From ef2a5247db0bf0c5c2ca3368bbd36153e7c00032 Mon Sep 17 00:00:00 2001
From: Eugeniy Mikhailov <evgmik@gmail.com>
Date: Wed, 27 Apr 2016 11:00:38 -0400
Subject: moved files to subdir

---
 Makefile                                         |  37 ------
 delta_2photon_noise.xmds                         | 148 -----------------------
 pp.m                                             |  21 ----
 simple_thin_layer_model/Makefile                 |  37 ++++++
 simple_thin_layer_model/delta_2photon_noise.xmds | 148 +++++++++++++++++++++++
 simple_thin_layer_model/pp.m                     |  21 ++++
 6 files changed, 206 insertions(+), 206 deletions(-)
 delete mode 100644 Makefile
 delete mode 100644 delta_2photon_noise.xmds
 delete mode 100644 pp.m
 create mode 100644 simple_thin_layer_model/Makefile
 create mode 100644 simple_thin_layer_model/delta_2photon_noise.xmds
 create mode 100644 simple_thin_layer_model/pp.m

diff --git a/Makefile b/Makefile
deleted file mode 100644
index 83877ee..0000000
--- a/Makefile
+++ /dev/null
@@ -1,37 +0,0 @@
-###  -*- make -*-
-### This file is part of the Debian xmds package
-### Copyright (C) 2006 Rafael Laboissiere
-### This file is relased under the GNU General Public License
-### NO WARRANTIES!
-
-### This makefile can be used to build and run the XMDS examples
-
-XMDS_FILES = $(shell ls *.xmds)
-RUN_FILES = $(patsubst %.xmds,%.run,$(XMDS_FILES))
-CC_FILES = $(patsubst %.xmds,%.cc,$(XMDS_FILES))
-XSIL_FILES = delta_2photon_noise.xsil
-M_FILES = $(patsubst %.xsil,%.m,$(XSIL_FILES))
-
-XMDS = xmds2
-XSIL2GRAPHICS = xsil2graphics2
-
-all: $(M_FILES) 
-
-%.run: %.xmds
-	$(XMDS) $<
-	mv $(patsubst %.xmds,%,$<) $@
-
-$(XSIL_FILES): %.xsil: $(RUN_FILES)
-	./$<
-
-$(M_FILES): %.m : %.xsil
-	$(XSIL2GRAPHICS) $<
-
-plot: $(M_FILES)
-	octave pp.m
-
-clean:
-	rm -f $(CC_FILES) $(RUN_FILES) $(M_FILES) $(XSIL_FILES) *.wisdom.fftw3 *.dat octave-core *.wisdom *.pdf
-
-.PRECIOUS: %.run %.xsil %.m
-.PHONY: all clean
diff --git a/delta_2photon_noise.xmds b/delta_2photon_noise.xmds
deleted file mode 100644
index 2cb3a52..0000000
--- a/delta_2photon_noise.xmds
+++ /dev/null
@@ -1,148 +0,0 @@
-<?xml version="1.0"?>
-<simulation xmds-version="2">
-
-	<name>delta_2photon_noise</name>
-
-	<author>E. Mikhailov, M. Guidry</author>
-	<description>
-		Solving 3 level atom in lambda field configuration,
-		no field propagation included. Noise on delta_2photon.
-	</description>
-
-	<features>
-		<benchmark />
-		<bing />
-		<fftw plan="patient" />
-		<openmp />
-		<auto_vectorise />
-		<globals>
-			<![CDATA[
-			const complex g=10;
-			const complex gbc=.001;
-			const complex Split = .1;
-			const double tset=5;
-			const double alpha = 0.001;
-
-			complex Gab, Gca, Gcb, GCB;
-			complex Ep,Ed,Epc,Edc;
-			complex noise;
-			double delta_2photon, delta_d;
-			complex rba,rac,rbc;
-			complex rBA,rAC,rBC;
-			complex drive_field0=1, probe_field0=1;
-			]]>
-		</globals>
-	</features>
-
-	<geometry>
-		<propagation_dimension> t </propagation_dimension>
-		<transverse_dimensions>
-			<dimension name="delta_2photon" lattice="256"  domain="(-2, 2)" />
-		</transverse_dimensions>
-	</geometry>
-
-	<driver name="multi-path" paths="16" />
-
-	<noise_vector name="drivingNoise" kind="wiener" type="real" method="dsfmt" >
-    		<components>Eta</components>
-  	</noise_vector>
-
-	<vector name="density_matrix" type="complex" dimensions="delta_2photon">
-		<components>raa rbb rcc rab rca rcb rAB rCA rCB</components>
-		<initialisation>
-			<![CDATA[
-			raa = 0;
-			rbb = 1;
-			rcc = 0;
-			rab = 0;
-			rca = 0;
-			rcb= 0;
-			rAB = 0;
-			rCA = 0;
-			rCB= 0;
-			]]>
-		</initialisation>
-	</vector>
-
-	<sequence>
-		<integrate algorithm="ARK45" interval="13.0" tolerance="1e-7">
-			<samples>100</samples>
-			<operators>
-				<integration_vectors>density_matrix</integration_vectors>
-				<dependencies>drivingNoise</dependencies>
-				<![CDATA[
-				delta_d=0;
-
-				noise = Eta*alpha;
-				Ed=drive_field0;
-				Ep=probe_field0;
-
-				Epc = conj(Ep);
-				Edc = conj(Ed);
-
-				Gab=g+i*(delta_d+delta_2photon+1*noise);
-				Gca=g-i*(delta_d);
-				Gcb=gbc+i*(Split + delta_2photon+0*noise);
-				GCB=gbc+i*(-Split + delta_2photon+0*noise);
-
-
-				rba=conj(rab);
-				rac=conj(rca);
-				rbc=conj(rcb);
-				rBA=conj(rAB);
-				rAC=conj(rCA);
-				rBC=conj(rCB);
-
-				draa_dt = -i*Epc*rab+i*Ep*rba-i*Edc*rac+i*Ed*rca-2*g*raa
-				          -i*Edc*rAB+i*Ed*rBA-i*Epc*rAC+i*Ep*rCA;
-				drbb_dt =  i*Epc*rab-i*Ep*rba+g*raa-gbc*rbb+gbc*rcc
-				          +i*Edc*rAB-i*Ed*rBA;
-				drcc_dt =  i*Edc*rac-i*Ed*rca+g*raa-gbc*rcc+gbc*rbb
-				          +i*Epc*rAC-i*Ep*rCA;
-
-				drab_dt = -Gab*rab+i*Ep*(rbb-raa)+i*Ed*rcb;
-				drca_dt = -Gca*rca+i*Edc*(raa-rcc)-i*Epc*rcb;
-				drcb_dt = -Gcb*rcb-i*Ep*rca+i*Edc*rab;
-
-				drAB_dt = -Gab*rAB+i*Ed*(rbb-raa)+i*Ep*rCB;
-				drCA_dt = -Gca*rCA+i*Epc*(raa-rcc)-i*Edc*rCB;
-				drCB_dt = -GCB*rCB-i*Ed*rCA+i*Epc*rAB;
-					]]>
-				</operators>
-			</integrate>
-		</sequence>
-
-
-
-
-		<!-- The output to generate -->
-		<!--<output format="ascii" filename="delta_2photon_noise_alpha_1.xsil">-->
-		<output>
-			<group>
-				<sampling basis="delta_2photon" initial_sample="yes">
-					<dependencies>density_matrix </dependencies>
-					<moments>eit_signal mor_signal rab_rlOut rab_imOut rca_rlOut rca_imOut raaOut rbbOut rccOut noiseOut PDl PDr</moments>
-					<![CDATA[
-					rab_rlOut = rab.Re();
-					rab_imOut = rab.Im();
-					rca_rlOut = rca.Re();
-					rca_imOut = rca.Im();
-					raaOut = raa.Re();
-					rbbOut = rbb.Re();
-					rccOut = rcc.Re();
-					noiseOut = noise.Re();
-					PDl = norm( 1/sqrt(2)*(rab - rAB) + i/sqrt(2)*(rca + rCA) );
-					PDr = norm( 1/sqrt(2)*(rab - rAB) - i/sqrt(2)*(rca + rCA) );
-					eit_signal = PDl + PDr;
-					mor_signal = PDl - PDr;
-					]]>
-				</sampling>
-			</group>
-		</output>
-
-	</simulation>
-	
-<!-- 
-vim: ts=2 sw=2 foldmethod=indent: 
--->
-
diff --git a/pp.m b/pp.m
deleted file mode 100644
index f59f19c..0000000
--- a/pp.m
+++ /dev/null
@@ -1,21 +0,0 @@
-delta_2photon_noise
-
-figure(1)
-plot(delta_2photon_1,  mean_mor_signal_1(end,:) )
-hold all
-plot(delta_2photon_1,  mean_eit_signal_1(end,:) )
-
-legend( {'mor', 'eit'} )
-
-figure(2)
-plot(delta_2photon_1,  stderr_mor_signal_1(end,:) )
-hold all
-plot(delta_2photon_1,  stderr_eit_signal_1(end,:) )
-
-legend( {'mor', 'eit'} )
-
-figure(3)
-plot(delta_2photon_1, stderr_eit_signal_1(end,:)./stderr_mor_signal_1(end,:) )
-hold all
-
-legend( {'noise eit/mor'} )
diff --git a/simple_thin_layer_model/Makefile b/simple_thin_layer_model/Makefile
new file mode 100644
index 0000000..83877ee
--- /dev/null
+++ b/simple_thin_layer_model/Makefile
@@ -0,0 +1,37 @@
+###  -*- make -*-
+### This file is part of the Debian xmds package
+### Copyright (C) 2006 Rafael Laboissiere
+### This file is relased under the GNU General Public License
+### NO WARRANTIES!
+
+### This makefile can be used to build and run the XMDS examples
+
+XMDS_FILES = $(shell ls *.xmds)
+RUN_FILES = $(patsubst %.xmds,%.run,$(XMDS_FILES))
+CC_FILES = $(patsubst %.xmds,%.cc,$(XMDS_FILES))
+XSIL_FILES = delta_2photon_noise.xsil
+M_FILES = $(patsubst %.xsil,%.m,$(XSIL_FILES))
+
+XMDS = xmds2
+XSIL2GRAPHICS = xsil2graphics2
+
+all: $(M_FILES) 
+
+%.run: %.xmds
+	$(XMDS) $<
+	mv $(patsubst %.xmds,%,$<) $@
+
+$(XSIL_FILES): %.xsil: $(RUN_FILES)
+	./$<
+
+$(M_FILES): %.m : %.xsil
+	$(XSIL2GRAPHICS) $<
+
+plot: $(M_FILES)
+	octave pp.m
+
+clean:
+	rm -f $(CC_FILES) $(RUN_FILES) $(M_FILES) $(XSIL_FILES) *.wisdom.fftw3 *.dat octave-core *.wisdom *.pdf
+
+.PRECIOUS: %.run %.xsil %.m
+.PHONY: all clean
diff --git a/simple_thin_layer_model/delta_2photon_noise.xmds b/simple_thin_layer_model/delta_2photon_noise.xmds
new file mode 100644
index 0000000..2cb3a52
--- /dev/null
+++ b/simple_thin_layer_model/delta_2photon_noise.xmds
@@ -0,0 +1,148 @@
+<?xml version="1.0"?>
+<simulation xmds-version="2">
+
+	<name>delta_2photon_noise</name>
+
+	<author>E. Mikhailov, M. Guidry</author>
+	<description>
+		Solving 3 level atom in lambda field configuration,
+		no field propagation included. Noise on delta_2photon.
+	</description>
+
+	<features>
+		<benchmark />
+		<bing />
+		<fftw plan="patient" />
+		<openmp />
+		<auto_vectorise />
+		<globals>
+			<![CDATA[
+			const complex g=10;
+			const complex gbc=.001;
+			const complex Split = .1;
+			const double tset=5;
+			const double alpha = 0.001;
+
+			complex Gab, Gca, Gcb, GCB;
+			complex Ep,Ed,Epc,Edc;
+			complex noise;
+			double delta_2photon, delta_d;
+			complex rba,rac,rbc;
+			complex rBA,rAC,rBC;
+			complex drive_field0=1, probe_field0=1;
+			]]>
+		</globals>
+	</features>
+
+	<geometry>
+		<propagation_dimension> t </propagation_dimension>
+		<transverse_dimensions>
+			<dimension name="delta_2photon" lattice="256"  domain="(-2, 2)" />
+		</transverse_dimensions>
+	</geometry>
+
+	<driver name="multi-path" paths="16" />
+
+	<noise_vector name="drivingNoise" kind="wiener" type="real" method="dsfmt" >
+    		<components>Eta</components>
+  	</noise_vector>
+
+	<vector name="density_matrix" type="complex" dimensions="delta_2photon">
+		<components>raa rbb rcc rab rca rcb rAB rCA rCB</components>
+		<initialisation>
+			<![CDATA[
+			raa = 0;
+			rbb = 1;
+			rcc = 0;
+			rab = 0;
+			rca = 0;
+			rcb= 0;
+			rAB = 0;
+			rCA = 0;
+			rCB= 0;
+			]]>
+		</initialisation>
+	</vector>
+
+	<sequence>
+		<integrate algorithm="ARK45" interval="13.0" tolerance="1e-7">
+			<samples>100</samples>
+			<operators>
+				<integration_vectors>density_matrix</integration_vectors>
+				<dependencies>drivingNoise</dependencies>
+				<![CDATA[
+				delta_d=0;
+
+				noise = Eta*alpha;
+				Ed=drive_field0;
+				Ep=probe_field0;
+
+				Epc = conj(Ep);
+				Edc = conj(Ed);
+
+				Gab=g+i*(delta_d+delta_2photon+1*noise);
+				Gca=g-i*(delta_d);
+				Gcb=gbc+i*(Split + delta_2photon+0*noise);
+				GCB=gbc+i*(-Split + delta_2photon+0*noise);
+
+
+				rba=conj(rab);
+				rac=conj(rca);
+				rbc=conj(rcb);
+				rBA=conj(rAB);
+				rAC=conj(rCA);
+				rBC=conj(rCB);
+
+				draa_dt = -i*Epc*rab+i*Ep*rba-i*Edc*rac+i*Ed*rca-2*g*raa
+				          -i*Edc*rAB+i*Ed*rBA-i*Epc*rAC+i*Ep*rCA;
+				drbb_dt =  i*Epc*rab-i*Ep*rba+g*raa-gbc*rbb+gbc*rcc
+				          +i*Edc*rAB-i*Ed*rBA;
+				drcc_dt =  i*Edc*rac-i*Ed*rca+g*raa-gbc*rcc+gbc*rbb
+				          +i*Epc*rAC-i*Ep*rCA;
+
+				drab_dt = -Gab*rab+i*Ep*(rbb-raa)+i*Ed*rcb;
+				drca_dt = -Gca*rca+i*Edc*(raa-rcc)-i*Epc*rcb;
+				drcb_dt = -Gcb*rcb-i*Ep*rca+i*Edc*rab;
+
+				drAB_dt = -Gab*rAB+i*Ed*(rbb-raa)+i*Ep*rCB;
+				drCA_dt = -Gca*rCA+i*Epc*(raa-rcc)-i*Edc*rCB;
+				drCB_dt = -GCB*rCB-i*Ed*rCA+i*Epc*rAB;
+					]]>
+				</operators>
+			</integrate>
+		</sequence>
+
+
+
+
+		<!-- The output to generate -->
+		<!--<output format="ascii" filename="delta_2photon_noise_alpha_1.xsil">-->
+		<output>
+			<group>
+				<sampling basis="delta_2photon" initial_sample="yes">
+					<dependencies>density_matrix </dependencies>
+					<moments>eit_signal mor_signal rab_rlOut rab_imOut rca_rlOut rca_imOut raaOut rbbOut rccOut noiseOut PDl PDr</moments>
+					<![CDATA[
+					rab_rlOut = rab.Re();
+					rab_imOut = rab.Im();
+					rca_rlOut = rca.Re();
+					rca_imOut = rca.Im();
+					raaOut = raa.Re();
+					rbbOut = rbb.Re();
+					rccOut = rcc.Re();
+					noiseOut = noise.Re();
+					PDl = norm( 1/sqrt(2)*(rab - rAB) + i/sqrt(2)*(rca + rCA) );
+					PDr = norm( 1/sqrt(2)*(rab - rAB) - i/sqrt(2)*(rca + rCA) );
+					eit_signal = PDl + PDr;
+					mor_signal = PDl - PDr;
+					]]>
+				</sampling>
+			</group>
+		</output>
+
+	</simulation>
+	
+<!-- 
+vim: ts=2 sw=2 foldmethod=indent: 
+-->
+
diff --git a/simple_thin_layer_model/pp.m b/simple_thin_layer_model/pp.m
new file mode 100644
index 0000000..f59f19c
--- /dev/null
+++ b/simple_thin_layer_model/pp.m
@@ -0,0 +1,21 @@
+delta_2photon_noise
+
+figure(1)
+plot(delta_2photon_1,  mean_mor_signal_1(end,:) )
+hold all
+plot(delta_2photon_1,  mean_eit_signal_1(end,:) )
+
+legend( {'mor', 'eit'} )
+
+figure(2)
+plot(delta_2photon_1,  stderr_mor_signal_1(end,:) )
+hold all
+plot(delta_2photon_1,  stderr_eit_signal_1(end,:) )
+
+legend( {'mor', 'eit'} )
+
+figure(3)
+plot(delta_2photon_1, stderr_eit_signal_1(end,:)./stderr_mor_signal_1(end,:) )
+hold all
+
+legend( {'noise eit/mor'} )
-- 
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