Index

_

__getitem__() (pyrid.data_structures.dynamic_array_util.HolesArray method) __init__() (pyrid.data_structures.cell_list_util.CellListMesh method) (pyrid.data_structures.dynamic_array_util.DenseArray method) (pyrid.data_structures.dynamic_array_util.DenseArrayReact method) (pyrid.data_structures.dynamic_array_util.HolesArray method) (pyrid.data_structures.dynamic_array_util.HolesArrayReact method) (pyrid.evaluation.evaluation_util.Evaluation method) (pyrid.molecules.particles_util.Particles method) (pyrid.molecules.rigidbody_util.RBs method) (pyrid.observables.observables_util.Observables method) (pyrid.reactions.reactions_registry_util.Reaction method)

__setitem__() (pyrid.data_structures.dynamic_array_util.HolesArray method) _append() (pyrid.data_structures.dynamic_array_util.HolesArray method) _resize() (pyrid.data_structures.cell_list_util.CellListMesh method) (pyrid.data_structures.dynamic_array_util.DenseArray method) (pyrid.data_structures.dynamic_array_util.DenseArrayReact method) (pyrid.data_structures.dynamic_array_util.HolesArray method) (pyrid.data_structures.dynamic_array_util.HolesArrayReact method) _resize_index() (pyrid.data_structures.dynamic_array_util.DenseArray method)

A

A() (in module pyrid.molecules.hydro_util) add() (pyrid.data_structures.dynamic_array_util.DenseArray method) add_barostat_berendsen() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) add_bm_reaction() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) add_border_2d() (pyrid.system.system_util.Compartment method) add_border_3d() (pyrid.system.system_util.Compartment method) (pyrid.system.system_util.System method) add_bp_reaction() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) add_checkpoints() (pyrid.run.Simulation method) add_edges() (pyrid.system.system_util.System method) add_group() (pyrid.system.system_util.Compartment method) add_interaction() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) add_mesh() (pyrid.system.system_util.System method) add_molecule_single() (in module pyrid.system.distribute_surface_util) (in module pyrid.system.distribute_vol_util) add_molecules() (in module pyrid.system.distribute_surface_util) (in module pyrid.system.distribute_vol_util) (pyrid.run.Simulation method)

add_neighbours() (pyrid.system.system_util.System method) add_particle() (pyrid.molecules.particles_util.Particles method) (pyrid.molecules.rigidbody_util.RBs method) add_path() (pyrid.reactions.reactions_registry_util.Reaction method) add_RB() (pyrid.molecules.rigidbody_util.RBs method) add_release_site() (pyrid.run.Simulation method) add_system_grid() (pyrid.system.system_util.System method) add_to_occupied() (pyrid.data_structures.dynamic_array_util.HolesArray method) add_um_reaction() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) add_up_reaction() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) allocate_slot() (pyrid.data_structures.cell_list_util.CellListMesh method) (pyrid.data_structures.dynamic_array_util.HolesArrayReact method) any_ray_mesh_intersection_test() (in module pyrid.geometry.intersections_util) append_reaction() (pyrid.reactions.reactions_registry_util.Reaction method) axis_angle_parameters() (in module pyrid.math.transform_util) axis_halfangle_parameters() (in module pyrid.math.transform_util)

B

barycentric_coord() (in module pyrid.math.transform_util) barycentric_coord_projection_method() (in module pyrid.math.transform_util)

barycentric_direction() (in module pyrid.math.transform_util) barycentric_params() (in module pyrid.math.transform_util) bisect_right() (in module pyrid.math.random_util)

C

calc_A_B() (in module pyrid.evaluation.diffusion_util) calc_centroid_radius_AABB() (pyrid.system.system_util.Compartment method) calc_CoD() (in module pyrid.molecules.hydro_util) calc_D() (in module pyrid.molecules.hydro_util) calc_MSD_population() (in module pyrid.evaluation.diffusion_util) calc_mu() (in module pyrid.molecules.hydro_util) calc_orientation_quat() (in module pyrid.evaluation.diffusion_util) (pyrid.molecules.rigidbody_util.RBs method) calc_P_theory() (in module pyrid.evaluation.diffusion_util) calc_phase_diagram() (in module pyrid.evaluation.direct_coexistence_method_util) calc_profile() (in module pyrid.evaluation.direct_coexistence_method_util) calc_Xi() (in module pyrid.molecules.hydro_util) calc_zeta() (in module pyrid.molecules.hydro_util) calcP2_anisotropic() (in module pyrid.evaluation.diffusion_util) calcP2_anisotropic_Population() (in module pyrid.evaluation.diffusion_util) cantor_pairing() (in module pyrid.math.transform_util) cartesian_coord() (in module pyrid.math.transform_util) cartesian_direction() (in module pyrid.math.transform_util) CellListMesh (class in pyrid.data_structures.cell_list_util) center_of_mass() (in module pyrid.molecules.hydro_util) center_profile() (in module pyrid.evaluation.direct_coexistence_method_util) clear() (pyrid.data_structures.dynamic_array_util.DenseArray method) (pyrid.data_structures.dynamic_array_util.DenseArrayReact method) (pyrid.data_structures.dynamic_array_util.HolesArrayReact method) (pyrid.reactions.reactions_registry_util.Reaction method)

clear_force() (pyrid.molecules.particles_util.Particles method) clear_number_reactions() (pyrid.molecules.particles_util.Particles method) close_hdf() (pyrid.evaluation.evaluation_util.Evaluation method) closest_boundary_point() (in module pyrid.geometry.mesh_util) collision_response() (in module pyrid.math.transform_util) Compartment (class in pyrid.system.system_util) convert_dict() (in module pyrid.run) convert_molecule_type() (in module pyrid.reactions.update_reactions) convert_particle_type() (in module pyrid.reactions.update_reactions) create_cell_list() (pyrid.system.system_util.System method) create_cell_list_mesh() (in module pyrid.data_structures.cell_list_util) create_cell_list_points() (in module pyrid.data_structures.cell_list_util) create_hgrid() (in module pyrid.data_structures.h_grid_util) create_rb_hgrid() (in module pyrid.evaluation.rdf_util) critical_Density() (in module pyrid.evaluation.direct_coexistence_method_util) critical_point_fit() (in module pyrid.evaluation.direct_coexistence_method_util) critical_Temp() (in module pyrid.evaluation.direct_coexistence_method_util) cross() (in module pyrid.math.transform_util) CSW() (in module pyrid.system.potentials_util) cuboid_data() (in module pyrid.observables.plot_util)

D

data_id() (in module pyrid.observables.write_util) decrease_number_reactions() (pyrid.molecules.particles_util.Particles method) delete() (pyrid.data_structures.dynamic_array_util.HolesArray method) delete_molecule() (in module pyrid.reactions.update_reactions) delete_particles() (in module pyrid.reactions.update_reactions) delete_reaction() (pyrid.reactions.reactions_registry_util.Reaction method) delete_reaction_all() (pyrid.reactions.reactions_registry_util.Reaction method) delete_reactions() (in module pyrid.reactions.update_reactions)

DenseArray (class in pyrid.data_structures.dynamic_array_util) DenseArrayReact (class in pyrid.data_structures.dynamic_array_util) density_hyperbolic_tangent() (in module pyrid.evaluation.direct_coexistence_method_util) diffusion_tensor() (in module pyrid.molecules.hydro_util) diffusion_tensor_off_center() (in module pyrid.molecules.hydro_util) distribute() (pyrid.run.Simulation method) draw_cuboid() (in module pyrid.observables.plot_util) draw_sphere() (in module pyrid.observables.plot_util) dx_cum_prob() (in module pyrid.math.random_util)

E

edge_intersection_barycentric() (in module pyrid.geometry.intersections_util) eij() (in module pyrid.math.transform_util) ek() (in module pyrid.math.transform_util)

erfc() (in module pyrid.math.random_util) Evaluation (class in pyrid.evaluation.evaluation_util) evenly_on_sphere() (in module pyrid.system.distribute_surface_util) execute_force() (in module pyrid.system.potentials_util)

F

FENE() (in module pyrid.system.potentials_util)

fixed_concentration_at_boundary() (pyrid.run.Simulation method) (pyrid.system.system_util.System method)

G

get() (pyrid.reactions.reactions_registry_util.Reaction method) get_AABB_centers() (pyrid.system.system_util.System method)

get_random() (pyrid.reactions.reactions_registry_util.Reaction method) get_triangles() (pyrid.data_structures.cell_list_util.CellListMesh method)

H

half_angle() (in module pyrid.math.transform_util) harmonic_repulsion() (in module pyrid.system.potentials_util)

HolesArray (class in pyrid.data_structures.dynamic_array_util) HolesArrayReact (class in pyrid.data_structures.dynamic_array_util)

I

increase_force() (pyrid.molecules.particles_util.Particles method) increase_number_reactions() (pyrid.molecules.particles_util.Particles method) increase_pos() (pyrid.molecules.particles_util.Particles method) increase_pos_local() (pyrid.molecules.particles_util.Particles method)

insert() (pyrid.data_structures.dynamic_array_util.HolesArray method) Interpolate (class in pyrid.math.random_util) is_diagonal() (in module pyrid.math.transform_util) isclose() (in module pyrid.math.transform_util) iterator() (pyrid.data_structures.dynamic_array_util.HolesArray method)

K

k_macro() (in module pyrid.reactions.reactions_util) (pyrid.run.Simulation method)

k_micro() (in module pyrid.reactions.reactions_util) (pyrid.run.Simulation method)

L

len() (pyrid.data_structures.dynamic_array_util.HolesArray method) Lennard_Jones() (in module pyrid.system.potentials_util) levi_civita() (in module pyrid.molecules.hydro_util) load_checkpoint() (in module pyrid.observables.checkpoint_util) (pyrid.run.Simulation method)

load_compartments() (in module pyrid.geometry.load_wavefront) load_file() (pyrid.evaluation.evaluation_util.Evaluation method) load_hdf() (pyrid.evaluation.evaluation_util.Evaluation method) local_coord() (in module pyrid.math.transform_util)

M

make_array() (pyrid.data_structures.cell_list_util.CellListMesh method) (pyrid.data_structures.dynamic_array_util.DenseArray method) (pyrid.data_structures.dynamic_array_util.DenseArrayReact method) (pyrid.data_structures.dynamic_array_util.HolesArray method) (pyrid.data_structures.dynamic_array_util.HolesArrayReact method) (pyrid.reactions.reactions_registry_util.Reaction method) make_head() (pyrid.data_structures.cell_list_util.CellListMesh method) make_index() (pyrid.data_structures.dynamic_array_util.DenseArray method) mc() (in module pyrid.system.distribute_surface_util) (in module pyrid.system.distribute_vol_util) mesh_inside_box_test() (in module pyrid.geometry.intersections_util) mesh_volume() (in module pyrid.geometry.mesh_util) module pyrid.data_structures.cell_list_util pyrid.data_structures.h_grid_util pyrid.evaluation.diffusion_util pyrid.evaluation.direct_coexistence_method_util pyrid.evaluation.rdf_util pyrid.geometry.intersections_util pyrid.geometry.load_wavefront pyrid.geometry.mesh_util pyrid.geometry.ray_march_util pyrid.math.random_util pyrid.math.transform_util pyrid.molecules.hydro_util pyrid.observables.checkpoint_util pyrid.observables.plot_util pyrid.observables.write_util pyrid.reactions.reactions_util pyrid.reactions.update_reactions pyrid.run pyrid.system.distribute_surface_util pyrid.system.distribute_vol_util pyrid.system.potentials_util pyrid.system.update_force pyrid.system.update_pos

MoleculeType (class in pyrid.system.system_util) monte_carlo_distribution_2D() (in module pyrid.system.distribute_surface_util) monte_carlo_distribution_3D() (in module pyrid.system.distribute_vol_util) MSD() (in module pyrid.evaluation.diffusion_util) (pyrid.evaluation.evaluation_util.Evaluation method)

N

nearest_triangle() (in module pyrid.geometry.ray_march_util) next_um_reaction() (pyrid.molecules.rigidbody_util.RBs method) next_up_reaction() (pyrid.molecules.particles_util.Particles method)

normal() (in module pyrid.system.distribute_surface_util) (in module pyrid.system.distribute_vol_util) normal_vector() (in module pyrid.math.transform_util) normalize() (in module pyrid.math.transform_util)

O

Observables (class in pyrid.observables.observables_util) observe() (pyrid.observables.observables_util.Observables method) (pyrid.run.Simulation method)

observe_rdf() (pyrid.observables.observables_util.Observables method) (pyrid.run.Simulation method) orthogonal_vector() (in module pyrid.math.transform_util)

P

P() (in module pyrid.molecules.hydro_util) P2() (in module pyrid.evaluation.diffusion_util) (pyrid.evaluation.evaluation_util.Evaluation method) Particles (class in pyrid.molecules.particles_util) pds() (in module pyrid.system.distribute_surface_util) (in module pyrid.system.distribute_vol_util) pds_uniform() (in module pyrid.system.distribute_vol_util) PHS() (in module pyrid.system.potentials_util) piecewise_harmonic() (in module pyrid.system.potentials_util) place_particles() (pyrid.molecules.rigidbody_util.RBs method) plot_cell_grid() (in module pyrid.observables.plot_util) plot_compartment_0() (in module pyrid.observables.plot_util) plot_compartments() (in module pyrid.observables.plot_util) plot_concentration_profile() (in module pyrid.observables.plot_util) plot_mobility_matrix() (in module pyrid.observables.plot_util) plot_MSD() (pyrid.evaluation.evaluation_util.Evaluation method) plot_observable() (pyrid.evaluation.evaluation_util.Evaluation method) plot_P2() (pyrid.evaluation.evaluation_util.Evaluation method) plot_path() (in module pyrid.observables.plot_util) plot_path_mesh() (in module pyrid.observables.plot_util) plot_potential() (in module pyrid.observables.plot_util) plot_rdf() (pyrid.evaluation.evaluation_util.Evaluation method) plot_reactions_graph() (pyrid.evaluation.evaluation_util.Evaluation method) plot_scene() (in module pyrid.observables.plot_util) plot_sphere_packing() (in module pyrid.observables.plot_util) plot_triangle() (in module pyrid.observables.plot_util) plot_triangles() (in module pyrid.observables.plot_util) point_in_disc() (in module pyrid.system.distribute_surface_util) point_in_sphere_simple() (in module pyrid.system.distribute_vol_util) point_in_triangle_barycentric() (in module pyrid.geometry.intersections_util) point_inside_AABB_test() (in module pyrid.geometry.intersections_util) point_inside_mesh_test() (in module pyrid.geometry.intersections_util) point_inside_mesh_test_raycasting() (in module pyrid.geometry.intersections_util) point_inside_triangle_test() (in module pyrid.geometry.intersections_util) point_on_sphere() (in module pyrid.system.distribute_surface_util) (in module pyrid.system.distribute_vol_util) point_triangle_distance() (in module pyrid.geometry.mesh_util) poisson_disc_sampling() (in module pyrid.system.distribute_vol_util) poisson_disc_sampling_2D() (in module pyrid.system.distribute_surface_util) poisson_disc_sampling_uniform() (in module pyrid.system.distribute_vol_util) pos_data() (in module pyrid.observables.write_util) print_timer() (pyrid.run.Simulation method) progress() (pyrid.run.Simulation method) pyrid.data_structures.cell_list_util module

pyrid.data_structures.h_grid_util module pyrid.evaluation.diffusion_util module pyrid.evaluation.direct_coexistence_method_util module pyrid.evaluation.rdf_util module pyrid.geometry.intersections_util module pyrid.geometry.load_wavefront module pyrid.geometry.mesh_util module pyrid.geometry.ray_march_util module pyrid.math.random_util module pyrid.math.transform_util module pyrid.molecules.hydro_util module pyrid.observables.checkpoint_util module pyrid.observables.plot_util module pyrid.observables.write_util module pyrid.reactions.reactions_util module pyrid.reactions.update_reactions module pyrid.run module pyrid.system.distribute_surface_util module pyrid.system.distribute_vol_util module pyrid.system.potentials_util module pyrid.system.update_force module pyrid.system.update_pos module

Q

quat_mult() (in module pyrid.math.transform_util) quaternion_plane_to_plane() (in module pyrid.math.transform_util)

quaternion_random_axis_rot() (in module pyrid.math.transform_util) quaternion_to_plane() (in module pyrid.math.transform_util)

R

radial_distr_function() (in module pyrid.evaluation.rdf_util) random_choice() (in module pyrid.math.random_util) random_direction_Halfsphere() (in module pyrid.system.distribute_vol_util) random_direction_sphere() (in module pyrid.system.distribute_vol_util) random_point_in_triangle() (in module pyrid.system.distribute_surface_util) random_point_on_edge() (in module pyrid.system.distribute_surface_util) random_quaternion() (in module pyrid.run) (in module pyrid.system.distribute_vol_util) random_quaternion_tuple() (in module pyrid.system.distribute_vol_util) ray_march_surface() (in module pyrid.geometry.ray_march_util) ray_march_volume() (in module pyrid.geometry.ray_march_util) ray_mesh_intersection_count() (in module pyrid.geometry.intersections_util) ray_mesh_intersection_test() (in module pyrid.geometry.intersections_util) ray_triangle_intersection() (in module pyrid.geometry.intersections_util) RBs (class in pyrid.molecules.rigidbody_util) react_interact_test() (in module pyrid.system.update_force) Reaction (class in pyrid.reactions.reactions_registry_util)

reactions_left_pointer() (pyrid.reactions.reactions_registry_util.Reaction method) read_molecule_data() (pyrid.evaluation.evaluation_util.Evaluation method) read_observable() (pyrid.evaluation.evaluation_util.Evaluation method) read_xyz() (in module pyrid.observables.write_util) register_molecule_type() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) register_particle_type() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) release_molecules() (pyrid.run.Simulation method) release_molecules_boundary() (in module pyrid.system.distribute_vol_util) release_molecules_boundary_2d() (in module pyrid.system.distribute_surface_util) remove() (pyrid.data_structures.dynamic_array_util.DenseArray method) repulsive_membrane() (in module pyrid.system.potentials_util) rescale_pos() (pyrid.molecules.rigidbody_util.RBs method) reverse_cell_mapping() (in module pyrid.data_structures.cell_list_util) rodrigues_rot() (in module pyrid.math.transform_util) rot_quaternion() (in module pyrid.math.transform_util) run() (pyrid.run.Simulation method)

S

save() (in module pyrid.observables.checkpoint_util) screened_electrostatics() (in module pyrid.system.potentials_util) set() (pyrid.reactions.reactions_registry_util.Reaction method) set_compartments() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) set_coord() (pyrid.molecules.particles_util.Particles method) set_diffusion_tensor() (pyrid.run.Simulation method) (pyrid.system.system_util.System method) set_force() (pyrid.molecules.particles_util.Particles method) set_orientation_quat() (pyrid.molecules.rigidbody_util.RBs method)

set_pos() (pyrid.molecules.particles_util.Particles method) (pyrid.molecules.rigidbody_util.RBs method) set_pos_local() (pyrid.molecules.particles_util.Particles method) set_rb_id() (pyrid.molecules.particles_util.Particles method) set_triangle() (pyrid.molecules.rigidbody_util.RBs method) set_type() (pyrid.molecules.particles_util.Particles method) Simulation (class in pyrid.run) solid_angle() (in module pyrid.math.transform_util) sqrt_matrix() (in module pyrid.math.transform_util) supermatrix_inverse() (in module pyrid.molecules.hydro_util) System (class in pyrid.system.system_util)

T

trace_direction_vector() (in module pyrid.system.distribute_surface_util) (in module pyrid.system.distribute_vol_util) transform_reverse_supermatrix() (in module pyrid.molecules.hydro_util) transform_supermatrix() (in module pyrid.molecules.hydro_util)

tri_area_2D() (in module pyrid.math.transform_util) triangle_area() (in module pyrid.geometry.mesh_util) triangle_cell_intersection_test() (in module pyrid.geometry.intersections_util) triangle_centroid() (in module pyrid.geometry.mesh_util) triangle_volume_signed() (in module pyrid.geometry.mesh_util)

U

unique_pairing() (in module pyrid.math.transform_util) update() (pyrid.observables.observables_util.Observables method) update_B() (pyrid.molecules.rigidbody_util.RBs method) update_bins() (pyrid.observables.observables_util.Observables method) update_dq() (pyrid.molecules.rigidbody_util.RBs method) update_dX() (pyrid.molecules.rigidbody_util.RBs method) update_force_append_reactions() (in module pyrid.system.update_force) update_force_torque() (pyrid.molecules.rigidbody_util.RBs method) update_hgrid() (in module pyrid.data_structures.h_grid_util) update_orientation_quat() (pyrid.molecules.rigidbody_util.RBs method) update_particle_level() (in module pyrid.data_structures.h_grid_util)

update_particle_pos() (pyrid.molecules.rigidbody_util.RBs method) update_particle_pos_2D() (pyrid.molecules.rigidbody_util.RBs method) update_pressure() (in module pyrid.run) update_rb() (in module pyrid.system.update_pos) update_rb_compartments() (in module pyrid.system.update_pos) update_rb_hgrid() (in module pyrid.evaluation.rdf_util) update_rb_level() (in module pyrid.evaluation.rdf_util) update_rdf() (pyrid.observables.observables_util.Observables method) update_reactions() (in module pyrid.reactions.update_reactions) update_to_nearest_triangle() (in module pyrid.geometry.ray_march_util) update_topology() (pyrid.molecules.rigidbody_util.RBs method) update_um_reaction() (pyrid.system.system_util.MoleculeType method)

V

valid_mobility_tensor_test() (in module pyrid.math.transform_util)

W

wall() (in module pyrid.system.potentials_util) Weeks_Chandler_Anderson() (in module pyrid.system.potentials_util)

WLC_force() (in module pyrid.system.potentials_util) write() (in module pyrid.observables.write_util) write_init() (in module pyrid.observables.write_util)