From 3a4ba8676f1c265e4631c065efa5c67476886326 Mon Sep 17 00:00:00 2001
From: Eugeniy Mikhailov <evgmik@gmail.com>
Date: Wed, 28 Nov 2012 22:58:07 -0500
Subject: now we use proper xml includes in xmds file for generated code

---
 xmds2/realistic_Rb/realistic_Rb.xmds | 109 +++++------------------------------
 1 file changed, 15 insertions(+), 94 deletions(-)

(limited to 'xmds2/realistic_Rb/realistic_Rb.xmds')

diff --git a/xmds2/realistic_Rb/realistic_Rb.xmds b/xmds2/realistic_Rb/realistic_Rb.xmds
index 94b398c..7744dd8 100644
--- a/xmds2/realistic_Rb/realistic_Rb.xmds
+++ b/xmds2/realistic_Rb/realistic_Rb.xmds
@@ -1,4 +1,11 @@
 <?xml version="1.0"?>
+<!--Below text defines necessary included files and references to them-->
+<!DOCTYPE simulation [
+<!ENTITY RbAtomConstansFile SYSTEM "RbAtomConstans.cdata" >
+<!ENTITY RbChosenRhoFile SYSTEM "RbChosenRho.txt" >
+<!ENTITY RbInitsFile SYSTEM "RbInits.cdata" >
+<!ENTITY RbEquationsFile SYSTEM "RbEquations.cdata" >
+]>
 <simulation xmds-version="2">
 	<testing>
 		<arguments> --Ndens=1e15 --Lcell=10.0e-2  --Temperature=1e-3  --Pwidth=0.4e-6  --delta1=0 --delta2=0 --delta3=0  --E1o=0 --E2o=1e2 --E3o=0 --E4o=0</arguments>
@@ -49,28 +56,12 @@
 
 	<features>
 		<globals>
+			<!-- read from Mathematica generated RbAtomConstans.cdata-->
+			&RbAtomConstansFile;
 			<![CDATA[
 				// Some numerical constants
 				const double pi = M_PI; 
 
-				// atom related constants
-				//read from Mathematica generated Constants.txt
-//---------------- Constants.txt starts ------------------
-const double ha0 = 2.1471788680034824e10;
-const double ha1 = 2.558764384495815e9;
-const double g1 = 3.612847284945266e7;
-const double ha2 = 5.323020344462938e8;
-const double hb2 = 7.85178251911697e7;
-const double g2 = 3.8117309832741246e7;
-const double lambda1 = 7.949788511562656e-7;
-const double lambda2 = 7.802412096860509e-7;
-const double eta1 = 5.450949336831401e-6;
-const double eta2 = 5.5397657647874e-6;
-const double rt6 = 2.449489742783178;
-const double rt3 = 1.7320508075688772;
-const double rt2 = 1.4142135623730951;
-//---------------- Constants.txt ends   ------------------
-
 				const double c=3.e8;
 				const double k_boltzmann= 1.3806505e-23; // Boltzmann knostant in [J/K]
 				const double lambda=794.7e-9; //wavelength in m
@@ -228,9 +219,7 @@ const double rt2 = 1.4142135623730951;
 	<vector name="density_matrix" type="complex" initial_space="t">
 		<components>
 			<!-- read from Mathematica generated RbChosenRho.txt -->
-<!-- ############### RbChosenRho.txt starts ################ -->
-r0101 r0113 r0202 r0214 r0303 r0309 r0315 r0404 r0410 r0416 r0505 r0511 r0602 r0606 r0614 r0703 r0707 r0709 r0715 r0804 r0808 r0810 r0816 r0909 r0915 r1010 r1016 r1111 r1313 r1414 r1515 r1616 
-<!-- ############### RbChosenRho.txt ends  ################# -->
+			&RbChosenRhoFile;
 		</components>
 		<initialisation>
 			<!--This sets boundary condition at all times and left border of z (i.e. z=0)-->
@@ -245,42 +234,9 @@ r0101 r0113 r0202 r0214 r0303 r0309 r0315 r0404 r0410 r0416 r0505 r0511 r0602 r0
 			//       and express other level, let's say r44
 			//       through population normalization
 
-			//read from Mathematica generated RbInits.txt
-//---------------- RbInits.txt starts ------------------
-r0101 = 0.125;
-r0113 = 0;
-r0202 = 0.125;
-r0214 = 0;
-r0303 = 0.125;
-r0309 = 0;
-r0315 = 0;
-r0404 = 0.125;
-r0410 = 0;
-r0416 = 0;
-r0505 = 0.125;
-r0511 = 0;
-r0602 = 0;
-r0606 = 0.125;
-r0614 = 0;
-r0703 = 0;
-r0707 = 0.125;
-r0709 = 0;
-r0715 = 0;
-r0804 = 0;
-r0808 = 0.125;
-r0810 = 0;
-r0816 = 0;
-r0909 = 0;
-r0915 = 0;
-r1010 = 0;
-r1016 = 0;
-r1111 = 0;
-r1313 = 0;
-r1414 = 0;
-r1515 = 0;
-r1616 = 0;
-//---------------- RbInits.txt ends  ------------------
 			]]>
+			<!--read from Mathematica generated RbInits.cdata-->
+			&RbInitsFile;
 		</initialisation>
 	</vector>
 
@@ -317,44 +273,9 @@ r1616 = 0;
             ]]>
 						-->
           </boundary_condition>
-					<![CDATA[
-						// Equations of motions according to Simon's mathematica code
-						//read from Mathematica generated RbEquations.txt
-//---------------- RbEquations.txt starts ------------------
-dr0101_dt = gt/8. - gt*r0101 + (g1*r0909)/2. + (g2*r1313)/6. - i*((r0113*E4a)/(4.*rt6) - (conj(r0113)*conj(E4a))/(4.*rt6));
-dr0113_dt = (-(gt*r0113) - (gt + g2)*r0113)/2. - i*(WL*r0113 - ((2*WL)/3. - delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r0113 + (r0101*conj(E4a))/(4.*rt6) - (r1313*conj(E4a))/(4.*rt6));
-dr0202_dt = gt/8. - gt*r0202 + (g1*r0909)/4. + (g1*r1010)/4. + (g2*r1313)/12. + (g2*r1414)/4. - i*((r0214*E4a)/8. - (conj(r0214)*conj(E4a))/8.);
-dr0214_dt = (-(gt*r0214) - (gt + g2)*r0214)/2. - i*((WL*r0214)/2. - (-delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r0214 - (conj(r0602)*conj(E3a))/(8.*rt3) + (r0202*conj(E4a))/8. - (r1414*conj(E4a))/8.);
-dr0303_dt = gt/8. - gt*r0303 + (g1*r0909)/12. + (g1*r1010)/3. + (g1*r1111)/12. + (g2*r1313)/4. + (g2*r1515)/4. - i*((r0309*E1a)/(4.*rt6) + (r0315*E4a)/8. - (conj(r0309)*conj(E1a))/(4.*rt6) - (conj(r0315)*conj(E4a))/8.);
-dr0309_dt = (-(gt*r0309) - (gt + g1)*r0309)/2. - i*(-((-WL/6. - delta1 - v*Kvec1)*r0309) + (r0303*conj(E1a))/(4.*rt6) - (r0909*conj(E1a))/(4.*rt6) - (conj(r0703)*conj(E2a))/(4.*rt6) - (conj(r0915)*conj(E4a))/8.);
-dr0315_dt = (-(gt*r0315) - (gt + g2)*r0315)/2. - i*(-(((-2*WL)/3. - delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r0315) - (r0915*conj(E1a))/(4.*rt6) - (conj(r0703)*conj(E3a))/8. + (r0303*conj(E4a))/8. - (r1515*conj(E4a))/8.);
-dr0404_dt = gt/8. - gt*r0404 + (g1*r1010)/4. + (g1*r1111)/4. + (g2*r1414)/4. + (g2*r1515)/12. + (g2*r1616)/6. - i*((r0410*E1a)/(4.*rt2) + (r0416*E4a)/(4.*rt6) - (conj(r0410)*conj(E1a))/(4.*rt2) - (conj(r0416)*conj(E4a))/(4.*rt6));
-dr0410_dt = (-(gt*r0410) - (gt + g1)*r0410)/2. - i*(-(WL*r0410)/2. + (delta1 + v*Kvec1)*r0410 + (r0404*conj(E1a))/(4.*rt2) - (r1010*conj(E1a))/(4.*rt2) - (conj(r0804)*conj(E2a))/(4.*rt6) - (conj(r1016)*conj(E4a))/(4.*rt6));
-dr0416_dt = (-(gt*r0416) - (gt + g2)*r0416)/2. - i*(-(WL*r0416)/2. - ((-4*WL)/3. - delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r0416 - (r1016*conj(E1a))/(4.*rt2) - (conj(r0804)*conj(E3a))/(4.*rt2) + (r0404*conj(E4a))/(4.*rt6) - (r1616*conj(E4a))/(4.*rt6));
-dr0505_dt = gt/8. - gt*r0505 + (g1*r1111)/2. + (g2*r1515)/6. + (g2*r1616)/3. - i*((r0511*E1a)/4. - (conj(r0511)*conj(E1a))/4.);
-dr0511_dt = (-(gt*r0511) - (gt + g1)*r0511)/2. - i*(-(WL*r0511) - (WL/6. - delta1 - v*Kvec1)*r0511 + (r0505*conj(E1a))/4. - (r1111*conj(E1a))/4.);
-dr0602_dt = -(gt*r0602) - i*(-(WL*r0602)/2. + (-WL/2. - delta1 + delta2 - v*Kvec1 + v*Kvec2)*r0602 + (r0614*E4a)/8. + (conj(r0214)*conj(E3a))/(8.*rt3));
-dr0606_dt = gt/8. - gt*r0606 + (g1*r0909)/12. + (g1*r1010)/12. + (g2*r1313)/4. + (g2*r1414)/12. - i*(-(r0614*E3a)/(8.*rt3) + (conj(r0614)*conj(E3a))/(8.*rt3));
-dr0614_dt = (-(gt*r0614) - (gt + g2)*r0614)/2. - i*((-WL/2. - delta1 + delta2 - v*Kvec1 + v*Kvec2)*r0614 - (-delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r0614 - (r0606*conj(E3a))/(8.*rt3) + (r1414*conj(E3a))/(8.*rt3) + (r0602*conj(E4a))/8.);
-dr0703_dt = -(gt*r0703) - i*((-delta1 + delta2 - v*Kvec1 + v*Kvec2)*r0703 + (r0709*E1a)/(4.*rt6) + (r0715*E4a)/8. + (conj(r0309)*conj(E2a))/(4.*rt6) + (conj(r0315)*conj(E3a))/8.);
-dr0707_dt = gt/8. - gt*r0707 + (g1*r0909)/12. + (g1*r1111)/12. + (g2*r1313)/4. + (g2*r1414)/3. + (g2*r1515)/4. - i*(-(r0709*E2a)/(4.*rt6) - (r0715*E3a)/8. + (conj(r0709)*conj(E2a))/(4.*rt6) + (conj(r0715)*conj(E3a))/8.);
-dr0709_dt = (-(gt*r0709) - (gt + g1)*r0709)/2. - i*(-((-WL/6. - delta1 - v*Kvec1)*r0709) + (-delta1 + delta2 - v*Kvec1 + v*Kvec2)*r0709 + (r0703*conj(E1a))/(4.*rt6) - (r0707*conj(E2a))/(4.*rt6) + (r0909*conj(E2a))/(4.*rt6) + (conj(r0915)*conj(E3a))/8.);
-dr0715_dt = (-(gt*r0715) - (gt + g2)*r0715)/2. - i*((-delta1 + delta2 - v*Kvec1 + v*Kvec2)*r0715 - ((-2*WL)/3. - delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r0715 + (r0915*conj(E2a))/(4.*rt6) - (r0707*conj(E3a))/8. + (r1515*conj(E3a))/8. + (r0703*conj(E4a))/8.);
-dr0804_dt = -(gt*r0804) - i*((WL*r0804)/2. + (WL/2. - delta1 + delta2 - v*Kvec1 + v*Kvec2)*r0804 + (r0810*E1a)/(4.*rt2) + (r0816*E4a)/(4.*rt6) + (conj(r0410)*conj(E2a))/(4.*rt6) + (conj(r0416)*conj(E3a))/(4.*rt2));
-dr0808_dt = gt/8. - gt*r0808 + (g1*r1010)/12. + (g1*r1111)/12. + (g2*r1414)/12. + (g2*r1515)/4. + (g2*r1616)/2. - i*(-(r0810*E2a)/(4.*rt6) - (r0816*E3a)/(4.*rt2) + (conj(r0810)*conj(E2a))/(4.*rt6) + (conj(r0816)*conj(E3a))/(4.*rt2));
-dr0810_dt = (-(gt*r0810) - (gt + g1)*r0810)/2. - i*((delta1 + v*Kvec1)*r0810 + (WL/2. - delta1 + delta2 - v*Kvec1 + v*Kvec2)*r0810 + (r0804*conj(E1a))/(4.*rt2) - (r0808*conj(E2a))/(4.*rt6) + (r1010*conj(E2a))/(4.*rt6) + (conj(r1016)*conj(E3a))/(4.*rt2));
-dr0816_dt = (-(gt*r0816) - (gt + g2)*r0816)/2. - i*((WL/2. - delta1 + delta2 - v*Kvec1 + v*Kvec2)*r0816 - ((-4*WL)/3. - delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r0816 + (r1016*conj(E2a))/(4.*rt6) - (r0808*conj(E3a))/(4.*rt2) + (r1616*conj(E3a))/(4.*rt2) + (r0804*conj(E4a))/(4.*rt6));
-dr0909_dt = -((gt + g1)*r0909) - i*(-(r0309*E1a)/(4.*rt6) + (r0709*E2a)/(4.*rt6) + (conj(r0309)*conj(E1a))/(4.*rt6) - (conj(r0709)*conj(E2a))/(4.*rt6));
-dr0915_dt = (-((gt + g1)*r0915) - (gt + g2)*r0915)/2. - i*((-WL/6. - delta1 - v*Kvec1)*r0915 - ((-2*WL)/3. - delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r0915 - (r0315*E1a)/(4.*rt6) + (r0715*E2a)/(4.*rt6) - (conj(r0709)*conj(E3a))/8. + (conj(r0309)*conj(E4a))/8.);
-dr1010_dt = -((gt + g1)*r1010) - i*(-(r0410*E1a)/(4.*rt2) + (r0810*E2a)/(4.*rt6) + (conj(r0410)*conj(E1a))/(4.*rt2) - (conj(r0810)*conj(E2a))/(4.*rt6));
-dr1016_dt = (-((gt + g1)*r1016) - (gt + g2)*r1016)/2. - i*(-((delta1 + v*Kvec1)*r1016) - ((-4*WL)/3. - delta1 + delta2 - delta3 - v*Kvec1 + v*Kvec2 - v*Kvec3)*r1016 - (r0416*E1a)/(4.*rt2) + (r0816*E2a)/(4.*rt6) - (conj(r0810)*conj(E3a))/(4.*rt2) + (conj(r0410)*conj(E4a))/(4.*rt6));
-dr1111_dt = -((gt + g1)*r1111) - i*(-(r0511*E1a)/4. + (conj(r0511)*conj(E1a))/4.);
-dr1313_dt = -((gt + g2)*r1313) - i*(-(r0113*E4a)/(4.*rt6) + (conj(r0113)*conj(E4a))/(4.*rt6));
-dr1414_dt = -((gt + g2)*r1414) - i*((r0614*E3a)/(8.*rt3) - (r0214*E4a)/8. - (conj(r0614)*conj(E3a))/(8.*rt3) + (conj(r0214)*conj(E4a))/8.);
-dr1515_dt = -((gt + g2)*r1515) - i*((r0715*E3a)/8. - (r0315*E4a)/8. - (conj(r0715)*conj(E3a))/8. + (conj(r0315)*conj(E4a))/8.);
-dr1616_dt = -((gt + g2)*r1616) - i*((r0816*E3a)/(4.*rt2) - (r0416*E4a)/(4.*rt6) - (conj(r0816)*conj(E3a))/(4.*rt2) + (conj(r0416)*conj(E4a))/(4.*rt6));
-//---------------- RbEquations.txt ends  ------------------
-					]]>
+						<!-- Equations of motions according to Simon's mathematica code-->
+						<!-- read from Mathematica generated RbEquations.cdata-->
+						&RbEquationsFile;
         </operator>
 				<!--
 							 According to xmds2 docs operator kind="ip" should be faster
-- 
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