crm_amir

The crm_amir script is designed to specifically estimate the parameters of the bending experiment performed by Amir et. al [5]. With our developed methods we are able to properly estimate the parameters of our model. More details are contained in our upcoming publication.

Usage of the crm_amir script

usage: crm_amir [-h] [-w WORKERS] [--maxiter MAXITER] [--popsize POPSIZE] [--skip-polish]
            [--maxiter-profiles MAXITER_PROFILES] [--optim-tol-profiles OPTIM_TOL_PROFILES]
            [--optim-atol-profiles OPTIM_ATOL_PROFILES] [--init INIT]
            [--popsize-profiles POPSIZE_PROFILES] [--skip-polish-profiles]
            [--samples-profiles SAMPLES_PROFILES]

options:
-h, --help            show this help message and exit
-w, --workers WORKERS
                        Number of threads (default: -1)
--maxiter MAXITER     Maximum iterations of the optimization routine (default: 350)
--popsize POPSIZE     Population Size of the optimization routine (default: 30)
--skip-polish         Skips polishing the result of the differential evolution algorithm (default:
                        False)
--maxiter-profiles MAXITER_PROFILES
                        See MAXITER (default: 350)
--optim-tol-profiles OPTIM_TOL_PROFILES
                        Relative Tolerance for optimization within profiles (default: 0.0001)
--optim-atol-profiles OPTIM_ATOL_PROFILES
                        Absolute Tolerance for optimization within profiles (default: 0.01)
--init INIT           Initialization method for the sampling of parameters. (default: latinhypercube)
--popsize-profiles POPSIZE_PROFILES
                        See POPSIZE (default: 30)
--skip-polish-profiles
                        See POLISH (default: False)
--samples-profiles SAMPLES_PROFILES
                        Number of sample points for profile likelihood plots (default: 100)

class FixedRod

Bases: object

RodAgent which is based on the RodAgent class.

It applies a fixed value to the first vertex of the rod and ensures that vertices can only move along a one-dimensional line when inside the nanochamber given by the block_size value.

agent

block_size

domain_size

class Parameters

Bases: object

Contains all parameters required for the simulation

block_size: Size for which to block movement along additional coordinate

damping: Damping constant

domain_size: Overall Domain Size

drag_force: Drag force exerted by the flow

dt: Time increment for solving the equations

growth_rate: Growth rate of the rod

n_vertices: Number of vertices to use for Rod

progressbar: Show/hide progressbar during solving of simulation

rod_length: Overall starting length of the rod

rod_rigidity: Rigidity of the rod

save_interval: Interval in which to save Agent data

spring_tension: Tension with which the segment lengths are enforced

t_max: Maximum simulation time

tube_width: Overall width of the tube

run_sim(parameters, initial_pos=None)

run_sim_with_relaxation(parameters, t_relax, initial_pos=None)