FINDS: The Fish INteraction and Dynamics Simulator

Contents:

• Constants
  • FISH_LENGTH
  • VOLUMETRIC_FLOW_RATE
  • FISH_SELF_PROPELLED_SPEED
  • ROOT_OUTPUT_PATH
  • SIMULATION_OUTPUT_DIR
  • SIMULATION_LATEST_DIR
  • SIMULATION_OUTPUT_NAME
  • VALIDATION_OUTPUT_PATH
  • BENCHMARK_OUTPUT_PATH
  • DATA_FILE_NAME
• Utility Functions
  • split()
  • rejoin()
• Non-Mathematical Fish/System Management Functions
  • normalize_orientation_vectors()
  • perturb_orientations()
  • generate_positions_random()
  • generate_positions_lattice()
  • generate_positions_sphere()
  • generate_positions_square()
  • generate_positions_circle()
  • generate_system()
• Simulation Functions
  • perform_simulation()
• Differential Calculation Functions
  • The Far-Field Model of Fish
  • Computing the Derivative of the System Matrix
  • Barnes-Hut Clustering Approximation
  • Functions
• File I/O
  • IO
  • init_input_filestream()
  • init_output_filestream()
  • close_filestream()
  • serialize_to_file()
• Post-Processing
  • Main Postprocessing Function
  • Post-Processing Modules
• Scripts: Validation and Benchmarking
  • Validation
  • Benchmarking
• Function Unit Tests
  • test_calculate_feature_positions()
  • helper_test_interaction()
  • test_compute_interaction_pairwise()
  • test_compute_interaction_barnes_hut()
  • test_calculate_feature_velocities()
  • test_calculate_system_derivative()
  • test_positions_and_orientations()
  • helper_test_fish()
  • helper_test_system()
  • test_generate_system()
  • test_normalize_orientation_vectors()

[1]

Josh Barnes and Piet Hut. A hierarchical o(n log n) force-calculation algorithm. Nature, 324:446–449, 1986. URL: https://www.nature.com/articles/324446a0, doi:10.1038/324446a0.

[2]

Jeffrey Heer. The barnes-hut approximation. 2018. Accessed: 2026-06-04. URL: https://jheer.github.io/barnes-hut/.

[3]

Mohamed Niged Mabrouk and Daniel Floryan. Group cohesion and passive dynamics of a pair of inertial swimmers with three-dimensional hydrodynamic interactions. Bioinspiration & Biomimetics, 20(1):016014, November 2024. URL: https://doi.org/10.1088/1748-3190/ad936d, doi:10.1088/1748-3190/ad936d.

[4]

Mohamed Niged Mabrouk and Daniel Floryan. Effects of symmetry and hydrodynamics on the cohesion of groups of swimmers. Bioinspiration & Biomimetics, 20(6):066005, October 2025. URL: https://doi.org/10.1088/1748-3190/ae0bd9, doi:10.1088/1748-3190/ae0bd9.

[5]

Tom Ventimiglia and Kevin Wayne. The barnes-hut algorithm. 2003. URL: https://arborjs.org/docs/barnes-hut (visited on 2026-06-23).