Index

A

AnimationGenerator (class in finds.processingmodules.AnimationGenerator) append_state() (finds.processingmodules.AnimationGenerator.AnimationGenerator method) (finds.processingmodules.CrossSectionGenerator.CrossSectionGenerator method) (finds.processingmodules.DensityAnimationGenerator.DensityAnimationGenerator method) (finds.processingmodules.MeanRadialDistancePlot.MeanRadialDistancePlot method) (finds.processingmodules.ProcessingModule.ProcessingModule method)

average (finds.calculations.OctreeNode attribute)

B

back_pos (finds.calculations.OctreeNode attribute) begin() (finds.processingmodules.AnimationGenerator.AnimationGenerator method) (finds.processingmodules.CrossSectionGenerator.CrossSectionGenerator method) (finds.processingmodules.DensityAnimationGenerator.DensityAnimationGenerator method) (finds.processingmodules.MeanRadialDistancePlot.MeanRadialDistancePlot method) (finds.processingmodules.ProcessingModule.ProcessingModule method)

BENCHMARK_OUTPUT_PATH (in module finds.constants) build_octree() (in module finds.calculations)

C

calculate_child_center() (finds.calculations.OctreeNode method) calculate_feature_interaction() (in module finds.calculations) calculate_feature_positions() (finds.calculations.OctreeNode method) (in module finds.calculations) calculate_feature_velocities() (in module finds.calculations) calculate_fish_interaction() (in module finds.calculations) calculate_octant_index() (finds.calculations.OctreeNode method) calculate_system_derivative() (in module finds.calculations) center (finds.calculations.OctreeNode attribute)

children (finds.calculations.OctreeNode attribute) close_filestream() (in module finds.io) cluster (finds.calculations.OctreeNode attribute) cluster_size (finds.calculations.OctreeNode attribute) compute_interaction() (finds.calculations.OctreeNode method) compute_interaction_barnes_hut() (in module finds.calculations) compute_interaction_pairwise() (in module finds.calculations) compute_octree_2d_positions_recurse() (in module scripts.validators.octree_validation) coplanar_simulation() (in module scripts.validators.figure_reproduction) CrossSectionGenerator (class in finds.processingmodules.CrossSectionGenerator)

D

data (finds.calculations.OctreeNode attribute) DATA_FILE_NAME (in module finds.constants) DensityAnimationGenerator (class in finds.processingmodules.DensityAnimationGenerator) draw_octree_2d() (in module scripts.validators.octree_validation)

draw_octree_3d() (in module scripts.validators.octree_validation) draw_octree_3d_recurse() (in module scripts.validators.octree_validation) draw_octree_node_2d_recurse() (in module scripts.validators.octree_validation) draw_wireframe_cube() (in module scripts.validators.octree_validation)

E

end() (finds.processingmodules.AnimationGenerator.AnimationGenerator method) (finds.processingmodules.CrossSectionGenerator.CrossSectionGenerator method) (finds.processingmodules.DensityAnimationGenerator.DensityAnimationGenerator method) (finds.processingmodules.MeanRadialDistancePlot.MeanRadialDistancePlot method) (finds.processingmodules.ProcessingModule.ProcessingModule method)

F

filename (scripts.validators.common.ValidationFunction attribute) filestream (finds.io.IO attribute) finds.calculations module finds.constants module finds.fish module finds.io module finds.postprocessing module finds.processingmodules.AnimationGenerator module

finds.processingmodules.CrossSectionGenerator module finds.processingmodules.DensityAnimationGenerator module finds.processingmodules.MeanRadialDistancePlot module finds.processingmodules.ProcessingModule module finds.simulation module finds.util module FISH_LENGTH (in module finds.constants) FISH_SELF_PROPELLED_SPEED (in module finds.constants) front_pos (finds.calculations.OctreeNode attribute)

G

generate_comparison_figure() (in module scripts.benchmark) generate_fish_circle() (in module scripts.validators.figure_reproduction) generate_octree_figures() (in module scripts.validators.octree_validation) generate_positions_circle() (in module finds.fish)

generate_positions_lattice() (in module finds.fish) generate_positions_random() (in module finds.fish) generate_positions_sphere() (in module finds.fish) generate_positions_square() (in module finds.fish) generate_system() (in module finds.fish)

H

helper_test_fish() (in module test.test_fish)

helper_test_interaction() (in module test.test_calculations) helper_test_system() (in module test.test_fish)

I

init_input_filestream() (in module finds.io) init_output_filestream() (in module finds.io) insert_data() (finds.calculations.OctreeNode method)

insert_into_children() (finds.calculations.OctreeNode method) IO (class in finds.io) is_leaf (finds.calculations.OctreeNode attribute)

M

MeanRadialDistancePlot (class in finds.processingmodules.MeanRadialDistancePlot) module finds.calculations finds.constants finds.fish finds.io finds.postprocessing finds.processingmodules.AnimationGenerator finds.processingmodules.CrossSectionGenerator finds.processingmodules.DensityAnimationGenerator finds.processingmodules.MeanRadialDistancePlot finds.processingmodules.ProcessingModule finds.simulation finds.util scripts.benchmark scripts.validation scripts.validators.common scripts.validators.figure_reproduction scripts.validators.octree_validation test.test_calculations test.test_fish test.test_simulation

N

name (scripts.validators.common.ValidationFunction attribute)

normalize_orientation_vectors() (in module finds.fish)

O

OctreeNode (class in finds.calculations)

output_dir (finds.processingmodules.ProcessingModule.ProcessingModule attribute)

P

perform_simulation() (in module finds.simulation) perform_time_test() (in module scripts.benchmark) perturb_orientations() (in module finds.fish)

process_data() (in module finds.postprocessing) ProcessingModule (class in finds.processingmodules.ProcessingModule) produces_validation() (in module scripts.validators.common)

R

rejoin() (in module finds.util) reproduce_2024_fig_16() (in module scripts.validators.figure_reproduction)

reproduce_2025_fig_8() (in module scripts.validators.figure_reproduction) ROOT_OUTPUT_PATH (in module finds.constants)

S

scripts.benchmark module scripts.validation module scripts.validators.common module scripts.validators.figure_reproduction module

scripts.validators.octree_validation module serialize_to_file() (in module finds.io) side_length (finds.calculations.OctreeNode attribute) SIMULATION_LATEST_DIR (in module finds.constants) SIMULATION_OUTPUT_DIR (in module finds.constants) SIMULATION_OUTPUT_NAME (in module finds.constants) split() (in module finds.util) state_dataset (finds.io.IO attribute)

T

test.test_calculations module test.test_fish module test.test_simulation module test_calculate_feature_positions() (in module test.test_calculations)

test_calculate_feature_velocities() (in module test.test_calculations) test_calculate_system_derivative() (in module test.test_calculations) test_compute_interaction_barnes_hut() (in module test.test_calculations) test_compute_interaction_pairwise() (in module test.test_calculations) test_generate_system() (in module test.test_fish) test_normalize_orientation_vectors() (in module test.test_fish) test_positions_and_orientations() (in module test.test_fish) time_dataset (finds.io.IO attribute)

V

validation_main() (in module scripts.validation) VALIDATION_OUTPUT_DIR (in module scripts.validators.common)

VALIDATION_OUTPUT_PATH (in module finds.constants) ValidationFunction (class in scripts.validators.common) VOLUMETRIC_FLOW_RATE (in module finds.constants)