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/RbAtomConstans.cdata |  18 ++++++
 xmds2/realistic_Rb/RbEquations.cdata    |  37 +++++++++++
 xmds2/realistic_Rb/RbInits.cdata        |  37 +++++++++++
 xmds2/realistic_Rb/realistic_Rb.xmds    | 109 +++++---------------------------
 4 files changed, 107 insertions(+), 94 deletions(-)
 create mode 100644 xmds2/realistic_Rb/RbAtomConstans.cdata
 create mode 100644 xmds2/realistic_Rb/RbEquations.cdata
 create mode 100644 xmds2/realistic_Rb/RbInits.cdata

(limited to 'xmds2/realistic_Rb')

diff --git a/xmds2/realistic_Rb/RbAtomConstans.cdata b/xmds2/realistic_Rb/RbAtomConstans.cdata
new file mode 100644
index 0000000..040d3c9
--- /dev/null
+++ b/xmds2/realistic_Rb/RbAtomConstans.cdata
@@ -0,0 +1,18 @@
+<![CDATA[
+//---------------- RbAtomConstans.cdata 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;
+//---------------- RbAtomConstans.cdata ends   ------------------
+]]>
+
diff --git a/xmds2/realistic_Rb/RbEquations.cdata b/xmds2/realistic_Rb/RbEquations.cdata
new file mode 100644
index 0000000..1c9f18a
--- /dev/null
+++ b/xmds2/realistic_Rb/RbEquations.cdata
@@ -0,0 +1,37 @@
+<![CDATA[
+//---------------- RbEquations.cdata 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.cdata ends  ------------------
+]]>
+
diff --git a/xmds2/realistic_Rb/RbInits.cdata b/xmds2/realistic_Rb/RbInits.cdata
new file mode 100644
index 0000000..77a5cf7
--- /dev/null
+++ b/xmds2/realistic_Rb/RbInits.cdata
@@ -0,0 +1,37 @@
+<![CDATA[
+//---------------- RbInits.cdata 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.cdata ends  ------------------
+]]>
+
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
-- 
cgit v1.2.3


From 3d3c605845be51eaf7a8d1085567797d71dc8d7e Mon Sep 17 00:00:00 2001
From: Eugeniy Mikhailov <evgmik@gmail.com>
Date: Wed, 28 Nov 2012 22:58:50 -0500
Subject: Makefile test properly works with included to xmds files

---
 xmds2/realistic_Rb/Makefile | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

(limited to 'xmds2/realistic_Rb')

diff --git a/xmds2/realistic_Rb/Makefile b/xmds2/realistic_Rb/Makefile
index ae7d4a9..583bc6a 100644
--- a/xmds2/realistic_Rb/Makefile
+++ b/xmds2/realistic_Rb/Makefile
@@ -1,9 +1,11 @@
 ###  -*- 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
+### This file is released under the GNU General Public License
 ### NO WARRANTIES!
 
+INSTALL = install --mode=664 -D 
+
 ### This makefile can be used to build and run the XMDS examples
 
 XMDS_FILES = $(shell ls *.xmds)
@@ -12,6 +14,12 @@ CC_FILES = $(patsubst %.xmds,%.cc,$(XMDS_FILES))
 XSIL_FILES = $(patsubst %.xmds,%.xsil,$(XMDS_FILES))
 M_FILES = $(patsubst %.xmds,%.m,$(XMDS_FILES))
 
+test_dir = tests
+test_result_dir = $(test_dir)/testsuite_results
+XMDS_INCLUDES_misc  = RbChosenRho.txt RbInits.cdata RbEquations.cdata RbAtomConstans.cdata
+XMDS_INCLUDES_xmds_in_target_dir = $(XMDS_INCLUDES_misc:%=$(test_dir)/%)
+XMDS_INCLUDES_cdata_in_target_dir = $(XMDS_INCLUDES_misc:%=$(test_result_dir)/%)
+
 XMDS = xmds2
 XSIL2GRAPHICS = xsil2graphics
 
@@ -46,8 +54,14 @@ $(png_targets): %.png : %.pdf
 
 pdf: $(pdf_targets) 
 
-test:
-	cp $(XMDS_FILES) tests/testsuite/
+$(XMDS_INCLUDES_cdata_in_target_dir): $(test_result_dir)/% : %
+	$(INSTALL) $< $@
+
+$(XMDS_INCLUDES_xmds_in_target_dir): $(test_dir)/% : %
+	$(INSTALL) $< $@
+
+test: $(XMDS_INCLUDES_cdata_in_target_dir) $(XMDS_INCLUDES_xmds_in_target_dir)
+	$(INSTALL) $(XMDS_FILES) tests/testsuite/
 	cd tests; ./run_tests.py
 
 test_from_scratch:
-- 
cgit v1.2.3


From f2891fa6f6ea67b9fd6a3fbec4cc6344debfba64 Mon Sep 17 00:00:00 2001
From: Eugeniy Mikhailov <evgmik@gmail.com>
Date: Wed, 28 Nov 2012 23:28:39 -0500
Subject: typo in makefile

---
 xmds2/realistic_Rb/Makefile            |  3 ++-
 xmds2/realistic_Rb_and_fields/Makefile | 25 ++++++++++++++++++-------
 2 files changed, 20 insertions(+), 8 deletions(-)

(limited to 'xmds2/realistic_Rb')

diff --git a/xmds2/realistic_Rb/Makefile b/xmds2/realistic_Rb/Makefile
index 583bc6a..1f5c4fd 100644
--- a/xmds2/realistic_Rb/Makefile
+++ b/xmds2/realistic_Rb/Makefile
@@ -16,7 +16,8 @@ M_FILES = $(patsubst %.xmds,%.m,$(XMDS_FILES))
 
 test_dir = tests
 test_result_dir = $(test_dir)/testsuite_results
-XMDS_INCLUDES_misc  = RbChosenRho.txt RbInits.cdata RbEquations.cdata RbAtomConstans.cdata
+XMDS_INCLUDES_misc  = RbChosenRho.txt RbInits.cdata RbEquations.cdata \
+		      RbAtomConstants.cdata RbPropEquations.cdata
 XMDS_INCLUDES_xmds_in_target_dir = $(XMDS_INCLUDES_misc:%=$(test_dir)/%)
 XMDS_INCLUDES_cdata_in_target_dir = $(XMDS_INCLUDES_misc:%=$(test_result_dir)/%)
 
diff --git a/xmds2/realistic_Rb_and_fields/Makefile b/xmds2/realistic_Rb_and_fields/Makefile
index d485891..1f5c4fd 100644
--- a/xmds2/realistic_Rb_and_fields/Makefile
+++ b/xmds2/realistic_Rb_and_fields/Makefile
@@ -1,9 +1,11 @@
 ###  -*- 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
+### This file is released under the GNU General Public License
 ### NO WARRANTIES!
 
+INSTALL = install --mode=664 -D 
+
 ### This makefile can be used to build and run the XMDS examples
 
 XMDS_FILES = $(shell ls *.xmds)
@@ -12,14 +14,19 @@ CC_FILES = $(patsubst %.xmds,%.cc,$(XMDS_FILES))
 XSIL_FILES = $(patsubst %.xmds,%.xsil,$(XMDS_FILES))
 M_FILES = $(patsubst %.xmds,%.m,$(XMDS_FILES))
 
-XMDS_INCLUDES = RbAtomConstants.h RbInits.h
+test_dir = tests
+test_result_dir = $(test_dir)/testsuite_results
+XMDS_INCLUDES_misc  = RbChosenRho.txt RbInits.cdata RbEquations.cdata \
+		      RbAtomConstants.cdata RbPropEquations.cdata
+XMDS_INCLUDES_xmds_in_target_dir = $(XMDS_INCLUDES_misc:%=$(test_dir)/%)
+XMDS_INCLUDES_cdata_in_target_dir = $(XMDS_INCLUDES_misc:%=$(test_result_dir)/%)
 
 XMDS = xmds2
 XSIL2GRAPHICS = xsil2graphics
 
 all: $(RUN_FILES) 
 
-%.run: %.xmds $(XMDS_INCLUDES)
+%.run: %.xmds
 	$(XMDS) $<
 	mv $(patsubst %.xmds,%,$<) $@
 
@@ -48,10 +55,14 @@ $(png_targets): %.png : %.pdf
 
 pdf: $(pdf_targets) 
 
-test:
-	cp $(XMDS_FILES) tests/testsuite/
-	mkdir -p tests/testsuite_results
-	cp $(XMDS_INCLUDES) tests/testsuite_results/
+$(XMDS_INCLUDES_cdata_in_target_dir): $(test_result_dir)/% : %
+	$(INSTALL) $< $@
+
+$(XMDS_INCLUDES_xmds_in_target_dir): $(test_dir)/% : %
+	$(INSTALL) $< $@
+
+test: $(XMDS_INCLUDES_cdata_in_target_dir) $(XMDS_INCLUDES_xmds_in_target_dir)
+	$(INSTALL) $(XMDS_FILES) tests/testsuite/
 	cd tests; ./run_tests.py
 
 test_from_scratch:
-- 
cgit v1.2.3


From aeeeb3a41ba3df163dede45c37efe74c6ce71ca3 Mon Sep 17 00:00:00 2001
From: Eugeniy Mikhailov <evgmik@gmail.com>
Date: Wed, 28 Nov 2012 23:36:08 -0500
Subject: completed move of mathematica generated files to includes

---
 xmds2/realistic_Rb/RbAtomConstans.cdata  | 18 ------------------
 xmds2/realistic_Rb/RbAtomConstants.cdata | 18 ++++++++++++++++++
 xmds2/realistic_Rb/RbPropEquations.cdata |  8 ++++++++
 xmds2/realistic_Rb/realistic_Rb.xmds     | 16 +++++-----------
 4 files changed, 31 insertions(+), 29 deletions(-)
 delete mode 100644 xmds2/realistic_Rb/RbAtomConstans.cdata
 create mode 100644 xmds2/realistic_Rb/RbAtomConstants.cdata
 create mode 100644 xmds2/realistic_Rb/RbPropEquations.cdata

(limited to 'xmds2/realistic_Rb')

diff --git a/xmds2/realistic_Rb/RbAtomConstans.cdata b/xmds2/realistic_Rb/RbAtomConstans.cdata
deleted file mode 100644
index 040d3c9..0000000
--- a/xmds2/realistic_Rb/RbAtomConstans.cdata
+++ /dev/null
@@ -1,18 +0,0 @@
-<![CDATA[
-//---------------- RbAtomConstans.cdata 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;
-//---------------- RbAtomConstans.cdata ends   ------------------
-]]>
-
diff --git a/xmds2/realistic_Rb/RbAtomConstants.cdata b/xmds2/realistic_Rb/RbAtomConstants.cdata
new file mode 100644
index 0000000..040d3c9
--- /dev/null
+++ b/xmds2/realistic_Rb/RbAtomConstants.cdata
@@ -0,0 +1,18 @@
+<![CDATA[
+//---------------- RbAtomConstans.cdata 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;
+//---------------- RbAtomConstans.cdata ends   ------------------
+]]>
+
diff --git a/xmds2/realistic_Rb/RbPropEquations.cdata b/xmds2/realistic_Rb/RbPropEquations.cdata
new file mode 100644
index 0000000..2a30be4
--- /dev/null
+++ b/xmds2/realistic_Rb/RbPropEquations.cdata
@@ -0,0 +1,8 @@
+<![CDATA[
+//---------------- RbPropEquations.cdata starts ------------------
+dE1_dz = 0.16666666666666666*i*Ndens*(2.449489742783178*conj(r0309) + 4.242640687119286*conj(r0410) + 6.*conj(r0511))*eta1 - Lt[E1];
+dE2_dz = -0.4082482904638631*i*Ndens*(conj(r0709) + conj(r0810))*eta1 - Lt[E2];
+dE3_dz = -0.3333333333333333*i*Ndens*(1.7320508075688772*conj(r0614) + 3.*conj(r0715) + 4.242640687119286*conj(r0816))*eta2 - Lt[E3];
+dE4_dz = (i*Ndens*(2.449489742783178*conj(r0113) + 3*conj(r0214) + 3*conj(r0315) + 2.449489742783178*conj(r0416))*eta2)/3. - Lt[E4];
+//---------------- RbPropEquations.cdata ends  ------------------
+]]>
diff --git a/xmds2/realistic_Rb/realistic_Rb.xmds b/xmds2/realistic_Rb/realistic_Rb.xmds
index 7744dd8..e3a5367 100644
--- a/xmds2/realistic_Rb/realistic_Rb.xmds
+++ b/xmds2/realistic_Rb/realistic_Rb.xmds
@@ -1,10 +1,11 @@
 <?xml version="1.0"?>
 <!--Below text defines necessary included files and references to them-->
 <!DOCTYPE simulation [
-<!ENTITY RbAtomConstansFile SYSTEM "RbAtomConstans.cdata" >
+<!ENTITY RbAtomConstantsFile SYSTEM "RbAtomConstants.cdata" >
 <!ENTITY RbChosenRhoFile SYSTEM "RbChosenRho.txt" >
 <!ENTITY RbInitsFile SYSTEM "RbInits.cdata" >
 <!ENTITY RbEquationsFile SYSTEM "RbEquations.cdata" >
+<!ENTITY RbPropEquationsFile SYSTEM "RbPropEquations.cdata" >
 ]>
 <simulation xmds-version="2">
 	<testing>
@@ -57,7 +58,7 @@
 	<features>
 		<globals>
 			<!-- read from Mathematica generated RbAtomConstans.cdata-->
-			&RbAtomConstansFile;
+			&RbAtomConstantsFile;
 			<![CDATA[
 				// Some numerical constants
 				const double pi = M_PI; 
@@ -291,15 +292,8 @@
 				</operator>
         <integration_vectors>E_field</integration_vectors>
 				<dependencies>density_matrix</dependencies>
-				<![CDATA[
-				//read from Mathematica generated RbPropEquations.txt
-//---------------- RbPropEquations.txt starts ------------------
-dE1_dz = 0.16666666666666666*i*Ndens*(2.449489742783178*conj(r0309) + 4.242640687119286*conj(r0410) + 6.*conj(r0511))*eta1 - Lt[E1];
-dE2_dz = -0.4082482904638631*i*Ndens*(conj(r0709) + conj(r0810))*eta1 - Lt[E2];
-dE3_dz = -0.3333333333333333*i*Ndens*(1.7320508075688772*conj(r0614) + 3.*conj(r0715) + 4.242640687119286*conj(r0816))*eta2 - Lt[E3];
-dE4_dz = (i*Ndens*(2.449489742783178*conj(r0113) + 3*conj(r0214) + 3*conj(r0315) + 2.449489742783178*conj(r0416))*eta2)/3. - Lt[E4];
-//---------------- RbPropEquations.txt ends  ------------------
-				]]>
+				<!-- read from Mathematica generated RbPropEquations.cdata-->
+				&RbPropEquationsFile;
 			</operators>
 		</integrate>
 	</sequence>
-- 
cgit v1.2.3