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;
theta=0;
%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=31;
min_angle=0; max_angle=pi; 
thetas=min_angle:((max_angle-min_angle)/N_angle_steps):max_angle;
for theta=thetas;
	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 into the cell as linearly polarized 
		% let's make circularly polarized light out of incident linear one
		E_field_lab_pos_freq.x = E_field_lab_pos_freq.linear/sqrt(2);
		E_field_lab_pos_freq.y = E_field_lab_pos_freq.linear/sqrt(2)*(1i);
		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);
% strangely parcell is slower than cellfun 20 seconds vs 29
%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  thetas problem_cntr;

compass_circ_output_results;

elapsed_time = etime (clock (), t0)

% vim: ts=2:sw=2:fdm=indent