax_md.simulate.NoseHooverChain attribute) (jax_md.simulate.NPTNoseHooverState attribute) (jax_md.simulate.NVEState attribute) (jax_md.simulate.NVTLangevinState attribute) (jax_md.simulate.NVTNoseHooverState attribute) masses (jax_md.rigid_body.RigidPointUnion attribute) max_occupancy (jax_md.partition.NeighborList attribute) metric() (in module jax_md.space) module jax_md.elasticity jax_md.energy jax_md.minimize jax_md.nn jax_md.partition jax_md.quantity jax_md.rigid_body jax_md.simulate jax_md.smap jax_md.space momentum (jax_md.simulate.NoseHooverChain attribute) (jax_md.simulate.NPTNoseHooverState attribute) (jax_md.simulate.NVEState attribute) (jax_md.simulate.NVTLangevinState attribute) (jax_md.simulate.NVTNoseHooverState attribute) morse() (in module jax_md.energy) morse_neighbor_list() (in module jax_md.energy) morse_pair() (in module jax_md.energy) multiplicative_isotropic_cutoff() (in module jax_md.energy) N n_pos (jax_md.minimize.FireDescentState attribute) named_buffer (jax_md.partition.CellList attribute) neighbor_list() (in module jax_md.partition) neighbor_list_mask() (in module jax_md.partition) NeighborList (class in jax_md.partition) NeighborListFns (class in jax_md.partition) NeighborListFormat (class in jax_md.partition) nodes (jax_md.nn.GraphsTuple attribute) nose_hoover_chain() (in module jax_md.simulate) NoseHooverChain (class in jax_md.simulate) npt_box() (in module jax_md.simulate) npt_nose_hoover() (in module jax_md.simulate) npt_nose_hoover_invariant() (in module jax_md.simulate) NPTNoseHooverState (class in jax_md.simulate) nve() (in module jax_md.simulate) NVEState (class in jax_md.simulate) nvt_langevin() (in module jax_md.simulate) nvt_nose_hoover() (in module jax_md.simulate) nvt_nose_hoover_invariant() (in module jax_md.simulate) NVTLangevinState (class in jax_md.simulate) NVTNoseHooverState (class in jax_md.simulate) O OrderedSparse (jax_md.partition.NeighborListFormat attribute) orientation (jax_md.rigid_body.RigidBody attribute) P pair() (in module jax_md.smap) pair_correlation() (in module jax_md.quantity) pair_correlation_neighbor_list() (in module jax_md.quantity) pair_neighbor_list() (in module jax_md.smap) pairwise_displacement() (in module jax_md.space) ParameterTree (class in jax_md.smap) ParameterTreeMapping (class in jax_md.smap) PerBond (jax_md.smap.ParameterTreeMapping attribute) periodic() (in module jax_md.space) periodic_general() (in module jax_md.space) periodic_shift() (in module jax_md.space) PerParticle (jax_md.smap.ParameterTreeMapping attribute) PerSpecies (jax_md.smap.ParameterTreeMapping attribute) phop() (in module jax_md.quantity) PHopState (class in jax_md.quantity) point_count (jax_md.rigid_body.RigidPointUnion attribute) point_energy() (in module jax_md.rigid_body) point_energy_neighbor_list() (in module jax_md.rigid_body) point_offset (jax_md.rigid_body.RigidPointUnion attribute) point_radius (jax_md.rigid_body.RigidPointUnion attribute) point_species (jax_md.rigid_body.RigidPointUnion attribute) point_union_shape() (in module jax_md.rigid_body) points (jax_md.rigid_body.RigidPointUnion attribute) position (jax_md.minimize.FireDescentState attribute) (jax_md.simulate.BrownianState attribute) (jax_md.simulate.NoseHooverChain attribute) (jax_md.simulate.NPTNoseHooverState attribute) (jax_md.simulate.NVEState attribute) (jax_md.simulate.NVTLangevinState attribute) (jax_md.simulate.NVTNoseHooverState attribute) position_buffer (jax_md.partition.CellList attribute) pressure() (in module jax_md.quantity) Q Quaternion (class in jax_md.rigid_body) quaternion_rotate() (in module jax_md.rigid_body) R radial_symmetry_functions() (in module jax_md._nn.behler_parrinello) radial_symmetry_functions_neighbor_list() (in module jax_md._nn.behler_parrinello) random_quaternion() (in module jax_md.rigid_body) reference_box (jax_md.simulate.NPTNoseHooverState attribute) reference_position (jax_md.partition.NeighborList attribute) RigidBody (class in jax_md.rigid_body) RigidPointUnion (class in jax_md.rigid_body) rng (jax_md.simulate.BrownianState attribute) (jax_md.simulate.NVTLangevinState attribute) S simple_spring() (in module jax_md.energy) simple_spring_bond() (in module jax_md.energy) soft_sphere() (in module jax_md.energy) soft_sphere_neighbor_list() (in module jax_md.energy) soft_sphere_pair() (in module jax_md.energy) Sparse (jax_md.partition.NeighborListFormat attribute) square_distance() (in module jax_md.space) stillinger_weber() (in module jax_md.energy) stillinger_weber_neighbor_list() (in module jax_md.energy) stress() (in module jax_md.quantity) sy_steps (in module jax_md.simulate) T tau (in module jax_md.simulate) (jax_md.simulate.NoseHooverChain attribute) temperature() (in module jax_md.quantity) (in module jax_md.rigid_body) tensor_to_mandel() (in module jax_md.elasticity) tersoff() (in module jax_md.energy) tersoff_from_lammps_parameters_neighbor_list() (in module jax_md.energy) tersoff_neighbor_list() (in module jax_md.energy) thermostsat (jax_md.simulate.NPTNoseHooverState attribute) to_dense() (in module jax_md.partition) to_jraph() (in module jax_md.partition) transform() (in module jax_md.rigid_body) (in module jax_md.space) tree (jax_md.smap.ParameterTree attribute) triplet() (in module jax_md.smap) U union_to_points() (in module jax_md.rigid_body) update (jax_md.partition.NeighborListFns attribute) update_fn (jax_md.partition.CellList attribute) (jax_md.partition.NeighborList attribute) V vec (jax_md.rigid_body.Quaternion attribute) velocity (jax_md.minimize.FireDescentState attribute) velocity_verlet() (in module jax_md.simulate)