Index

A

A1_analysis module A2_dla module A3_salesman module A4_2dmd module A5_fem module accelerate() (A4_2dmd.Particle method) (ballistic.Ball method) (dynamics.Planet method) (flocking.Animal method) (pbc.Atom method) (temp.Atom method) activation() (neuralnetwork.NeuralNetwork method) activation_derivative() (neuralnetwork.NeuralNetwork method) add_alignment_force() (flocking.Prey method) add_avoidance_force() (flocking.Prey method) add_chase_force() (flocking.Predator method) add_circle() (genetic.Solution method) add_cohesion_force() (flocking.Prey method) add_gaussian() (in module fourier) (in module waves) (in module waves_2d) add_scalar() (in module vectors) add_separation_force() (flocking.Predator method) (flocking.Prey method) add_sinusoidal() (in module fourier) (in module waves) add_triangle() (in module fourier) (in module waves) AI (class in game_ai) all_plays() (in module n_in_a_row) (in module tictac) all_reasonable_plays() (in module n_in_a_row) (in module tictac)

all_reasonable_plays_alternative() (in module tictac) alter() (genetic.Circle method) Animal (class in flocking) animate() (in module A2_dla) (in module A4_2dmd) (in module A5_fem) (in module ballistic) (in module dynamics) (in module etching) (in module flocking) (in module fourier) (in module genetic) (in module gradients) (in module heat) (in module ising) (in module motion) (in module pbc) (in module random_walk_free) (in module random_walk_lattice) (in module temp) (in module waves) (in module waves_2d) animate_3d() (in module waves_2d) animate_profile() (in module clustering) animate_scatter() (in module clustering) Animation (class in A4_2dmd) apply_air_resistance() (ballistic.Ball method) apply_bounce() (ballistic.Ball method) apply_constraints() (in module A4_2dmd) apply_gravity() (ballistic.Ball method) ask_for_move() (in module n_in_a_row) (in module tictac) assign_maxwell_boltzmann_velocities() (in module temp) Atom (class in forces) (class in pbc) (class in temp)

B

backpropagate() (game_ai.MC_node method) (neuralnetwork.NeuralNetwork method) Ball (class in ballistic) ballistic module

berendsen_thermostat() (in module temp) best_solution() (in module genetic) bias_factor() (game_ai.MC_node method) black() (genetic.Solution method) Boltzmann_P() (in module A3_salesman) breed() (in module genetic)

C

calculate_average_and_error() (in module A4_2dmd) (in module temp) calculate_Binder_cumulant() (in module ising) calculate_cluster_centers() (in module clustering) calculate_cluster_radius() (in module A2_dla) calculate_density_histogram() (in module random_walk_lattice) calculate_distance_statistics() (in module random_walk_lattice) calculate_distances() (in module A3_salesman) calculate_fitness() (genetic.Solution method) calculate_flip_energy() (in module ising) calculate_forces() (flocking.Predator method) (flocking.Prey method) (in module A4_2dmd) (in module dynamics) (in module flocking) (in module forces) (in module pbc) (in module temp) calculate_fractal_dimension() (in module A2_dla) calculate_heat_flux() (in module A5_fem) calculate_inverse_transformation() (in module fourier) calculate_kinetic_energy() (in module A4_2dmd) (in module dynamics) (in module pbc) (in module temp) calculate_left_temperature_gradient() (in module A5_fem) calculate_lj_potential_energy() (in module A4_2dmd) calculate_load() (in module A5_fem) (in module heat) calculate_magnetic_moment() (in module ising) calculate_mass_matrix() (in module A5_fem) (in module heat) calculate_momentum() (in module A4_2dmd) (in module dynamics) (in module pbc) (in module temp) calculate_particles_in_cluster() (in module A2_dla) calculate_potential_energy() (in module dynamics) (in module forces) (in module pbc) (in module temp) calculate_power_vector() (in module A5_fem) (in module heat) calculate_pressure() (in module A4_2dmd) (in module temp) calculate_propagator() (in module A5_fem) (in module heat) calculate_right_temperature_gradient() (in module A5_fem) calculate_spring_potential_energy() (in module A4_2dmd) calculate_statistics() (in module coins) (in module ising)

calculate_statistics_for_distribution() (in module coins) calculate_stiffness_matrix() (in module A5_fem) (in module heat) calculate_temperature() (in module A4_2dmd) (in module temp) calculate_total_heating_power() (in module A5_fem) calculate_transformation() (in module fourier) can_continue() (in module n_in_a_row) (in module tictac) can_take_slot() (in module n_in_a_row) (in module tictac) change_center_element() (in module vectors) change_center_element_in_place() (in module vectors) change_route_randomly() (in module A3_salesman) check_performance() (in module neuralnetwork) check_results() (in module clustering) check_winner() (in module n_in_a_row) (in module tictac) Circle (class in genetic) clock() (A4_2dmd.Animation method) clustering module coins module conjugate_gradients_algorithm() (in module gradients) connected_atoms (A4_2dmd.Particle attribute) constraint_type (A4_2dmd.Particle attribute) constraint_value (A4_2dmd.Particle attribute) copy_game() (in module n_in_a_row) (in module tictac) cos_analysis() (in module fourier) cos_synthesis() (in module fourier) count_connections() (in module A4_2dmd) count_consecutives() (in module n_in_a_row) (in module tictac) count_max_streak() (in module coins) count_neighbors() (in module etching) count_particles_in_circle() (in module A2_dla) count_particles_in_square() (in module A2_dla) count_primes() (in module primes) count_probabilities() (in module etching) covers() (genetic.Circle method) create_branches() (game_ai.MC_node method) create_data() (in module clustering) create_grid() (in module A2_dla) create_random_configuration() (in module forces) create_random_flock() (in module flocking) create_random_route() (in module A3_salesman) create_random_solution() (genetic.Solution method) crossover() (genetic.Solution method) crossover_box() (genetic.Solution method) crossover_line() (genetic.Solution method)

D

data_to_matrix() (in module clustering) declare_winner() (in module n_in_a_row) (in module tictac) deepest_descent_algorithm() (in module gradients) diffusion_simulation() (in module A2_dla) distance_squared() (flocking.PeriodicBox method) (in module dynamics) (in module forces) (pbc.PeriodicBox method) (temp.PeriodicBox method) distance_squared_to() (A4_2dmd.Particle method) distance_to() (A4_2dmd.Particle method) draw() (genetic.Solution method) (in module A2_dla) (in module A5_fem) (in module dynamics) (in module etching) (in module flocking) (in module fourier) (in module genetic) (in module gradients) (in module heat) (in module ising) (in module motion) (in module n_in_a_row) (in module pbc) (in module random_walk_free) (in module random_walk_lattice) (in module temp) (in module tictac) (in module waves) (in module waves_2d)

draw_3d() (in module waves_2d) draw_animation_frame() (in module ballistic) draw_motion_blur_image() (in module ballistic) draw_particles_and_forces() (in module forces) draw_population_to_file() (in module genetic) draw_profile() (in module clustering) draw_scatter() (in module clustering) draw_solution() (in module genetic) draw_trajectory() (in module ballistic) dynamics module

E

energy_gradient() (in module forces) etching module

euler() (in module dynamics) expand_discretization() (in module waves) expand_supercell() (in module temp) explore_branches() (game_ai.MC_node method)

F

feedforward() (neuralnetwork.NeuralNetwork method) fill_population() (in module genetic) find_clusters() (in module clustering) find_connected_atoms() (in module A4_2dmd) find_info() (in module A4_2dmd) (in module flocking) find_top_cluster() (in module percolation) first_step() (in module waves) (in module waves_2d)

flip() (in module ising) flocking module force (A4_2dmd.Particle attribute) forces module fourier module fourier_analysis() (in module fourier) fourier_synthesis() (in module fourier)

G

game_ai module generate_empty_lattice() (in module random_walk_lattice) generate_grid() (in module ising) generate_lattice() (in module random_walk_lattice) generate_network() (in module percolation) generate_system() (in module etching) genetic module

get_bond_width_and_colour() (A4_2dmd.Animation method) get_distance_sq() (random_walk_lattice.Walker method) get_particle_size_and_colour() (A4_2dmd.Animation method) get_random_sequence() (in module coins) get_removal_rate() (in module etching) get_trip_length() (in module A3_salesman) gradient() (in module gradients) gradients module

H

has_branches() (game_ai.MC_node method)

heat module

I

index (A4_2dmd.Particle attribute) is_above_line() (genetic.Circle method) is_inside_box() (genetic.Circle method)

is_leaf() (game_ai.MC_node method) is_vertically_connected() (in module percolation) ising module

K

k_means_clustering_algorithm() (in module clustering)

kill_the_unfit() (in module genetic) kinetic_energy() (A4_2dmd.Particle method)

L

langevin_force() (in module A4_2dmd) linear() (in module A1_analysis) (in module random_walk_lattice) linear_fit() (in module A1_analysis) (in module random_walk_lattice) linear_search() (in module gradients)

linearfit() (in module A2_dla) linlin_analysis() (in module A1_analysis) linlog_analysis() (in module A1_analysis) lj_energy() (in module A4_2dmd) lj_force() (in module A4_2dmd) loglog_analysis() (in module A1_analysis)

M

main() (in module A1_analysis) (in module A2_dla) (in module A3_salesman) (in module A4_2dmd) (in module A5_fem) (in module ballistic) (in module coins) (in module dynamics) (in module etching) (in module flocking) (in module forces) (in module fourier) (in module genetic) (in module gradients) (in module heat) (in module ising) (in module motion) (in module neuralnetwork) (in module pbc) (in module random_walk_free) (in module random_walk_lattice) (in module temp) (in module vectors) (in module waves) (in module waves_2d) make_move() (in module n_in_a_row) (in module tictac) mass (A4_2dmd.Particle attribute) matrix() (in module vectors) matrix_as_lists() (in module vectors) matrix_to_vector() (in module waves_2d) MC_node (class in game_ai) metropolis_step() (in module ising) mind_the_gap() (in module A2_dla) module A1_analysis A2_dla A3_salesman A4_2dmd A5_fem ballistic clustering coins dynamics etching flocking forces fourier game_ai genetic gradients heat ising motion n_in_a_row neuralnetwork pbc percolation primes random_walk_free random_walk_lattice temp tictac vectors waves waves_2d

motion module move() (A4_2dmd.Particle method) (ballistic.Ball method) (dynamics.Planet method) (flocking.Animal method) (forces.Atom method) (in module motion) (in module random_walk_free) (in module random_walk_lattice) (pbc.Atom method) (temp.Atom method) move_linearly() (A4_2dmd.Particle method) move_randomly() (in module random_walk_free) (random_walk_lattice.Walker method) multiply_by_scalar() (in module vectors) mutate() (genetic.Solution method) mutate_all() (in module genetic)

N

n_in_a_row module name (A4_2dmd.Particle attribute) neighbor_is_in_cluster() (in module A2_dla) neuralnetwork module

NeuralNetwork (class in neuralnetwork) new_game() (in module n_in_a_row) (in module tictac) next_player() (in module n_in_a_row) (in module tictac) nudge() (neuralnetwork.NeuralNetwork method)

O

optimize_route() (in module A3_salesman)

P

parse_line() (in module A4_2dmd) (in module flocking) parse_xy_data() (in module A1_analysis) Particle (class in A4_2dmd) pbc module percolation module percolation_mean_and_error() (in module percolation) PeriodicBox (class in flocking) (class in pbc) (class in temp) pick_best_play() (game_ai.MC_node method) pick_class() (in module neuralnetwork) pick_move() (game_ai.AI method) pick_played_branch() (game_ai.MC_node method) pick_random_event() (in module etching) pick_random_point() (in module A2_dla) pick_target() (flocking.Predator method) pick_unplayed_branch() (game_ai.MC_node method) Pixel (class in genetic) Planet (class in dynamics) play_game() (in module game_ai) plot_function_and_average() (in module A4_2dmd) plot_line() (in module A1_analysis) plot_trajectory() (in module motion) (in module random_walk_free) plot_xy_data() (in module A1_analysis) Point (class in clustering)

position (A4_2dmd.Particle attribute) Predator (class in flocking) previous_player() (in module n_in_a_row) (in module tictac) Prey (class in flocking) primes module print_matrix() (in module vectors) print_progress() (game_ai.AI method) (in module A2_dla) (in module A3_salesman) (in module A4_2dmd) (in module clustering) (in module coins) (in module dynamics) (in module etching) (in module flocking) (in module fourier) (in module genetic) (in module ising) (in module neuralnetwork) (in module pbc) (in module percolation) (in module random_walk_lattice) (in module temp) (in module waves) (in module waves_2d) profile_plot() (in module clustering) propagator() (in module waves) (in module waves_2d)

R

random_displacement() (in module gradients) random_step() (in module A2_dla) random_walk_free module random_walk_lattice module randomize() (genetic.Circle method) randomize_velocities() (in module A4_2dmd) randomly_remove_atom() (in module etching) read_animal_info() (in module flocking) read_atom() (in module A4_2dmd) read_atoms_from_file() (in module forces) read_box() (in module A4_2dmd) read_box_info() (in module flocking) read_cities_from_file() (in module A3_salesman) read_constraint() (in module A4_2dmd) read_constraints() (in module A4_2dmd) read_data() (in module clustering) read_dynamics_file() (in module flocking) read_file() (in module motion) (in module random_walk_free) read_force_info() (in module flocking) read_grid_from_file() (in module A2_dla) read_image() (in module genetic) read_interactions() (in module A4_2dmd) read_mesh_from_file() (in module A5_fem) read_particles_from_file() (in module dynamics) (in module pbc) (in module temp)

read_physics() (in module A4_2dmd) read_recording() (in module A4_2dmd) read_route_from_file() (in module A3_salesman) read_solution_from_file() (in module genetic) read_system() (in module A4_2dmd) read_system_file() (in module flocking) read_temperature() (in module A4_2dmd) read_time_info() (in module flocking) read_timescale() (in module A4_2dmd) read_timing() (in module A4_2dmd) read_weights() (neuralnetwork.NeuralNetwork method) record_position() (ballistic.Ball method) remove_circle() (genetic.Solution method) reset_forces() (ballistic.Ball method) rgb_to_hex() (A4_2dmd.Animation method) run_annealing_cycle() (in module A3_salesman) run_cumulant_series() (in module ising) run_evolution() (in module genetic) run_metropolis_algorithm() (in module ising) run_series() (in module coins) (in module percolation) run_simulation() (in module A4_2dmd) (in module A5_fem) (in module ballistic) (in module fourier) (in module heat) (in module percolation) (in module waves) (in module waves_2d) run_temperature_series() (in module ising)

S

save_grid_image() (in module ising) save_plot() (in module A1_analysis) save_position() (A4_2dmd.Particle method) (dynamics.Planet method) (flocking.Animal method) (pbc.Atom method) (temp.Atom method) save_weights() (neuralnetwork.NeuralNetwork method) scale_velocities() (in module temp) scatter_plot() (in module clustering) shift_inside_box() (flocking.PeriodicBox method) (pbc.PeriodicBox method) (temp.PeriodicBox method) shift_particles() (A4_2dmd.Animation method) show_cluster() (in module A2_dla) show_convergence() (in module gradients) show_grid() (in module ising) show_history() (in module A5_fem) (in module heat) show_network() (in module percolation)

show_particles() (in module temp) show_route() (in module A3_salesman) show_system() (in module A4_2dmd) (in module etching) (in module random_walk_lattice) show_temperature() (in module heat) show_trajectories() (in module dynamics) (in module pbc) (in module temp) simulate() (game_ai.MC_node method) simulate_single_particle() (in module A2_dla) simulated_annealing() (in module gradients) sin_analysis() (in module fourier) sin_synthesis() (in module fourier) Solution (class in genetic) solve_equilibrium() (in module heat) sort_by_fitness() (in module genetic) spring_energy() (in module A4_2dmd) spring_force() (in module A4_2dmd) sq_distance() (clustering.Point method)

T

target() (in module gradients) temp module tictac module

train() (neuralnetwork.NeuralNetwork method) transform_data() (in module A1_analysis) transform_data_in_place() (in module A1_analysis)

U

unit_vector_to() (A4_2dmd.Particle method) update_neighbors() (in module flocking) update_positions() (in module A4_2dmd) (in module dynamics) (in module pbc) (in module temp) update_positions_no_force() (in module dynamics) (in module flocking) (in module pbc) (in module temp)

update_positions_without_force() (in module A4_2dmd) update_targets() (in module flocking) update_velocities() (in module A4_2dmd) (in module dynamics) (in module flocking) (in module pbc) (in module temp)

V

vector() (flocking.PeriodicBox method) (in module dynamics) (in module forces) (pbc.PeriodicBox method) (temp.PeriodicBox method) vector_to() (A4_2dmd.Particle method) vector_to_matrix() (in module waves_2d) vectors module

velocity (A4_2dmd.Particle attribute) velocity_verlet() (in module A4_2dmd) (in module dynamics) (in module flocking) (in module pbc) (in module temp) visualize() (neuralnetwork.NeuralNetwork method)

W

Walker (class in random_walk_lattice) waves module waves_2d module wrap() (A4_2dmd.Particle method) write_cluster_file() (in module A2_dla) write_data() (in module A1_analysis) write_data_to_file() (in module ising) write_file() (in module A1_analysis) (in module motion) (in module random_walk_free)

write_particles_to_file() (in module dynamics) (in module pbc) (in module temp) write_route_to_file() (in module A3_salesman) write_solution_to_file() (in module genetic) write_system_file() (in module A4_2dmd) write_temperatures_to_file() (in module A5_fem) write_xyz_file() (in module dynamics) (in module pbc) (in module temp)