Calculations/MOT Capture Process Simulation/@MOTSimulator/runSimulation.m

function [LoadingRate, StandardError, ConfidenceInterval] = runSimulation(this)
    
    %% - Sampling for initial positions and velocities
    % - sampling the position distribution
    this.InitialPositions  = this.initialPositionSampling();
    % - sampling the velocity distribution
    this.InitialVelocities = this.initialVelocitySampling();
    
    %% Solve ODE 
    progressbar  = Helper.parforNotifications();
    progressbar.PB_start(this.NumberOfAtoms,'Message',['Simulating capture process for ' num2str(this.NumberOfAtoms,'%.0f') ' atoms:']);
    
    % calculate the final position of the atoms
    ParticleDynamicalQuantities     = zeros(this.NumberOfAtoms,int64(this.SimulationTime/this.TimeStep),6);
    Positions   = this.InitialPositions;
    Velocities  = this.InitialVelocities; 
    parfor Index = 1:this.NumberOfAtoms
        ParticleDynamicalQuantities(Index,:, :) = this.solver(Positions(Index,:), Velocities(Index,:));
        progressbar.PB_iterate();
    end
    clear Index
    
    %% Calculate the Loading Rate
    [LoadingRate, StandardError, ConfidenceInterval] = this.calculateLoadingRate(ParticleDynamicalQuantities);
end