Index

A

absolute_sizer() (in module ilpm.pyopencl_scripts.network_visualization) acquire_opencl_devices() (in module ilpm.simple_cl) apply_basis() (ilpm.path.Path method) (ilpm.path.Tangle method) (in module ilpm.vector) arb_perp() (in module ilpm.vector)

args_unique_rows_threshold() (in module ilpm.networks) as_path() (in module ilpm.path) attach() (ilpm.mesh.Mesh method) azimuthalAverage() (in module ilpm.networks)

B

biot_savart_on_path() (ilpm.path.Path method) BL2BM() (in module ilpm.networks) BL2KL() (in module ilpm.networks) BL2NLandKL() (in module ilpm.networks) BL2PVxydict() (in module ilpm.networks) BL2TRI() (in module ilpm.networks) BM2bL() (in module ilpm.networks) BM2BSM() (in module ilpm.networks)

bond_length_list() (in module ilpm.networks) bond_strain_list() (in module ilpm.networks) bonds_are_in_region() (in module ilpm.networks) boundary_triangles() (in module ilpm.networks) buffer_points_for_periodicBC() (in module ilpm.networks) buffer_points_for_rectangular_periodicBC() (in module ilpm.networks) buffered_pts_to_periodic_network() (in module ilpm.networks) buffered_pts_to_periodic_network_parallelogram() (in module ilpm.networks)

C

calc_forces_and_cross() (in module ilpm.pyopencl_scripts.rk4_functions) calc_forces_and_cross_magnetic() (in module ilpm.pyopencl_scripts.rk4_functions) center() (ilpm.path.Path method) (ilpm.path.Tangle method) center_of_mass() (in module ilpm.networks) centroid_lattice_from_TRI() (in module ilpm.networks) Cine (class in ilpm.cine) clear_derived() (ilpm.path.Path method) clip() (ilpm.mesh.Mesh method) close() (ilpm.cine.Cine method) closest_opposed() (ilpm.path.Tangle method) closest_pt_along_line() (in module ilpm.networks) closest_pt_on_lineseg() (in module ilpm.networks) closest_pts_along_line() (in module ilpm.networks) closest_pts_on_lineseg() (in module ilpm.networks) closest_pts_on_lineseg_2D() (in module ilpm.networks) CLSession (class in ilpm.simple_cl) collect_lines() (in module ilpm.networks) color_by_proximity() (ilpm.mesh.Mesh method) (ilpm.path.Path method) (ilpm.path.Tangle method) colorize() (ilpm.mesh.Mesh method) (ilpm.path.Path method) (ilpm.path.Tangle method) com_periodic() (in module ilpm.networks)

compacted_segment_attribute() (ilpm.path.Tangle method) compacted_segments() (ilpm.path.Tangle method) compile() (ilpm.simple_cl.CLSession method) compile_code_in_external_session() (in module ilpm.geometry_extractor) compile_file() (ilpm.simple_cl.CLSession method) compute_bulk_z() (in module ilpm.networks) contains_sublist() (in module ilpm.networks) convert_colors() (ilpm.mesh.Mesh method) copy() (ilpm.mesh.Mesh method) (ilpm.path.Path method) (ilpm.path.Tangle method) count_NN() (in module ilpm.networks) cross() (in module ilpm.vector) cross_pts_triangle() (in module ilpm.networks) crossing_matrix() (ilpm.path.Tangle method) cubic_bezier_resample() (ilpm.path.Path method) cut_bonds() (in module ilpm.networks) cut_bonds_strain() (in module ilpm.networks) cut_bonds_strain_BL() (in module ilpm.networks) cut_bonds_z_highest() (in module ilpm.networks) cut_bonds_z_random() (in module ilpm.networks)

D

data2stills_2D() (in module ilpm.pyopencl_scripts.network_visualization) decimate() (ilpm.path.Path method) (ilpm.path.Tangle method) decode_ply() (in module ilpm.mesh) delaunay_centroid_lattice_from_pts() (in module ilpm.networks) delaunay_centroid_periodic_network_from_pts() (in module ilpm.networks) delaunay_centroid_rect_periodic_network_from_pts() (in module ilpm.networks) delaunay_cut_unnatural_boundary() (in module ilpm.networks) delaunay_cut_unnatural_boundary_singlepass() (in module ilpm.networks) delaunay_lattice_from_pts() (in module ilpm.networks) delaunay_periodic_network_from_pts() (in module ilpm.networks)

delaunay_rect_periodic_network_from_pts() (in module ilpm.networks) diff_matrix() (in module ilpm.networks) display_lattice_2D() (in module ilpm.networks) dist_pts() (in module ilpm.networks) distance_periodic() (in module ilpm.networks) dot() (in module ilpm.vector) dot1() (in module ilpm.vector) draw_lattice() (in module ilpm.networks) drop() (ilpm.path.Tangle method) drop_shorter_than() (ilpm.path.Tangle method)

E

eliminate_close_points() (ilpm.path.Path method) (ilpm.path.Tangle method) empty() (ilpm.simple_cl.CLSession method) empty_like() (ilpm.simple_cl.CLSession method) encode_ply() (in module ilpm.mesh) enqueue_copy() (ilpm.simple_cl.CLSession method) ensure_dir() (in module ilpm.pyopencl_scripts.network_visualization)

ensure_periodic_connectivity() (in module ilpm.networks) euler_char() (ilpm.mesh.Mesh method) extract_boundary() (in module ilpm.networks) extract_phase() (in module ilpm.networks) extract_polygons_lattice() (in module ilpm.networks) extrude_shape() (in module ilpm.mesh)

F

face_normals() (ilpm.mesh.Mesh method) fBrunGyro() (in module ilpm.pyopencl_scripts.rk4_functions) fdspring() (in module ilpm.pyopencl_scripts.rk4_functions) fft() (ilpm.simple_cl.CLSession method) fglidingHST_exact() (in module ilpm.pyopencl_scripts.rk4_functions) fglidingHST_PL() (in module ilpm.pyopencl_scripts.rk4_functions) fgyro_Nash() (in module ilpm.pyopencl_scripts.rk4_functions)

find_cut_bonds() (in module ilpm.networks) find_intersections() (in module ilpm.networks) find_nearest() (in module ilpm.networks) flexible_PVxydict2PVxPVy() (in module ilpm.networks) float2pstr() (in module ilpm.networks) fspring() (in module ilpm.pyopencl_scripts.rk4_functions) fspring_perp() (in module ilpm.pyopencl_scripts.rk4_functions)

G

gamma_corrected_frame() (ilpm.cine.Cine method) gen_normal() (ilpm.path.Path method) get_device_info() (ilpm.simple_cl.CLSession method) (in module ilpm.simple_cl) get_fname_and_index_size() (in module ilpm.pyopencl_scripts.network_visualization) get_fps() (ilpm.cine.Cine method)

get_frame() (ilpm.cine.Cine method) get_points_per_unit() (in module ilpm.pyopencl_scripts.network_visualization) get_time() (ilpm.cine.Cine method) GroupById (class in ilpm.misc)

H

highlight_bonds() (in module ilpm.networks)

I

ilpm.cine (module) ilpm.colormaps (module) ilpm.geometry_extractor (module) ilpm.mesh (module) ilpm.misc (module) ilpm.movies (module) ilpm.networks (module) ilpm.path (module) ilpm.pyopencl_scripts.network_visualization (module) ilpm.pyopencl_scripts.rk4_functions (module) ilpm.raw (module) ilpm.science_plot_style (module) ilpm.simple_cl (module) ilpm.vector (module) indices_within_r() (ilpm.misc.NeighborList method)

inds_in_polygon() (in module ilpm.networks) inductance_matrix() (ilpm.path.Tangle method) initialize() (ilpm.simple_cl.CLSession method) interpol_meshgrid() (in module ilpm.networks) intersect2d() (in module ilpm.networks) intersection_lines() (in module ilpm.networks) intersection_linesegs() (in module ilpm.networks) invert() (ilpm.mesh.Mesh method) inverted() (ilpm.mesh.Mesh method) is_closed() (ilpm.mesh.Mesh method) is_cyclic_permutation() (in module ilpm.networks) is_cyclic_permutation_numpy() (in module ilpm.networks) is_job_done() (in module ilpm.simple_cl) is_number() (in module ilpm.networks) ismember() (in module ilpm.networks)

K

keep() (ilpm.path.Path method) keys() (ilpm.misc.GroupById method)

KL2kL() (in module ilpm.networks)

L

line_pts_are_on_lineseg() (in module ilpm.networks) line_pts_are_on_lineseg_2D() (in module ilpm.networks) load_mesh() (in module ilpm.mesh) load_path() (in module ilpm.path)

load_raw() (in module ilpm.raw) load_tangle() (in module ilpm.path) local_memory() (ilpm.simple_cl.CLSession method)

M

mag() (in module ilpm.vector) mag1() (in module ilpm.vector) make_movie() (in module ilpm.movies) mean() (ilpm.path.Path method) (ilpm.path.Tangle method) memberIDs() (in module ilpm.networks) Mesh (class in ilpm.mesh) mesh_tube() (ilpm.path.Path method) (ilpm.path.Tangle method)

message() (ilpm.misc.StatusCounter method) midpoint() (ilpm.path.Path method) midpoint_delta() (in module ilpm.vector) minimum_distance_between_pts() (in module ilpm.networks) minus() (in module ilpm.vector) moment() (ilpm.path.Path method) (ilpm.path.Tangle method) movie_plot_2D() (in module ilpm.networks) (in module ilpm.pyopencl_scripts.network_visualization)

N

NeighborList (class in ilpm.misc) NL2BL() (in module ilpm.networks) NL2BM() (in module ilpm.networks)

NL2NLdict() (in module ilpm.networks) norm() (in module ilpm.vector) normalize_basis() (in module ilpm.vector)

O

ones() (ilpm.simple_cl.CLSession method) ones_like() (ilpm.simple_cl.CLSession method)

orient() (ilpm.path.Path method) (ilpm.path.Tangle method)

P

pairwise() (in module ilpm.networks) parallel_transport_framing() (ilpm.path.Path method) partial_s() (ilpm.path.Path method) Path (class in ilpm.path) PBCmap_for_rectangular_buffer() (in module ilpm.networks) periodic_complex_trace() (in module ilpm.geometry_extractor) periodic_interpolate() (in module ilpm.geometry_extractor) periodic_isosurface() (in module ilpm.geometry_extractor) periodic_label() (in module ilpm.geometry_extractor) periodic_path_unwrap() (in module ilpm.geometry_extractor) periodic_polygon_indices2xy() (in module ilpm.networks) periodic_separate() (ilpm.mesh.Mesh method) perp() (in module ilpm.networks)

plus() (in module ilpm.vector) point_is_on_linesegment_2D() (in module ilpm.networks) point_is_on_linesegment_2D_singlept() (in module ilpm.networks) polygons2PPC() (in module ilpm.networks) prepstr() (in module ilpm.networks) print_msg() (ilpm.misc.StatusCounter method) print_output_1stO() (in module ilpm.pyopencl_scripts.rk4_functions) print_output_test_actual_1stO() (in module ilpm.pyopencl_scripts.rk4_functions) proj() (in module ilpm.vector) pts_are_near_lineseg() (in module ilpm.networks) pts_in_polygon() (in module ilpm.networks) PVxy2PVxydict() (in module ilpm.networks) PVxydict2PVxPVy() (in module ilpm.networks)

R

reduce_by_curvature() (ilpm.path.Path method) (ilpm.path.Tangle method) reduce_topology() (ilpm.path.Tangle method) remove_degenerate_triangles() (ilpm.mesh.Mesh method) remove_pts() (in module ilpm.networks) resample_with_spacing() (ilpm.path.Path method) (ilpm.path.Tangle method) rk4_1stO() (in module ilpm.pyopencl_scripts.rk4_functions) rk4_BrunGyro() (in module ilpm.pyopencl_scripts.rk4_functions) rk4_damp() (in module ilpm.pyopencl_scripts.rk4_functions) rk4_damp_constvBC() (in module ilpm.pyopencl_scripts.rk4_functions) rk4_glidingHST_exact() (in module ilpm.pyopencl_scripts.rk4_functions) rk4_glidingHST_PL() (in module ilpm.pyopencl_scripts.rk4_functions)

rk4_perp() (in module ilpm.pyopencl_scripts.rk4_functions) rms_radius() (ilpm.path.Path method) (ilpm.path.Tangle method) rot() (ilpm.path.Path method) (ilpm.path.Tangle method) (in module ilpm.vector) rotate() (ilpm.mesh.Mesh method) rotate_tensor_cartesian() (in module ilpm.networks) rotate_vectors_2D() (in module ilpm.networks) rotated() (ilpm.mesh.Mesh method) rotation_matrix_3D() (in module ilpm.networks) row_is_in_array() (in module ilpm.networks) rows_matching() (in module ilpm.networks) running_mean() (in module ilpm.networks)

S

save() (ilpm.mesh.Mesh method) (ilpm.path.Path method) (ilpm.path.Tangle method) save_pov() (ilpm.mesh.Mesh method) save_raw() (in module ilpm.raw) scale() (ilpm.mesh.Mesh method) (ilpm.path.Path method) (ilpm.path.Tangle method) scaled() (ilpm.mesh.Mesh method) seg_length_per_point() (ilpm.path.Path method) separate() (ilpm.mesh.Mesh method) set_default_core_model() (in module ilpm.path)

set_opencl_params() (in module ilpm.geometry_extractor) (in module ilpm.mesh) (in module ilpm.path) setdiff2d() (in module ilpm.networks) sort_arrays_by_first_array() (in module ilpm.networks) StatusCounter (class in ilpm.misc) stills2mov_util() (in module ilpm.pyopencl_scripts.network_visualization) string_sequence_to_numpy_array() (in module ilpm.networks) string_to_array() (in module ilpm.networks) surface_of_revolution() (in module ilpm.mesh)

T

Tangle (class in ilpm.path) tensor_cartesian2polar2D() (in module ilpm.networks) tensor_polar2cartesian2D() (in module ilpm.networks) tensor_polar2cartesian_tractions() (in module ilpm.networks) to_device() (ilpm.simple_cl.CLSession method) to_dict() (ilpm.path.Path method) (ilpm.path.Tangle method) torus_knot() (in module ilpm.path) total_length() (ilpm.path.Tangle method) total_points() (ilpm.path.Tangle method) translate() (ilpm.mesh.Mesh method) (ilpm.path.Path method) (ilpm.path.Tangle method) translated() (ilpm.mesh.Mesh method)

TRI2BL() (in module ilpm.networks) Tri2BL() (in module ilpm.networks) TRI2centroidBL() (in module ilpm.networks) TRI2centroidNLandKL() (in module ilpm.networks) TRI2centroidNLandKLandBL() (in module ilpm.networks) TRI2NLandKL() (in module ilpm.networks) trigger_time_p (ilpm.cine.Cine attribute) tune_springs_connecting_regions() (in module ilpm.networks) twist() (ilpm.path.Path method) (ilpm.path.Tangle method) twist_rate() (ilpm.path.Tangle method)

U

unique_rows() (in module ilpm.networks) unique_rows_threshold() (in module ilpm.networks)

update() (ilpm.misc.StatusCounter method)

V

vec() (in module ilpm.vector) volume() (ilpm.mesh.Mesh method)

voronoi_lattice_from_pts() (in module ilpm.networks) voronoi_rect_periodic_from_pts() (in module ilpm.networks)

W

where_points_in_triangle() (in module ilpm.networks)

X

xyandTRI2centroid() (in module ilpm.networks)

Z

zeros() (ilpm.simple_cl.CLSession method)

zeros_like() (ilpm.simple_cl.CLSession method)