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coli chemotactic % foraging strategy for the surge tank example. % % Kevin Passino % Version: 9/27/00 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Initialize variables clear rand('state',0) % Reset the random number generator so each time you re-run % the program with no changes you will get the same results. % We assume that the parameters of the tank are: abar=0.01; bbar=0.2; cbar=1; 1) dbar=1; g=9.8; T=0.1; beta0=0.25; beta1=0.5; % Parameter characterizing tank shape (nominal value is 0.01) % Parameter characterizing tank shape (nominal value is 0.2) % Clogging factor representing dirty filter in pump (nominally, % % % % % Related to diameter of output pipe Gravity Sampling rate Set known lower bound on betahat and the upper bound

% Set the length of the simulation (here, also the number of chemotactic steps) Nnc=1000; % As a reference input, we use a square wave (define one extra % point since at the last time we need the reference value at % the last time plus one) timeref=1:Nnc+1; r(timeref)=3.25-3*square((2*pi/150)*timeref); % A square wave input %r(timeref)=3.25*ones(1,Nnc+1)-3*(2*rand(1,Nnc+1)-ones(1,Nnc+1)); % A noise input ref=r(1:Nnc); % Then, use this one for plotting time=1:Nnc; time=T*time; % Next, make the vector real time % Next, set plant initial conditions

h(1)=1; e(1)=r(1)-h(1);

A(1)=abs(abar*h(1)+bbar); alpha(1)=h(1)-T*dbar*sqrt(2*g*h(1))/A(1); beta(1)=T*cbar/A(1); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Initialize the foraging strategy parameters: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % We will use a very simple foraging strategy, one modeling the E. coli, but not % the reproduction and elimination-dispersal events. We align the increments for % chemotactic steps with time steps (of course you could take multiple steps per % time step, but that complicates the coding a bit). p=2; % Dimension of the search space

S=10; % The number of bacteria in the population (for convenience, require this to be an % an even number) Ns=4; % Limits the length of a swim when it is on a gradient

climbstepcounter=0*ones(S,1); % Set up a counter for each bacterium when for how long it % will climb down in a single direction runlengthunit=0.05; % For setting chemotactic step size (same for both dimensions), can % think of this as an adaptation gain % Allocate memory: %bestvalue=0*ones(Nnc+1,1); %bestmember=0*ones(Nnc+1,1); %bestindividual=0*ones(p,Nnc+1); % Generate an initial random direction for each bacterium (later these will change when % a bacterium tumbles) for i=1:S Delta(:,i)=(2*round(rand(p,1))-1).*rand(p,1); end % Initial population P(:,:,:)=0*ones(p,S,Nnc+1); % First, allocate needed memory

% Initialize locations of bacteria - initial guess at the plant dynamics (make each member of the % population the same initial guess)

thetaalpha(1)=2; thetabeta(1)=0.5; for m=1:S P(1,m,1)=thetaalpha(1); % Load into initial population of bacteria P(2,m,1)=thetabeta(1); end % Make the initial estimates of the plant dynamics based on this: alphahat(1)=thetaalpha(1)*h(1); betahat(1)=thetabeta(1); % Number of steps to look back in assessment of quality of identifier model: N=100; % Next, define the intial controller output u(1)=(1/(betahat(1)))*(-alphahat(1)+r(1+1)); % Initialize estimate of the plant dynamics (note that the % time indices are not properly aligned but this is just an estimate) hhat(1)=alphahat(1)+betahat(1)*u(1); % Estimate to be the same as at % the first time step %%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Next, start the main loop: %%%%%%%%%%%%%%%%%%%%%%%%%%%%% for k=2:Nnc % Define the plant % In implementation, the input flow is restricted % by some physical contraints. So we have to put a % limit for the input flow that is chosen as 50. if u(k-1)>50 u(k-1)=50; end if u(k-1)<-50 u(k-1)=-50; end h(k)=alpha(k-1)+beta(k-1)*u(k-1); h(k)=max([0.001,h(k)]); % Constraint liquid not to go % negative e(k)=r(k)-h(k); % For plotting, if needed

if k>N+1, % Next, we have to check how each member of the population would have % done over the last several steps if it had been used as the identifier % The objective is to compute Js which will be used in the fitness function for m=1:S % Initialize: Js(m,k)=0; % Compute S values of the cost, one for each bacterium for j=k-N:k, hhats(m,j)=P(1,m,k-1)*h(j-1)+P(2,m,k-1)*u(j-1); es(m,j)=hhats(m,j)-h(j); Js(m,k)=Js(m,k)+(es(m,j))^2; end end % Pick the best member to be used to specify the estimate [bestvalue(k),bestmember(k)]=min(Js(:,k)); bestindividual(:,k)=P(:,bestmember(k),k-1); thetaalpha(k)=P(1,bestmember(k),k-1); thetabeta(k)=P(2,bestmember(k),k-1); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Foraging strategy for searching for good model information (parameters) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % This part assumes that the parameters at time k-1 are in range to start with % This algorithm operates on P(:,:,k-1) to produce P(:,:,k) for i=1:S % For each bacterium % For plotting if needed

if Js(i,k)<Js(i,k-1) & climbstepcounter(i,1)<Ns; % Moving in good direction, and not for too long P(:,i,k)=P(:,i,k1)+runlengthunit*Delta(:,i)/sqrt(Delta(:,i)'*Delta(:,i)); climbstepcounter(i,1)=climbstepcounter(i,1)+1; % Increment climb counter since climbed in same direction as last time else % Not in good direction, or moved in good one too long Delta(:,i)=(2*round(rand(p,1))-1).*rand(p,1); % Generate new direction for this bacterium (tumble) P(:,i,k)=P(:,i,k1)+runlengthunit*Delta(:,i)/sqrt(Delta(:,i)'*Delta(:,i)); % Reset counter for any bacterium that has reached the max number of climb steps climbstepcounter(i,1)=0; end % Put parameters in range using projection:

if P(1,m,k)>6; P(1,m,k)=6; end if P(1,m,k)<-2; P(1,m,k)=-2; end if P(2,m,k)>0.5; P(2,m,k)=0.5; end if P(2,m,k)<0.25; P(2,m,k)=0.25; end end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % End foraging strategy %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% else % Hold estimates constant if have not gotten enough data % to be able to compute the cost function (hence, adaptation % does not start until after N steps) P(:,:,k)=P(:,:,k-1); % Pick the parameters to be the same (here, just pick it to be the first % population member - since they are all the same initially it does not % matter which one you pick) thetaalpha(k)=P(1,1,k-1); thetabeta(k)=P(2,1,k-1); end % Next, find the estimates of the plant dynamics (best member) betahat(k)=thetabeta(k); alphahat(k)=thetaalpha(k)*h(k); % Store the estimate of the plant dynamics hhat(k)=alphahat(k-1)+betahat(k-1)*u(k-1); % Next, use the certainty equivalence controller u(k)=(1/(betahat(k)))*(-alphahat(k)+r(k+1)); % Define some parameters to be used in the plant A(k)=abs(abar*h(k)+bbar); alpha(k)=h(k)-T*dbar*sqrt(2*g*h(k))/A(k); beta(k)=T*cbar/A(k);

end %%%%%%%% % Plot the results figure(1) clf subplot(211) plot(time,h,'b-',time,ref,'k--') grid ylabel('Liquid height, h') title('Liquid level h (solid) and reference input r') subplot(212) plot(time,u,'b-') grid title('Tank input, u') xlabel('Time, k') axis([min(time) max(time) -50 50]) %%%%%%%% figure(2) clf subplot(311) plot(time,h,'k--',time,hhat,'b-') grid title('Liquid level h and estimate of h (solid)') subplot(312) plot(time,alpha,'k--',time,alphahat,'b-') grid title('Plant nonlinearity \alpha and its estimate (solid)') subplot(313) plot(time,beta,'k--',time,betahat,'b-') grid xlabel('Time, k') title('Plant nonlinearity \beta and its estimate (solid)') %%%%%%%% figure(3) clf subplot(211) plot(time,bestvalue,'b-') grid title('Cost for best member') subplot(212) plot(time,bestmember,'b-') grid xlabel('Time, k') T=num2str(S); T=strcat('Index of best member in population of size=',T); title(T)

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