Cleaned up control functions.testing

Changed config for longer times and smaller ground state decay.
data/ is a symlink to an additional drive, may cause funny behavior when cloning.

8 files changed, 35 insertions, 45 deletions

diff --git a/config.m b/config.m
index 0d9b525..78bcd09 100644
--- a/config.m
+++ b/config.m
@@ -3,9 +3,9 @@
 % Always run this file first.
 %
 
-decay_ground = [0.00001];	% Ground state decay
+decay_ground = [0.000001];	% Ground state decay
 decay_upper = [6];	% Excited state decay
-drive = [linspace(1e-2,7e-2,10)];	% Drive/control field
+drive = [linspace(5e-3,5e-2,10)];	% Drive/control field
 drive = drive;	% Choose which drives you want 
 detuning1 = [0];	% Single photon detuning
 dephase_bc = [0];	% Ground state dephasing
diff --git a/control/getSimulation.m b/control/getSimulation.m
index 6eb964e..0c5b877 100644
--- a/control/getSimulation.m
+++ b/control/getSimulation.m
@@ -1,9 +1,8 @@
-function [detunings2, probe, absorptions, z] = getSimulation(dataFile)
+function [detunings2, probe, z] = getSimulation(dataFile)
 
 	data = load(dataFile);
 	detunings2 = data._1.detuning';
 	z = data._1.z;
-	absorptions = squeeze(data._2.PabI(:,end,:));
 	probe = squeeze(data._1.I1_out(:,end,:));
 
 end
diff --git a/control/getSimulations.m b/control/getSimulations.m
index e3d5851..19cce0e 100644
--- a/control/getSimulations.m
+++ b/control/getSimulations.m
@@ -1,9 +1,9 @@
-function [drives, widths, minAbsorptions, contrasts, z] = getSimulations(decay_bc, detuning, dephase_bc)
+function [drives, widths, transmissions, contrasts, z] = getSimulations(decay_bc, detuning, dephase_bc)
 
 	global data_dir
 	dataFiles = dir([data_dir, decay_bc, '*_*_', detuning, '*_', dephase_bc, '*.h5']);
 	widths = [];
-	minAbsorptions = [];
+	transmissions = [];
 	contrasts = [];
 	drives = [];
 	detunings1 = [];
@@ -11,18 +11,18 @@ function [drives, widths, minAbsorptions, contrasts, z] = getSimulations(decay_b
 
 	for i = 1:length(dataFiles)
 		dataFile = dataFiles(i).name;
-		[detunings2, probes, absorptions, z] = getSimulation([data_dir, dataFile]);
+		[detunings2, probes, z] = getSimulation([data_dir, dataFile]);
 		width_by_z = [];
 		contrast_by_z = [];
-		absorption_by_z = [];
+		transmission_by_z = [];
 		for j = 2:length(z)
-			[width, probe, contrast] = getPeak(detunings2, probes(:,j));
+			[width, transmission, contrast] = getPeak(detunings2, probes(:,j));
 			width_by_z = [width_by_z; width];
-			absorption_by_z = [absorption_by_z; probe];
+			transmission_by_z = [transmission_by_z; transmission];
 			contrast_by_z = [contrast_by_z; contrast];
 		end
 		widths = [widths; width_by_z'];
-		minAbsorptions = [minAbsorptions; absorption_by_z'];
+		transmissions = [transmissions; transmission_by_z'];
 		contrasts = [contrasts; contrast_by_z'];
 		sections = strfind(dataFile, '_');
 		drive = dataFile(sections(1)+1:sections(2)-1);
diff --git a/data b/data
new file mode 120000
index 0000000..a068fbc
--- /dev/null
+++ b/data
@@ -0,0 +1 @@
+/run/media/hunter/Media/Workspace/eit/data
\ No newline at end of file
diff --git a/data/.gitignore b/data/.gitignore
deleted file mode 100644
index 5e7d273..0000000
--- a/data/.gitignore
+++ /dev/null
@@ -1,4 +0,0 @@
-# Ignore everything in this directory
-*
-# Except this file
-!.gitignore
diff --git a/octave-workspace b/octave-workspace
index 8622b89..a4f53f9 100644
--- a/octave-workspace
+++ b/octave-workspace
diff --git a/source/eit.xmds b/source/eit.xmds
index 592c0fc..778309c 100644
--- a/source/eit.xmds
+++ b/source/eit.xmds
@@ -48,7 +48,7 @@
      <validation kind="run-time"/>
      <arguments>
       <argument name="decay_upper_arg" type="real" default_value="1e1" />
-      <argument name="decay_ground_arg" type="real" default_value="1e-3" />
+      <argument name="decay_ground_arg" type="real" default_value="1e-6" />
       <argument name="drive_arg" type="real" default_value="1e-1" />
       <argument name="probe_arg" type="real" default_value="1e-4" />
       <!-- Expected detuning width needed is: 
@@ -59,7 +59,7 @@
       <argument name="delta1_arg" type="real" default_value="0" />
       <argument name="dephase_bc_arg" type="real" default_value="0" />
       <argument name="start_time" type="real" default_value="0" />
-      <argument name="end_time" type="real" default_value="100" />
+      <argument name="end_time" type="real" default_value="5000" />
       <![CDATA[
         
         decay_upper = decay_upper_arg;
@@ -87,8 +87,8 @@
       <dimension name="detuning" lattice="256"  domain="(domain_min, domain_max)" />
       -->
       
-      <dimension name="t"   lattice="1000"   domain="(start_time, end_time)"  />
-      <dimension name="detuning" lattice="100"  domain="(detuning_min, detuning_max)" />
+      <dimension name="t"   lattice="50000"   domain="(start_time, end_time)"  />
+      <dimension name="detuning" lattice="10"  domain="(detuning_min, detuning_max)" />
     </transverse_dimensions>
   </geometry>
 
@@ -134,7 +134,7 @@
     and what algorithm we want to use.
     -->
     <integrate algorithm="ARK45" tolerance="1e-5" interval="7e-2">
-      <samples>100 100</samples>
+      <samples>100</samples>
       <operators>
         <operator kind="cross_propagation" algorithm="SI" propagation_dimension="t">
           <integration_vectors>population</integration_vectors>
@@ -195,35 +195,29 @@
   <output format="hdf5" >
     <sampling_group basis="t detuning" initial_sample="yes">
       <dependencies>E_field</dependencies>
-      <moments>I1_out I2_out</moments>
+      <moments>I1_out</moments>
       <![CDATA[
       I1_out = mod2(probe);
-      I2_out = mod2(drive);
+      //I2_out = mod2(drive);
       ]]>
     </sampling_group>
-    <sampling_group basis="t detuning" initial_sample="yes">
-      <!-- <moments>PaaR PaaI PbbR PbbI PccR PccI PabR PabI PcaR PcaI PcbR PcbI</moments>
+    <!--<sampling_group basis="t detuning" initial_sample="yes">
+      <moments>PaaR PaaI PbbR PbbI PccR PccI PabR PabI PcaR PcaI PcbR PcbI</moments>
       <dependencies>population</dependencies>
       <![CDATA[
-        PaaR = Paa.Re();
-        PaaI = Paa.Im();
-        PbbR = Pbb.Re();
-        PbbI = Pbb.Im();
-        PccR = Pcc.Re();
-        PccI = Pcc.Im();
-        PabR = Pab.Re();
+        //PaaR = Paa.Re();
+        //PaaI = Paa.Im();
+        //PbbR = Pbb.Re();
+        //PbbI = Pbb.Im();
+        //PccR = Pcc.Re();
+        //PccI = Pcc.Im();
+        //PabR = Pab.Re();
         PabI = Pab.Im();
-        PcaR = Pca.Re();
-        PcaI = Pca.Im();
-        PcbR = Pcb.Re();
-        PcbI = Pcb.Im();
-      ]]> -->
-      <moments>PabI PabR</moments>
-      <dependencies>population</dependencies>
-      <![CDATA[
-        PabI = Pab.Im();
-        PabR = Pab.Re();
+        //PcaR = Pca.Re();
+        //PcaI = Pca.Im();
+        //PcbR = Pcb.Re();
+        //PcbI = Pcb.Im();
       ]]>
-    </sampling_group>
+    </sampling_group>-->
   </output>
 </simulation>
diff --git a/source/simulate.py b/source/simulate.py
index c1dccaf..6807154 100644
--- a/source/simulate.py
+++ b/source/simulate.py
@@ -10,7 +10,7 @@ FNULL = open(os.devnull, 'w')
 
 # Wrapper for call function to forward output to /dev/null
 def bash(command):
-	call(command, shell=True, stdout=FNULL, stderr=STDOUT)
+	call(command, shell=True)#, stdout=FNULL, stderr=STDOUT)
 
 # Divide the given values into n arrays
 def splitRange(x, n):
@@ -96,8 +96,8 @@ def simulate((index, decays_upper, decays_ground, drives, detunings1, dephasings
 				for detuning1 in detunings1:
 					for dephase_bc in dephasings_bc:
 						
-						expected_width = (math.pow(drive,2)/decay_upper + dephase_bc + decay_ground)
-						domain_max = expected_width*50
+						expected_width = (math.pow(drive,2)/decay_upper)
+						domain_max = expected_width*10
 						domain_min = -1*domain_max
 						final_time = 1/expected_width*time_multiplier