From bd1e0f7cb84bf9b41e459c5f1d8a3b458b79fb09 Mon Sep 17 00:00:00 2001
From: Eugeniy Mikhailov <evgmik@gmail.com>
Date: Wed, 20 Mar 2013 17:15:15 -0400
Subject: added the penalty for final waist location mismatch and extra clean
 up

---
 fitness.m | 38 ++++++++------------------------------
 1 file changed, 8 insertions(+), 30 deletions(-)

diff --git a/fitness.m b/fitness.m
index e92879f..22699fd 100644
--- a/fitness.m
+++ b/fitness.m
@@ -1,34 +1,16 @@
 function [Energy, Waist, Penalty] = fitness( q_0, q_final, x_final, optics_positions, optics_focal_length, lambda )
 %Outputs fitness of suggested solution
     x0 = 0;
-    Np=20; % # of pts between start position and second lens
-    N_collimated = 10; % # of pts between second lens and third lens to be collimated region
     Energy = 0;
     
     x1=optics_positions(1);
     x2=optics_positions(2);
     x3=optics_positions(3);
     
-%     x_array1=linspace(x0,x2,Np);
-%     x_array2=linspace(x2, x3, N_collimated);
-%     x = cat(2,x_array1,x_array2);
-%     
-%     q_f_trial_forward = gbeam_propagation(x,q_0,x0,optics_placer(optics_positions, optics_focal_length));
-%     [Waist_trial_forward, Radius_trial_forward] = q2wr(q_f_trial_forward, lambda);
-%     q_f_trial_backward = gbeam_propagation(x,q_final,x_final,optics_placer(optics_positions, optics_focal_length));
-%     [Waist_trial_backward, Radius_trial_backward] = q2wr(q_f_trial_backward, lambda);
-% 
-%     Energy = 0;
-%     Penalty_waist_mismatch = sum(abs((Waist_trial_forward-Waist_trial_backward)./min(Waist_trial_forward, Waist_trial_backward)))/Np;
-%     
-%     Energy = 1e-2*Penalty_waist_mismatch;
-%     
     % penalty calculation
     % do not put lenses too close to each other and end positions
     lens_size=0.03;
     
-
-    
     d(1)=abs(x1-x2);
     d(2)=abs(x2-x3);
     d(3)=abs(x1-x3);
@@ -37,7 +19,6 @@ function [Energy, Waist, Penalty] = fitness( q_0, q_final, x_final, optics_posit
     d_from_end=abs(x_final-optics_positions);
     
     
-    
     d=cat(2, d, d_from_start, d_from_end);
     
     coef = 1;
@@ -64,7 +45,7 @@ function [Energy, Waist, Penalty] = fitness( q_0, q_final, x_final, optics_posit
     [ w, w_pos ] = self_gbeam_propagation( w0, optics_positions, optics_focal_length, x0, lambda );
     
     coef = 1;
-    d_object = ((optics_positions(end) - w_pos(end - 1))^2)^.5;
+    d_object = abs(optics_positions(end) - w_pos(end - 1));
     d_lens = optics_positions(end) - optics_positions(end - 1);
     penalty_not_collimated_beam = coef * exp(-(d_object/d_lens)^2);
     
@@ -72,20 +53,17 @@ function [Energy, Waist, Penalty] = fitness( q_0, q_final, x_final, optics_posit
     
 %     % waist at end matches desired waist
     coef = 10;
-    waist_desired = 3.709E-5;
+    [waist_desired, r_desired] = q2wr(q_final, lambda);
     
-    penalty_waist = coef *((waist_desired-w(end))^2)^.5;
+    penalty_waist = coef *((waist_desired-w(end))^2);
     
     Energy = Energy + penalty_waist;
 
-    %intialize intermediate points between lenses
-%     q_intermediate = q_f_trial_forward((x2<x) & (x<x3));
-%     lambda_over_waist_sq = (-imag(1./q_intermediate)); %with numerical factor
-%     
-%     coef = 1e-3;
-%     penalty_not_collimated_beam = coef * sum(exp((std(lambda_over_waist_sq)/mean(lambda_over_waist_sq)/abs(optics_positions(2) - optics_positions(3)))));
-%     Energy = Energy + penalty_not_collimated_beam;
-%     
+    dist_between_desired_and_final_waist_location =w_pos(end) - x_final;
+    penalty_final_waist_position = dist_between_desired_and_final_waist_location^2;
+
+    Energy = Energy + penalty_final_waist_position;
+
    Penalty = [ penalty_lenses_too_closely_spaced; penalty_lenses_outside_optical_path; penalty_not_collimated_beam; penalty_waist];
 end
 
-- 
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