22 files changed, 3 insertions, 440 deletions
diff --git a/faraday/Makefile b/faraday/Makefile
deleted file mode 100644
index 0a84c81..0000000
--- a/faraday/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-
-
-PROBLEMS = $(wildcard tasks/*.mat)
-RESULTS = $(PROBLEMS:tasks/%=results/%)
-
-
-calculate: problems  solutions
-
-solutions: results $(RESULTS)
-
-results:
-	@mkdir results
-
-
-problems: problems_prepared.stamp
-
-tasks:
-	@mkdir tasks
-
-problems_prepared.stamp: tasks tasks_builder.m
-	@./tasks_builder.m
-	@touch $@
-	@echo "Please run again:  make calculate"
-
-$(RESULTS): results/% : tasks/%
-	./task_solver.m $< $@
-
-clean:
-	rm -f problems_prepared.stamp
-	rm -rf tasks
-	rm -rf results
-	
-
-real_clean:
-	rm -rf L0m.cache
diff --git a/faraday/output_faraday_results_vs_B.m b/faraday/output_faraday_results_vs_B.m
deleted file mode 100644
index 8387a92..0000000
--- a/faraday/output_faraday_results_vs_B.m
+++ /dev/null
@@ -1,59 +0,0 @@
-function psr_rad=output_faraday_results_vs_B()
-load '/tmp/xi_vs_B.mat' ;
-
-Er=(1+I*xi_right)*E_field_pos_freq.right;
-El=(1+I*xi_left) *E_field_pos_freq.left;
-
-Ex=(Er+El)/sqrt(2);
-Ey=I*(Er-El)/sqrt(2);
-
-%extra rotation to compensate rotation due to ellipticity
-% actually no need for it since x-polarization shifts by positive phase 
-% and y-pol by negative phase 
-%el_rot=0*psi_el;
-%Ex=cos(el_rot)*Ex-sin(el_rot)*Ey;
-%Ey=sin(el_rot)*Ex+cos(el_rot)*Ey;
-
-Ipos=(abs(Ey).^2)/2;
-Ineg=(abs(Ex).^2)/2;
-
-figure(1);
-hold off;
-plot(B_fields, real(xi_left-xi_right), '-');  
-title("differential real xi");
-xlabel("two photon detuning (MHz)");
-
-figure(2);
-hold off;
-plot(B_fields, imag(xi_left-xi_right), '-');  
-title("differential imag xi");
-xlabel("two photon detuning (MHz)");
-
-figure(3);
-hold off;
-plot(B_fields, real(xi_left), '-', detuning_freq, real(xi_right), '-');  
-title("real xi");
-xlabel("two photon detuning (MHz)");
-
-figure(4);
-hold off;
-plot(B_fields, imag(xi_left), '-', detuning_freq, imag(xi_right), '-');  
-title("imag xi");
-xlabel("two photon detuning (MHz)");
-
-figure(5);
-hold off;
-I_probe=E_field_probe^2;
-psr_rad=(Ipos-Ineg)/(2*I_probe);
-plot(B_fields, psr_rad, '-');  
-subt_str=sprintf("Laser Rabi freq normalized to upper state decay %.3f, ellipticity %.1f degree, \n B field ground level splitting %.3f Gauss", I_probe, psi_el*180/pi, detuning_freq); 
-title(cstrcat("BPD normilized PSR signal at F_g=2 to F_e=1,2.\n ",subt_str) );
-xlabel("two photon detuning (MHz)");
-ylabel("PSR (radians)");
-
-print("psr_vs_detuning.ps");
-
-fname= sprintf("psr_vs_B_Fg=2toFe=1,2_Ip=%.3f_el_%.1f_detun=%.3fMHz.mat", I_probe, psi_el*180/pi,detuning_freq); 
-save(fname,'B_fields', 'psr_rad', 'xi_left', 'xi_right', 'xi_linear');
-
-return;
diff --git a/faraday/susceptibility_problem.m b/faraday/susceptibility_problem.m
deleted file mode 100644
index 56808e9..0000000
--- a/faraday/susceptibility_problem.m
+++ /dev/null
@@ -1,99 +0,0 @@
-function [xi_linear, xi_left, xi_right]=susceptibility_problem(detuning_freq, Ep, psi_el, B_field, theta, phi) 
-% calculates transmission  if light polarizations  vs B field in the cell
-% for given laser probe and B fields array
-% Probe field defined by field strength (Ep) and ellipticity angle (pse_el)
-% Magnetic field defined by magnitude (B_field) and angles theta and phi. 
-%
-% Note: it is expensive to recalculate atom property for each given B_field strength
-% so run as many calculation for constant magnetic field as possible
-
-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;
-
-
-B_str=num2str(B_field(1),"%g");
-% the child  file to which calculated matrices are  written 
-cfile='L0m.cache/L0m_and_polarizability_calculated_for_B=';
-cfile=strcat(cfile,B_str,'.mat');
-
-need_update=true;
-[s, err, msg] = stat (cfile); 
-if(err) 
-	%file does not exist
-	need_update=true; 
-else
-	need_update=false; 
-endif; 
-if ( !need_update)
-		% matrices already calculated and up to date, all we need to load them
-		load(cfile);
-	else
-		% 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 ...
-		);
-		save(cfile, 'L0m', 'polarizability_m');
-	endif
-
-global atom_properties;
-atom_properties.L0m=L0m;
-atom_properties.polarizability_m=polarizability_m;
-atom_properties.dipole_elements=dipole_elements;
-
-%light_positive_freq  = [wp];
-E_field_drive         = [0    ];
-E_field_probe         = [Ep   ];
-E_field_zero          = [0    ];
-E_field_lab_pos_freq.linear = E_field_zero + (1.00000+0.00000i)*E_field_probe  + (1.00000+0.00000i)*E_field_drive; 
-
-% we define light as linearly polarized 
-% where phi is angle between light polarization and axis x
-% only sign of modulation frequency is important now
-% we define actual frequency later on
-[E_field_lab_pos_freq.x, E_field_lab_pos_freq.y] = rotXpolarization(phi, E_field_lab_pos_freq.linear);
-% we add required ellipticity
-E_field_lab_pos_freq.x*=exp(I*psi_el);
-E_field_lab_pos_freq.y*=exp(-I*psi_el);
-E_field_lab_pos_freq.z=E_field_zero;
-
-E_field_pos_freq=xyz_lin2atomic_axis_polarization(theta, E_field_lab_pos_freq);
-
-
-wp0=w_pf1-w_sf2;  %Fg=2 -> Fe=1
-wp=wp0+detuning_freq;
-light_positive_freq=[ wp];
-% we calculate dc and negative frequencies 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=atom_field_problem;
-
-[xi_linear, xi_left, xi_right]=susceptibility_steady_state_at_freq( problems_cell_array);
-
-
-elapsed_time = etime (clock (), t0)
-return
-
-endfunction
-
-% vim: ts=2:sw=2:fdm=indent
diff --git a/faraday/task_solver.m b/faraday/task_solver.m
deleted file mode 100755
index 0ba57ea..0000000
--- a/faraday/task_solver.m
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/octave -qf
-% reads parameters file (argv1)  and output results of the calculations into output file (argv(2)
-
-arg_list = argv ();
-
-if (nargin < 2) 
-	error("need at least two parameters");
-end
-params_file=arg_list{1};
-output_fname=arg_list{2};
-
-load(params_file);
-
-[xi_linear, xi_left, xi_right]=susceptibility_problem(detuning_freq, Ep, psi_el, B_field, theta, phi)
-
-save(output_fname, 'detuning_freq', 'Ep', 'psi_el', 'B_field', 'theta', 'phi', ...
-	'xi_linear', 'xi_left', 'xi_right' ...
-	);
-
diff --git a/faraday/tasks_builder.m b/faraday/tasks_builder.m
deleted file mode 100755
index 3cc76b9..0000000
--- a/faraday/tasks_builder.m
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/octave -qf
-
-task_dir='tasks/';
-task_base_name='task_';
-task_ext='.mat';
-data_dir='results/';
-output_dir='results/';
-detuning_freq=0;
-
-
-% assign some defaults
-gmg=.7; % gyro magnetic ration for ground level
-
-%[psr_rad]=psr_vs_detuning(Ep, psi_el, B_field, theta, phi) 
-
-% phi is angle between linear polarization and axis x
-%phi=pi/4;
-phi=pi/2;
-% theta is angle between lab z axis (light propagation direction) and magnetic field axis (z')
-theta=0;
-% psi_el is the ellipticity parameter (phase difference between left and right polarization)
-psi_el=0/180*pi*e-8;
-
-Ep=sqrt(0.1);
-
-% we are going to sweep B so parts related to sweep paramer(s)
-zeeman_splitting=+0.1;
-Nsteps=100;
-B_fields=linspace(-zeeman_splitting/gmg, zeeman_splitting/gmg, Nsteps);
-
-for i=1:Nsteps
-	filename_task=strcat(task_dir, task_base_name);
-	i_str=num2str(i, "%04d");
-	filename_task=strcat(filename_task,i_str, task_ext);
-	B_field = B_fields(i);
-	save(filename_task, 'detuning_freq', 'Ep', 'psi_el', 'B_field', 'theta', 'phi');
-endfor
-
-disp("Tasks creation done");
diff --git a/faraday/tasks_pp.m b/faraday/tasks_pp.m
deleted file mode 100644
index f17d0d1..0000000
--- a/faraday/tasks_pp.m
+++ /dev/null
@@ -1,35 +0,0 @@
-basis_transformation;
-
-fnames=glob('results/*.mat');
-
-Nsteps=length(fnames)
-B_field=zeros(1,Nsteps);
-xi_linear=zeros(1,Nsteps);
-xi_left=zeros(1,Nsteps);
-xi_right=zeros(1,Nsteps);
-
-% read the information from resulting files
-for i=1:Nsteps
-	d=load(fnames{i});
-	B_field(i)=d.B_field;
-	xi_linear(i)=d.xi_linear;
-	xi_left(i)=d.xi_left;
-	xi_right(i)=d.xi_right;
-endfor
-
-figure(1);
-plot(B_field, real((xi_right+xi_left))/sqrt(2));
-title('phase of linear x-polarization');
-
-figure(2);
-plot(B_field, imag((xi_right+xi_left))/sqrt(2));
-title('absorption of linear x-polarization');
-
-figure(3);
-plot(B_field, real((1i*xi_right-1i*xi_left))/sqrt(2));
-title('phase of linear y-polarization');
-
-figure(4);
-plot(B_field, imag((1i*xi_right-1i*xi_left))/sqrt(2));
-title('absorption of linear y-polarization');
-
diff --git a/faraday_and_psr/L0m.cache b/faraday_and_psr/L0m.cache
new file mode 120000
index 0000000..c9b0aa9
--- /dev/null
+++ b/faraday_and_psr/L0m.cache
@@ -0,0 +1 @@
+../L0m.cache
+\ No newline at end of file
diff --git a/squeezing_filter/Makefile b/faraday_and_psr/Makefile
index 1cfd0de..39f5e1e 100644
--- a/squeezing_filter/Makefile
+++ b/faraday_and_psr/Makefile
@@ -12,7 +12,7 @@ results:
 	@mkdir results
 
 
-problems: problems_prepared.stamp
+problems: tasks problems_prepared.stamp
 
 tasks:
 	@mkdir tasks
@@ -36,7 +36,7 @@ clean: tasks_clean results_clean
 	rm -f problems_prepared.stamp
 	
 
-real_clean:
+real_clean: clean
 	rm -rf tasks
 	rm -rf results
 	rm -rf L0m.cache
diff --git a/faraday/basis_transformation.m b/faraday_and_psr/basis_transformation.m
index 28d8beb..28d8beb 120000
--- a/faraday/basis_transformation.m
+++ b/faraday_and_psr/basis_transformation.m
diff --git a/faraday/dipole_elementRb87D1line.m b/faraday_and_psr/dipole_elementRb87D1line.m
index 6a11745..6a11745 120000
--- a/faraday/dipole_elementRb87D1line.m
+++ b/faraday_and_psr/dipole_elementRb87D1line.m
diff --git a/faraday/rb87_D1_line.m b/faraday_and_psr/rb87_D1_line.m
index 74a52f0..74a52f0 100644
--- a/faraday/rb87_D1_line.m
+++ b/faraday_and_psr/rb87_D1_line.m
diff --git a/squeezing_filter/susceptibility_problem.m b/faraday_and_psr/susceptibility_problem.m
index 140204c..140204c 100644
--- a/squeezing_filter/susceptibility_problem.m
+++ b/faraday_and_psr/susceptibility_problem.m
diff --git a/squeezing_filter/task_solver.m b/faraday_and_psr/task_solver.m
index c044cf6..c044cf6 100755
--- a/squeezing_filter/task_solver.m
+++ b/faraday_and_psr/task_solver.m
diff --git a/squeezing_filter/tasks_builder.m b/faraday_and_psr/tasks_builder.m
index 78eea9e..78eea9e 100755
--- a/squeezing_filter/tasks_builder.m
+++ b/faraday_and_psr/tasks_builder.m
diff --git a/squeezing_filter/tasks_pp.m b/faraday_and_psr/tasks_pp.m
index 82bcdac..82bcdac 100644
--- a/squeezing_filter/tasks_pp.m
+++ b/faraday_and_psr/tasks_pp.m
diff --git a/faraday/useful_constants.m b/faraday_and_psr/useful_constants.m
index fc5b92d..fc5b92d 120000
--- a/faraday/useful_constants.m
+++ b/faraday_and_psr/useful_constants.m
diff --git a/faraday/useful_functions.m b/faraday_and_psr/useful_functions.m
index a2d3237..a2d3237 120000
--- a/faraday/useful_functions.m
+++ b/faraday_and_psr/useful_functions.m
diff --git a/squeezing_filter/basis_transformation.m b/squeezing_filter/basis_transformation.m
deleted file mode 120000
index 28d8beb..0000000
--- a/squeezing_filter/basis_transformation.m
+++ /dev/null
@@ -1 +0,0 @@
-../basis_transformation.m
-\ No newline at end of file
diff --git a/squeezing_filter/dipole_elementRb87D1line.m b/squeezing_filter/dipole_elementRb87D1line.m
deleted file mode 120000
index 6a11745..0000000
--- a/squeezing_filter/dipole_elementRb87D1line.m
+++ /dev/null
@@ -1 +0,0 @@
-../dipole_elementRb87D1line.m
-\ No newline at end of file
diff --git a/squeezing_filter/rb87_D1_line.m b/squeezing_filter/rb87_D1_line.m
deleted file mode 100644
index 74a52f0..0000000
--- a/squeezing_filter/rb87_D1_line.m
+++ /dev/null
@@ -1,148 +0,0 @@
-1;
-useful_constants;
-
-% note all frequency values are in MHz
-
-%  87Rb D1 line
-%
-%     m=-2   m=-1   m=0    m=1    m=2
-%     ----   ----   ----   ----   ----   |P,F=2>
-%
-%            ----   ----   ----          |P,F=1>
-%            m=-1   m=0    m=1        
-%
-%
-%
-%
-%
-%     m=-2   m=-1   m=0    m=1    m=2
-%     ----   ----   ----   ----   ----   |S,F=2>
-%
-%            ----   ----   ----          |S,F=1>
-%            m=-1   m=0    m=1        
-
-
-w_hpf_ground=6834;
-w_hpf_exited=817;
-w_sf2 = w_hpf_ground; %            Distance from |S,F=1> to |S,F=2>
-w_pf1       =1e9;  % something big Distance from |S,F=1> to |P,F=1>
-w_pf2       = w_pf1+w_hpf_exited; %Distance from |S,F=1> to |P,F=2> 
-gmg=.7; % gyro magnetic ration for ground level
-gme=.23; % gyro magnetic ration for exited level % CHECKME
-
-
-%bottom level   |F=1>
-levels( 1)=struct( "ang_momentum",  0, "total_momentum",   1, "m",  -1,  "energy",       0, "gm",  -gmg);
-levels( 2)=struct( "ang_momentum",  0, "total_momentum",   1, "m",   0,  "energy",       0, "gm",  -gmg);
-levels( 3)=struct( "ang_momentum",  0, "total_momentum",   1, "m",   1,  "energy",       0, "gm",  -gmg);
-
-%second bottom level |F=2>
-levels( 4)=struct( "ang_momentum",  0, "total_momentum",   2, "m",  -2,  "energy",   w_sf2, "gm",   gmg);
-levels( 5)=struct( "ang_momentum",  0, "total_momentum",   2, "m",  -1,  "energy",   w_sf2, "gm",   gmg);
-levels( 6)=struct( "ang_momentum",  0, "total_momentum",   2, "m",   0,  "energy",   w_sf2, "gm",   gmg);
-levels( 7)=struct( "ang_momentum",  0, "total_momentum",   2, "m",   1,  "energy",   w_sf2, "gm",   gmg);
-levels( 8)=struct( "ang_momentum",  0, "total_momentum",   2, "m",   2,  "energy",   w_sf2, "gm",   gmg);
-
-% first exited level |F=1>
-levels( 9)=struct( "ang_momentum",  1, "total_momentum",   1, "m",  -1,  "energy",   w_pf1, "gm",  -gme);
-levels(10)=struct( "ang_momentum",  1, "total_momentum",   1, "m",   0,  "energy",   w_pf1, "gm",  -gme);
-levels(11)=struct( "ang_momentum",  1, "total_momentum",   1, "m",   1,  "energy",   w_pf1, "gm",  -gme);
-
-% second exited level |F=2>
-levels(12)=struct( "ang_momentum",  1, "total_momentum",   2, "m",  -2,  "energy",   w_pf2, "gm",   gme);
-levels(13)=struct( "ang_momentum",  1, "total_momentum",   2, "m",  -1,  "energy",   w_pf2, "gm",   gme);
-levels(14)=struct( "ang_momentum",  1, "total_momentum",   2, "m",   0,  "energy",   w_pf2, "gm",   gme);
-levels(15)=struct( "ang_momentum",  1, "total_momentum",   2, "m",   1,  "energy",   w_pf2, "gm",   gme);
-levels(16)=struct( "ang_momentum",  1, "total_momentum",   2, "m",   2,  "energy",   w_pf2, "gm",   gme);
-
-Nlevels=size(levels)(2);
-
-
-H0=zeros(Nlevels);
-energy            = [1:Nlevels].*0;
-ang_momentum      = [1:Nlevels].*0;
-total_momentum    = [1:Nlevels].*0;
-m                 = [1:Nlevels].*0;
-gm                = [1:Nlevels].*0;
-
-for i=1:Nlevels
-	energy(i)         = levels(i).energy;
-	ang_momentum(i)   = levels(i).ang_momentum;
-	total_momentum(i) = levels(i).total_momentum;
-	m(i)              = levels(i).m;
-	gm(i)             = levels(i).gm;
-endfor
-H0=diag(energy)*hbar;
-
-
-dipole_elements.left   = zeros(Nlevels);
-dipole_elements.right  = zeros(Nlevels);
-dipole_elements.linear = zeros(Nlevels);
-% define dipole elements for transition from level j->k
-for j=1:Nlevels
-	for k=1:Nlevels
-		if ( abs(ang_momentum(j) - ang_momentum(k)) == 1)
-			%transition allowed for L =L' +/- 1
-			% but they correct within a factor, but not sign
-			if ( ( H0(j,j) < H0(k,k)) )
-				de=dipole_elementRb87D1line(...
-					total_momentum(j),m(j), ...
-					total_momentum(k),m(k)  ...
-				);
-				dipole_elements.left(j,k)   = de.left;
-				dipole_elements.right(j,k)  = de.right;
-				dipole_elements.linear(j,k) = de.linear;
-			endif	
-		endif
-	endfor
-endfor
-dipole_elements.linear+=dipole_elements.linear';
-dipole_elements.left+=dipole_elements.left';
-dipole_elements.right+=dipole_elements.right';
-
-maximum_dipole_elements=abs(dipole_elements.linear) + abs(dipole_elements.left) + abs(dipole_elements.right);
-
-%defasing matrix
-g_deph=0;
-g_dephasing=zeros(Nlevels);
-% dephasing only for non zero dipole elements (am I right?)
-g_dephasing=g_deph*(abs(maximum_dipole_elements) != 0);
-
-% decay matrix g(i,j) correspnds to decay from i-->j
-gamma=6;
-g_decay=zeros(Nlevels);
-for i=1:Nlevels
-	for j=1:Nlevels
-		if (  H0(i,i) > H0(j,j) )
-			% only upper levels decaying and decay is always positive
-			g_decay(i,j)=gamma * abs( maximum_dipole_elements(i,j) );
-		endif
-	endfor
-endfor
-
-% ground level mixing need to be artificial
-gamma_hpf=.0001;
-for i=1:Nlevels
-	for j=1:Nlevels
-		% it would be better to introduce a level corresponding to the bath
-		% but this slows calculations
-		% So 
-		% ground hyperfine are equally mixed together
-		if (  (abs( H0(i,i) - H0(j,j)) == w_hpf_ground*hbar ) || ...
-			    (abs( H0(i,i) - H0(j,j)) == 0 ) )
-			% i and j correspond to 2 ground levels
-			% we cannot decay to itself
-			if ( i != j )	
-				% total eight ground levels F=2 and F=1 so we decay in 7 channels
-				g_decay(i,j)+=gamma_hpf/7; 
-			endif
-		endif
-	endfor
-endfor
-
-% apply B field Zeeman splitting
-energy+=B_field * ( gm .* m);
-% convert frequency to energy units
-H0=diag(energy)*hbar;
-
-% vim: ts=2:sw=2:fdm=indent
diff --git a/squeezing_filter/useful_constants.m b/squeezing_filter/useful_constants.m
deleted file mode 120000
index fc5b92d..0000000
--- a/squeezing_filter/useful_constants.m
+++ /dev/null
@@ -1 +0,0 @@
-../useful_constants.m
-\ No newline at end of file
diff --git a/squeezing_filter/useful_functions.m b/squeezing_filter/useful_functions.m
deleted file mode 120000
index a2d3237..0000000
--- a/squeezing_filter/useful_functions.m
+++ /dev/null
@@ -1 +0,0 @@
-../useful_functions.m
-\ No newline at end of file