init of the calculations with Doppler broadening

1 files changed, 190 insertions, 0 deletions

diff --git a/xmds2/Nlevels_with_doppler_with_z_4wm/pp.m b/xmds2/Nlevels_with_doppler_with_z_4wm/pp.m
new file mode 100644
index 0000000..b88fa6e
--- /dev/null
+++ b/xmds2/Nlevels_with_doppler_with_z_4wm/pp.m
@@ -0,0 +1,190 @@
+Nlevels_no_dopler_with_z_4wm
+
+%% field propagation
+z_1=z_1*100; % z in cm
+t_1=t_1*1e6; % time now measured in uS
+figure(1)
+subplot(2,2,1); imagesc(z_1, t_1, I1_out_1); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('I_1')
+title('I_1')
+subplot(2,2,2); imagesc(z_1, t_1, I2_out_1); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('I_2')
+title('I_2')
+subplot(2,2,3); imagesc(z_1, t_1, I3_out_1); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('I_3')
+title('I_3')
+subplot(2,2,4); imagesc(z_1, t_1, I4_out_1); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('I_4')
+title('I_4')
+
+
+print('-color','fields_propagation.eps')
+
+
+
+%% fields before and after the cell
+figure(2)
+subplot(2,2,1);
+plot( ...
+	t_1,I1_out_1(:,1),'-;before;', "linewidth", 4,  ...
+	t_1,I1_out_1(:,end), '-;after;', "linewidth", 4 ...
+	)
+xlabel('t (uS)')
+ylabel('I_1 (1/s)^2')
+title('I_1 before and after cell')
+subplot(2,2,2);
+plot( ...
+	t_1,I2_out_1(:,1),'-;before;', "linewidth", 4,  ...
+	t_1,I2_out_1(:,end), '-;after;', "linewidth", 4 ...
+	)
+xlabel('t (uS)')
+ylabel('I_2 (1/s)^2')
+title('I_2 before and after cell')
+subplot(2,2,3);
+plot( ...
+	t_1,I3_out_1(:,1),'-;before;', "linewidth", 4,  ...
+	t_1,I3_out_1(:,end), '-;after;', "linewidth", 4 ...
+	)
+xlabel('t (uS)')
+ylabel('I_3 (1/s)^2')
+title('I_3 before and after cell')
+
+[b, a]=butter(3, 0.05);
+I2_out_after=I2_out_1(:,end);
+I2_out_after_filtered=filtfilt(b,a,I2_out_after);
+settling_time=0.8; %uS
+t_good_indx=t_1> min(t_1 + settling_time);
+[m,max_pos_before]=max(I2_out_1(t_good_indx,1) ); [m,max_pos_after]=max(I2_out_after_filtered(t_good_indx));
+delay_time=t_1(max_pos_after)-t_1(max_pos_before);
+printf('Second field delay time  = %f uS\n',delay_time);
+
+print('-color','fields_before_after_cell.eps')
+
+subplot(2,2,4);
+plot( ...
+	t_1,I4_out_1(:,1),'-;before;', "linewidth", 4,  ...
+	t_1,I4_out_1(:,end), '-;after;', "linewidth", 4 ...
+	)
+xlabel('t (uS)')
+ylabel('I_3 (1/s)^2')
+title('I_3 before and after cell')
+
+figure(4)
+I2_max_in=max(I2_out_1(t_good_indx,1));
+I2_max_out=max(I2_out_1(t_good_indx,end));
+I2_in_norm=(I2_out_1(:,1))/I2_max_in;
+I2_out_norm=(I2_out_1(:,end))/I2_max_out;
+tmin=-0.05;
+tmax=0.05;
+indx=(t_1>=tmin & t_1<=tmax);  % soom in in time to this region
+plot( ...
+	t_1(indx),I2_in_norm(indx),'-;before;', "linewidth", 4,  ...
+	t_1(indx),I2_out_norm(indx), '-;after;', "linewidth", 4 ...
+	)
+xlim([tmin,tmax],'manual');	
+xlabel('t (uS)')
+ylabel('I_2')
+title('I_2 before and after cell normalized')
+print('-color','probe_before_after_cell.eps')
+
+return;
+
+%% all density matrix elements in one plot
+% diagonal populations, 
+% upper triangle real part of coherences, 
+% lower diagonal imaginary part of coherences
+z_2=z_2*100; % z in cm
+t_2=t_2*1e6; % time now measured in uS
+figure(3)
+subplot(4,4,1); imagesc (z_2, t_2, r11_out_2);  caxis([0,1]); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('rho_{11}')
+title('rho_{11}')
+subplot(4,4,6); imagesc (z_2, t_2, r22_out_2);  caxis([0,1]); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('rho_{22}')
+title('rho_{22}')
+subplot(4,4,11); imagesc (z_2, t_2, r33_out_2);  caxis([0,1]); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('rho_{33}')
+title('rho_{33}')
+subplot(4,4,16); imagesc (z_2, t_2, r44_out_2); caxis([0,1]);  colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('rho_{44}')
+title('rho_{44}')
+% real parts of coherences
+subplot(4,4,2); imagesc(z_2, t_2, r12_re_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Real(rho_{12})')
+title('Real(rho_{12})')
+subplot(4,4,3); imagesc(z_2, t_2, r13_re_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Real(rho_{13})')
+title('Real(rho_{13})')
+subplot(4,4,4); imagesc(z_2, t_2, r14_re_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Real(rho_{14})')
+title('Real(rho_{14})')
+subplot(4,4,7); imagesc(z_2, t_2, r23_re_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Real(rho_{23})')
+title('Real(rho_{23})')
+subplot(4,4,8); imagesc(z_2, t_2, r24_re_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Real(rho_{24})')
+title('Real(rho_{24})')
+subplot(4,4,12); imagesc(z_2, t_2, r34_re_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Real(rho_{34})')
+title('Real(rho_{34})')
+% imaginary parts of coherences
+subplot(4,4,5); imagesc(z_2, t_2, r12_im_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Imag(rho_{12})')
+title('Imag(rho_{12})')
+subplot(4,4,9); imagesc(z_2, t_2, r13_im_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Imag(rho_{13})')
+title('Imag(rho_{13})')
+subplot(4,4,10); imagesc(z_2, t_2, r23_im_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Imag(rho_{23})')
+title('Imag(rho_{23})')
+subplot(4,4,13); imagesc(z_2, t_2, r14_im_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Imag(rho_{14})')
+title('Imag(rho_{14})')
+subplot(4,4,14); imagesc(z_2, t_2, r24_im_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Imag(rho_{24})')
+title('Imag(rho_{24})')
+subplot(4,4,15); imagesc(z_2, t_2, r34_im_out_2); colorbar
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('Imag(rho_{34})')
+title('Imag(rho_{34})')
+
+