Index

A

alf (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) allocate (jax_md.custom_partition.NeighborListMultiImageFns attribute) (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborListFns attribute) (jax_md.partition.NeighborListFns attribute) allocate() (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration method) allocate_fixed() (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration method) alpha (jax_md.minimize.FireDescentState attribute)

amas (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) angle() (in module jax_md.smap) 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) aval (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

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) bo131 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) bo132 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) bo133 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) body2_params_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) body34_params_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) body3_indices_dst (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) body3_indices_src (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

body3_params_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) body4_indices_dst (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) body4_indices_src (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) body4_params_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) body_34_candidate_fn() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) body_3_candidate_fn() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) body_4_candidate_fn() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) bond() (in module jax_md.smap) bop1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) bop2 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) box (jax_md.custom_partition.NeighborListMultiImage attribute), [1] 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

calculate_acks2_charges() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_acks2_coulomb_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_all_4_body_angles() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) calculate_all_angles_and_distances() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) calculate_all_hbond_angles_and_dists() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) calculate_angle() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) calculate_bo() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_boncor_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_charge_energy() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_charge_energy_acks2() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_coulomb_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_covbon_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_eem_charges() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_hb_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_lonpar_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_ovcor_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_reaxff_energy() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_torsion_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_valency_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) calculate_vdw_pot() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) candidate_fn (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration attribute), [1]

canonicalize() (in module jax_md.interpolate) 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) close_nbrs (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) concatenate_shapes() (in module jax_md.rigid_body) conjugate_momentum_to_angular_momentum() (in module jax_md.rigid_body) constant() (in module jax_md.interpolate) cosine_angles() (in module jax_md.quantity) count() (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration method) cutoff (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) cutoff2 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

D

dataclass() (in module jax_md.dataclasses) de1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) de2 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) de3 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) degrees_of_freedom (jax_md.simulate.NoseHooverChain attribute) dehb (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) Dense (jax_md.partition.NeighborListFormat attribute)

did_buffer_overflow (jax_md.custom_partition.NeighborListMultiImage attribute), [1] (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration attribute), [1] (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) (jax_md.partition.CellList attribute) distance() (in module jax_md.space) dt (in module jax_md.simulate) (jax_md.minimize.FireDescentState attribute) dUdV (jax_md.simulate.NPTNoseHooverState 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)

electronegativity (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) eps (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) error (jax_md.partition.NeighborList attribute) estimate_max_neighbors() (in module jax_md.custom_partition) estimate_max_neighbors_from_box() (in module jax_md.custom_partition) extract_elements() (in module jax_md.elasticity) extract_isotropic_moduli() (in module jax_md.elasticity)

F

far_nbrs (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) fill_off_diag() (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField method) fill_symm() (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField method) filter2 (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) filter3 (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) filter34 (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) filter4 (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) filter_hb (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) filter_hb_close (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) filter_hb_far (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists attribute) Filtration (class in jax_md.mm_forcefields.reaxff.reaxff_interactions) filtration() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) find_3_body_inter() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions)

find_body_4_inter() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) 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) ForceField (class in jax_md.mm_forcefields.reaxff.reaxff_forcefield) format (jax_md.custom_partition.NeighborListMultiImage attribute), [1] (jax_md.partition.NeighborList attribute) free() (in module jax_md.space)

G

gamma (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) Global (jax_md.smap.ParameterTreeMapping attribute) global_params (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) globals (jax_md.nn.GraphsTuple attribute) gradient_descent() (in module jax_md.minimize) graph_featurizer() (in module jax_md.custom_partition)

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

hb_close_cutoff (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) hb_far_cutoff (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

hb_params_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) hbond_candidate_fn() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) hybrid_swap_mc() (in module jax_md.simulate)

I

id_buffer (jax_md.partition.CellList attribute) idempotential (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) idx (jax_md.custom_partition.NeighborListMultiImage attribute), [1] (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration attribute), [1] (jax_md.partition.NeighborList attribute)

init_from_arg_dict() (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField class method) init_params_for_filler_atom_type() (in module jax_md.mm_forcefields.reaxff.reaxff_helper) is_dense (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration attribute), [1]

J

jax_md.custom_partition module jax_md.custom_smap module jax_md.dataclasses module jax_md.elasticity module jax_md.energy module jax_md.interpolate module jax_md.minimize module jax_md.mm_forcefields.reaxff module jax_md.mm_forcefields.reaxff.reaxff_energy module jax_md.mm_forcefields.reaxff.reaxff_forcefield module

jax_md.mm_forcefields.reaxff.reaxff_helper module jax_md.mm_forcefields.reaxff.reaxff_interactions 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) low_tap_rad (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

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) mask_fn (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration attribute), [1] mass (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) masses (jax_md.rigid_body.RigidPointUnion attribute) max_neighbors (jax_md.custom_partition.NeighborListMultiImage property) max_occupancy (jax_md.custom_partition.NeighborListMultiImage attribute), [1] (jax_md.partition.NeighborList attribute) metric() (in module jax_md.space) module jax_md.custom_partition jax_md.custom_smap jax_md.dataclasses jax_md.elasticity jax_md.energy jax_md.interpolate jax_md.minimize jax_md.mm_forcefields.reaxff jax_md.mm_forcefields.reaxff.reaxff_energy jax_md.mm_forcefields.reaxff.reaxff_forcefield jax_md.mm_forcefields.reaxff.reaxff_helper jax_md.mm_forcefields.reaxff.reaxff_interactions 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.minimize.FireDescentState 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) 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_edges (jax_md.custom_partition.NeighborListMultiImage property) n_node (jax_md.custom_partition.NeighborListMultiImage property) n_pos (jax_md.minimize.FireDescentState attribute) name_to_index (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) named_buffer (jax_md.partition.CellList attribute) neighbor_list() (in module jax_md.partition) neighbor_list_mask() (in module jax_md.partition) neighbor_list_multi_image() (in module jax_md.custom_partition) neighbor_list_multi_image_mask() (in module jax_md.custom_partition) NeighborList (class in jax_md.partition) NeighborListFns (class in jax_md.partition) NeighborListFormat (class in jax_md.partition) NeighborListMultiImage (class in jax_md.custom_partition) NeighborListMultiImageFns (class in jax_md.custom_partition) nodes (jax_md.nn.GraphsTuple attribute)

nose_hoover_chain() (in module jax_md.simulate) NoseHooverChain (class in jax_md.simulate) nphb (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) 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) num_atom_types (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) 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)

ovc (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) over_coord1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) over_coord2 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

P

p1co (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) p1co_off (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) p1co_off_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) p2co (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) p2co_off (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) p2co_off_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) p3co (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) p3co_off (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) p3co_off_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) 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) pair_neighbor_list_multi_image() (in module jax_md.custom_smap) pairwise_displacement() (in module jax_md.space) par_10 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_16 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_24 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_25 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_26 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_28 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_32 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_33 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_35 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_6 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_7 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) par_9 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) ParameterTree (class in jax_md.smap) ParameterTreeMapping (class in jax_md.smap) params_to_indices (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) particle_cell_id (jax_md.partition.CellList attribute)

pdo (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) pdp (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) 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) popi (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField 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) psi (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) psp (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) ptp (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

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) rapt (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rat (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) read_force_field() (in module jax_md.mm_forcefields.reaxff.reaxff_helper) reaxff_inter_list() (in module jax_md.mm_forcefields.reaxff.reaxff_interactions) ReaxFFNeighborListFns (class in jax_md.mm_forcefields.reaxff.reaxff_interactions) ReaxFFNeighborLists (class in jax_md.mm_forcefields.reaxff.reaxff_interactions) receivers (jax_md.custom_partition.NeighborListMultiImage property) reference_box (jax_md.custom_partition.NeighborListMultiImage attribute), [1] (jax_md.simulate.NPTNoseHooverState attribute) reference_position (jax_md.custom_partition.NeighborListMultiImage attribute), [1] (jax_md.partition.NeighborList attribute)

rhb (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField 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) rob1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rob1_off (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rob1_off_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rob2 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rob2_off (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rob2_off_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rob3 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rob3_off (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rob3_off_mask (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) rvdw (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

S

safe_sqrt_jvp() (in module jax_md.mm_forcefields.reaxff.reaxff_helper) search_shifts (jax_md.custom_partition.NeighborListMultiImage attribute), [1] self_energies (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) senders (jax_md.custom_partition.NeighborListMultiImage property) set() (jax_md.custom_partition.NeighborListMultiImage method) (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField method) (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration method) (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborListFns method) (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborLists method) shift (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) shifts (jax_md.custom_partition.NeighborListMultiImage attribute), [1] simple_spring() (in module jax_md.energy) simple_spring_bond() (in module jax_md.energy) smooth_lone_pair_casting() (in module jax_md.mm_forcefields.reaxff.reaxff_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) softcut (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) softcut_2d (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) Sparse (jax_md.partition.NeighborListFormat attribute) spline() (in module jax_md.interpolate) square_distance() (in module jax_md.space) static_field() (in module jax_md.dataclasses) stillinger_weber() (in module jax_md.energy) stillinger_weber_neighbor_list() (in module jax_md.energy) stlp (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) stress() (in module jax_md.quantity) sy_steps (in module jax_md.simulate)

T

taper() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) taper_inc() (in module jax_md.mm_forcefields.reaxff.reaxff_energy) 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) th0 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

thermostat (jax_md.simulate.NPTNoseHooverState attribute) to_dense() (in module jax_md.partition) to_jraph() (in module jax_md.partition) torsion() (in module jax_md.smap) transform() (in module jax_md.rigid_body) (in module jax_md.space) tree (jax_md.smap.ParameterTree attribute) trip_stab11 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) trip_stab4 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) trip_stab5 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) trip_stab8 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) triplet() (in module jax_md.smap)

U

union_to_points() (in module jax_md.rigid_body) unpack() (in module jax_md.dataclasses) up_tap_rad (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) update (jax_md.custom_partition.NeighborListMultiImageFns attribute) (jax_md.mm_forcefields.reaxff.reaxff_interactions.ReaxFFNeighborListFns attribute) (jax_md.partition.NeighborListFns attribute)

update() (jax_md.custom_partition.NeighborListMultiImage method) (jax_md.mm_forcefields.reaxff.reaxff_interactions.Filtration method) update_fn (jax_md.custom_partition.NeighborListMultiImage attribute), [1] (jax_md.partition.CellList attribute) (jax_md.partition.NeighborList attribute)

V

v1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) v13cor (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) v2 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) v3 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) v4 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par15 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par17 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par18 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par20 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par21 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par22 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par3 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par31 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par34 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) val_par39 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) valf (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) valp1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vconj (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vdw_shiedling (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)

vec (jax_md.rigid_body.Quaternion attribute) vectorized_cond() (in module jax_md.mm_forcefields.reaxff.reaxff_helper) velocity_verlet() (in module jax_md.simulate) vhb1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vhb2 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vka (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vka3 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vka8 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vkac (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vkap (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vlp1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vnq (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vop (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vover (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vovun (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vval1 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vval2 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vval3 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute) vval4 (jax_md.mm_forcefields.reaxff.reaxff_forcefield.ForceField attribute)