Index

B

bacteria (Options attribute)

BacteriaBranching (class in cr_bayesian_optim.cr_bayesian_optim) BacterialParameters (class in cr_bayesian_optim.cr_bayesian_optim)

C

calculate_discretization() (in module cr_bayesian_optim.sim_branching) calculate_fractal_dim_for_pos() (in module cr_bayesian_optim.sim_branching) callback_diffevol() (in module cr_bayesian_optim.optimization) cell_radius (BacterialParameters attribute) check_exists() (in module cr_bayesian_optim.sim_branching) cr_bayesian_optim module

cr_bayesian_optim.cr_bayesian_optim module cr_bayesian_optim.optimization module cr_bayesian_optim.plotting module cr_bayesian_optim.sim_branching module

D

damping_constant (BacterialParameters attribute) diffusion_constant (DomainParameters attribute) division_radius (BacteriaBranching attribute) division_threshold (BacterialParameters attribute)

domain (Options attribute) domain_size (DomainParameters attribute) domain_starting_size (DomainParameters attribute) DomainParameters (class in cr_bayesian_optim.cr_bayesian_optim) dt (TimeParameters attribute)

G

generate_movie() (in module cr_bayesian_optim.plotting) get_all_iterations() (in module cr_bayesian_optim.cr_bayesian_optim)

growth_rate (BacteriaBranching attribute) (BacterialParameters attribute)

I

initial_concentration (DomainParameters attribute)

interaction (BacteriaBranching attribute)

L

load_cells() (in module cr_bayesian_optim.cr_bayesian_optim) load_cells_at_iteration() (in module cr_bayesian_optim.cr_bayesian_optim) load_from_toml() (Options static method)

load_optimization_result() (in module cr_bayesian_optim.optimization) load_or_compute_full() (in module cr_bayesian_optim.sim_branching) load_or_compute_last_iter() (in module cr_bayesian_optim.sim_branching) load_subdomains_at_iteration() (in module cr_bayesian_optim.cr_bayesian_optim)

M

mechanics (BacteriaBranching attribute) module cr_bayesian_optim cr_bayesian_optim.cr_bayesian_optim cr_bayesian_optim.optimization cr_bayesian_optim.plotting cr_bayesian_optim.sim_branching

MorsePotential (class in cr_bayesian_optim.cr_bayesian_optim) my_cmap() (in module cr_bayesian_optim.plotting)

N

n_bacteria_initial (BacterialParameters attribute)

n_threads (Options attribute) NewtonDamped2D (class in cr_bayesian_optim.cr_bayesian_optim)

O

optimization_bayes() (in module cr_bayesian_optim.optimization)

optimization_diff_evolution() (in module cr_bayesian_optim.optimization) Options (class in cr_bayesian_optim.cr_bayesian_optim)

P

plot_1D_cost_approximation_bayes() (in module cr_bayesian_optim.plotting) plot_all_iterations() (in module cr_bayesian_optim.plotting) plot_discretizations() (in module cr_bayesian_optim.sim_branching) plot_iteration() (in module cr_bayesian_optim.plotting)

plot_objective_projection_bayes() (in module cr_bayesian_optim.plotting) plot_optimization_convergence_bayes() (in module cr_bayesian_optim.plotting) potential_stiffness (BacterialParameters attribute) potential_strength (BacterialParameters attribute)

R

reactions_dx (DomainParameters attribute)

rhs_fractal_dim() (in module cr_bayesian_optim.optimization) run_sim_branching() (in module cr_bayesian_optim.cr_bayesian_optim)

S

save_interval (TimeParameters attribute) save_optimization_result() (in module cr_bayesian_optim.optimization) save_to_toml() (Options method)

set_rcparams() (in module cr_bayesian_optim.plotting) show_progressbar (Options attribute) storage_location (Options attribute) SubDomainPlainIndex (class in cr_bayesian_optim.cr_bayesian_optim)

T

t_max (TimeParameters attribute)

time (Options attribute) TimeParameters (class in cr_bayesian_optim.cr_bayesian_optim)

U

uptake_rate (BacteriaBranching attribute) (BacterialParameters attribute)

V

voxel_size (DomainParameters attribute)