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diff --git a/compass_lin.m b/compass_lin.m
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+1;
+clear all;
+t0 = clock (); % we will use this latter to calculate elapsed time
+
+
+% load useful functions;
+useful_functions;
+
+% some physical constants
+useful_constants;
+
+basis_transformation; % load subroutines
+
+% load atom energy levels and decay description
+rb87_D1_line;
+%four_levels_with_polarization;
+%four_levels;
+%three_levels;
+%two_levels;
+
+% load EM field description
+field_description;
+
+%Nfreq=length(modulation_freq);
+
+
+
+%tune probe frequency
+detuning_p=0;
+N_detun_steps=100;
+%detuning_p_min=-B_field*gmg*4; % span +/-4 Zeeman splitting
+%detuning_p_max=-detuning_p_min;
+detuning_freq=zeros(1,N_detun_steps+1);
+kappa_p =zeros(1,N_detun_steps+1);
+kappa_m =zeros(1,N_detun_steps+1);
+%detun_step=(detuning_p_max-detuning_p_min)/N_detun_steps;
+
+fprintf (stderr, "calculating atom properties\n");
+fflush (stderr);
+% calculate E_field independent properties of the atom
+% to be used as sub matrix templates for Liouville operator matrix
+[L0m, polarizability_m]=L0_and_polarization_submatrices( ...
+ Nlevels, ...
+ H0, g_decay, g_dephasing, dipole_elements ...
+ );
+elapsed_time = etime (clock (), t0);
+fprintf (stderr, "elapsed time so far is %.3f sec\n",elapsed_time);
+fflush (stderr);
+
+global atom_properties;
+atom_properties.L0m=L0m;
+atom_properties.polarizability_m=polarizability_m;
+atom_properties.dipole_elements=dipole_elements;
+
+%Ed=.1; Edc=conj(Ed);
+%Ep=0.8*Ed; Epc=conj(Ep);
+
+%light_positive_freq = [wp, wd, wp-wd];
+E_field_drive = [0 , Ed, 0 ];
+E_field_probe = [Ep, 0 , 0 ];
+E_field_zero = [0 , 0 , 0 ];
+E_field_lab_pos_freq.linear = E_field_zero + (1.00000+0.00000i)*E_field_probe + (1.00000+0.00000i)*E_field_drive;
+%E_field_lab_pos_freq.right = E_field_zero + (0.00000+0.00000i)*E_field_probe + (0.00000+0.00000i)*E_field_drive;
+%E_field_lab_pos_freq.left = E_field_zero + (0.00000+0.00000i)*E_field_probe + (0.00000+0.00000i)*E_field_drive;
+
+
+% phi is angle between linear polarization and axis x
+phi=pi*2/8;
+% theta is angle between lab z axis (light propagation direction) and magnetic field axis (z')
+theta=0/4;
+theta=65/180*pi;
+%small ellipticity angle psi (0 to pi/2)
+% 0 will give linear polarization
+% pi/2 circular polarization
+psi=pi/2;
+
+
+
+
+fprintf (stderr, "tuning laser in forloop to set conditions vs detuning\n");
+fflush (stderr);
+
+detuning_freq=[-.075, -.05, -.025, 0 , .025, .05 , .075, .1];
+
+problem_cntr=1;
+N_angle_steps=15;
+min_angle=0; max_angle=pi;
+phis=min_angle:((max_angle-min_angle)/N_angle_steps):max_angle;
+for phi=phis;
+ for detuning_p_cntr=1:length(detuning_freq);
+
+ wp0=w_pf1;
+ wd=w_pf1-w_hpf_ground;
+ detuning_p=detuning_freq(detuning_p_cntr);
+ wp=wp0+detuning_p;
+ wm=wd-(wp-wd);
+
+ light_positive_freq=[ wp, wd, wp-wd];
+ % we define light as linearly polarized
+ % where phi is angle between light polarization and axis x
+ [E_field_lab_pos_freq.x, E_field_lab_pos_freq.y] = rotXpolarization(phi, E_field_lab_pos_freq.linear);
+ E_field_lab_pos_freq.z=E_field_zero;
+
+ % now we transfor x,y,z, to x',y', and z' with respect to magnetic field az z' axis
+ E_field_pos_freq=xyz_lin2atomic_axis_polarization(theta, E_field_lab_pos_freq);
+
+ % we calculate dc and negative frequiencies as well as amplitudes
+ [modulation_freq, E_field] = ...
+ light_positive_frequencies_and_amplitudes2full_set_of_modulation_frequencies_and_amlitudes(...
+ light_positive_freq, E_field_pos_freq);
+
+ freq_index=freq2index(wp,modulation_freq);
+
+ atom_field_problem.E_field = E_field;
+ atom_field_problem.modulation_freq = modulation_freq;
+ atom_field_problem.freq_index = freq_index;
+
+ problems_cell_array{problem_cntr}=atom_field_problem;
+ problem_cntr++;
+
+
+ %kappa_p(detuning_p_cntr)=susceptibility_steady_state_at_freq( atom_field_problem);
+ endfor
+endfor
+
+save '/tmp/problem_definition.mat' problems_cell_array atom_properties detuning_freq theta;
+fprintf (stderr, "now really hard calculations begin\n");
+fflush (stderr);
+% once we define all problems the main job is done here
+%kappa_p=cellfun( @susceptibility_steady_state_at_freq, problems_cell_array);
+%kappa_p=parcellfun(2, @susceptibility_steady_state_at_freq, problems_cell_array);
+%[xi_linear, xi_left, xi_right]=parcellfun(2, @susceptibility_steady_state_at_freq, problems_cell_array);
+total_relative_transmission_vs_phi=parcellfun(2, @total_relative_transmission, problems_cell_array);
+%total_relative_transmission_vs_phi=cellfun(@total_relative_transmission, problems_cell_array);
+
+%save 'xi_vs_detuning.mat' detuning_freq xi_linear xi_left xi_right ;
+problem_cntr--;
+save '/tmp/total_relative_transmission_vs_phi.mat' detuning_freq total_relative_transmission_vs_phi phis problem_cntr;
+
+compass_output_results;
+
+elapsed_time = etime (clock (), t0)
+
+% vim: ts=2:sw=2:fdm=indent