no Doppler: Temperature and Ndens argument properly treated

2 files changed, 32 insertions, 16 deletions

diff --git a/xmds2/Nlevels_no_dopler_with_z_4wm/Nlevels_no_dopler_with_z_4wm.xmds b/xmds2/Nlevels_no_dopler_with_z_4wm/Nlevels_no_dopler_with_z_4wm.xmds
index 045adac..bb0feb2 100644
--- a/xmds2/Nlevels_no_dopler_with_z_4wm/Nlevels_no_dopler_with_z_4wm.xmds
+++ b/xmds2/Nlevels_no_dopler_with_z_4wm/Nlevels_no_dopler_with_z_4wm.xmds
@@ -49,7 +49,7 @@
 				const double lambda=794.7e-9; //wavelength in m
 				const double Kvec = 2*M_PI/lambda;  // k-vector
 				const double Gamma_super=6*(2*M_PI*1e6);  // characteristic decay rate of upper level used for eta  calculations expressed in [1/s]
-				// eta will be calculated in the sequence -> filter element to use --Ndens parameter
+				// eta will be calculated in the <arguments> section
 				double eta = 0;  // eta constant in the wave equation for Rabi frequency. Units are [1/(m s)]
 				
 				//  ---------  Atom and cell properties -------------------------
@@ -58,9 +58,10 @@
 				// above mass expression is written as (expression is isotopic_mass * atomic_mass_unit)
 
 				// Average sqrt(v^2) in Maxwell distribution for one dimension
-				const double v_thermal_averaged=sqrt(k_boltzmann*Temperature/mass); 
+				// Maxwell related parameters will be calculated in <arguments> section
+				double v_thermal_averaged=0;
 				// Maxwell distribution velocities range to take in account in [m/s]
-				const double V_maxwell_min = -4*v_thermal_averaged, V_maxwell_max = -V_maxwell_min; // there is almost zero probability for higher velocity p(4*v_av) = 3.3e-04 * p(0)
+				double V_maxwell_min = 0, V_maxwell_max = 0;
 
 				// repopulation rate (atoms flying in/out the laser beam)  in [1/s]
 				const double gt=0.01 *(2*M_PI*1e6);
@@ -102,6 +103,18 @@
 					 I am guessing detunings are too large and thus it became a stiff equation-->
 			<!--! make sure it is not equal to zero!-->
 			<argument name="Temperature"  type="real" default_value="5" />
+			<!-- This will be executed after arguments/parameters are parsed -->
+			<!-- Read the code Luke: took me a while of reading the xmds2 sources to find it -->
+			<![CDATA[
+				// Average sqrt(v^2) in Maxwell distribution for one dimension
+				v_thermal_averaged=sqrt(k_boltzmann*Temperature/mass); 
+				// Maxwell distribution velocities range to take in account in [m/s]
+				// there is almost zero probability for higher velocity p(4*v_av) = 3.3e-04 * p(0)
+				V_maxwell_min = -4*v_thermal_averaged; V_maxwell_max = -V_maxwell_min; 
+
+				// eta constant in the wave equation for Rabi frequency. Units are [1/(m s)]
+				eta = 3*lambda*lambda*Ndens*Gamma_super/8.0/M_PI;
+			]]>
     </arguments>
 		<bing />
 		<fftw plan="patient" />
@@ -219,11 +232,6 @@
 	</vector>
 
 	<sequence>
-		<filter>
-			<![CDATA[
-			eta = 3*lambda*lambda*Ndens*Gamma_super/8.0/M_PI;  // eta constant in the wave equation for Rabi frequency. Units are [1/(m s)]
-			]]>
-		</filter>
 		<!--For this set of conditions ARK45 is faster than ARK89-->
 		<!--ARK45 is good for small detuning when all frequency like term are close to zero-->
 		<integrate algorithm="ARK45" tolerance="1e-5" interval="Lcell"> 
diff --git a/xmds2/Nlevels_no_dopler_with_z_4wm_with_perturbations/Nlevels_no_dopler_with_z_4wm_with_perturbations.xmds b/xmds2/Nlevels_no_dopler_with_z_4wm_with_perturbations/Nlevels_no_dopler_with_z_4wm_with_perturbations.xmds
index d662779..e336db7 100644
--- a/xmds2/Nlevels_no_dopler_with_z_4wm_with_perturbations/Nlevels_no_dopler_with_z_4wm_with_perturbations.xmds
+++ b/xmds2/Nlevels_no_dopler_with_z_4wm_with_perturbations/Nlevels_no_dopler_with_z_4wm_with_perturbations.xmds
@@ -54,7 +54,7 @@
 				const double lambda=794.7e-9; //wavelength in m
 				const double Kvec = 2*M_PI/lambda;  // k-vector
 				const double Gamma_super=6*(2*M_PI*1e6);  // characteristic decay rate of upper level used for eta  calculations expressed in [1/s]
-				// eta will be calculated in the sequence -> filter element to use --Ndens parameter
+				// eta will be calculated in the <arguments> section
 				double eta = 0;  // eta constant in the wave equation for Rabi frequency. Units are [1/(m s)]
 				
 				//  ---------  Atom and cell properties -------------------------
@@ -63,9 +63,10 @@
 				// above mass expression is written as (expression is isotopic_mass * atomic_mass_unit)
 
 				// Average sqrt(v^2) in Maxwell distribution for one dimension
-				const double v_thermal_averaged=sqrt(k_boltzmann*Temperature/mass); 
+				// Maxwell related parameters will be calculated in <arguments> section
+				double v_thermal_averaged=0;
 				// Maxwell distribution velocities range to take in account in [m/s]
-				const double V_maxwell_min = -4*v_thermal_averaged, V_maxwell_max = -V_maxwell_min; // there is almost zero probability for higher velocity p(4*v_av) = 3.3e-04 * p(0)
+				double V_maxwell_min = 0, V_maxwell_max = 0;
 
 				// repopulation rate (atoms flying in/out the laser beam)  in [1/s]
 				const double gt=0.01 *(2*M_PI*1e6);
@@ -108,6 +109,18 @@
 					 I am guessing detunings are too large and thus it became a stiff equation-->
 			<!--! make sure it is not equal to zero!-->
 			<argument name="Temperature"  type="real" default_value="5" />
+			<!-- This will be executed after arguments/parameters are parsed -->
+			<!-- Read the code Luke: took me a while of reading the xmds2 sources to find it -->
+			<![CDATA[
+				// Average sqrt(v^2) in Maxwell distribution for one dimension
+				v_thermal_averaged=sqrt(k_boltzmann*Temperature/mass); 
+				// Maxwell distribution velocities range to take in account in [m/s]
+				// there is almost zero probability for higher velocity p(4*v_av) = 3.3e-04 * p(0)
+				V_maxwell_min = -4*v_thermal_averaged; V_maxwell_max = -V_maxwell_min; 
+
+				// eta constant in the wave equation for Rabi frequency. Units are [1/(m s)]
+				eta = 3*lambda*lambda*Ndens*Gamma_super/8.0/M_PI;
+			]]>
     </arguments>
 		<bing />
 		<fftw plan="patient" />
@@ -226,11 +239,6 @@
 	</vector>
 
 	<sequence>
-		<filter>
-			<![CDATA[
-			eta = 3*lambda*lambda*Ndens*Gamma_super/8.0/M_PI;  // eta constant in the wave equation for Rabi frequency. Units are [1/(m s)]
-			]]>
-		</filter>
 		<!--For this set of conditions ARK45 is faster than ARK89-->
 		<!--ARK45 is good for small detuning when all frequency like term are close to zero-->
 		<integrate algorithm="ARK45" tolerance="1e-5" interval="Lcell">