Doppler: Temperature and Ndens argument properly treated

2 files changed, 20 insertions, 21 deletions

diff --git a/xmds2/Nlevels_with_doppler_with_z_4wm/Nlevels_with_doppler_with_z_4wm.xmds b/xmds2/Nlevels_with_doppler_with_z_4wm/Nlevels_with_doppler_with_z_4wm.xmds
index 7f13652..bcb6b39 100644
--- a/xmds2/Nlevels_with_doppler_with_z_4wm/Nlevels_with_doppler_with_z_4wm.xmds
+++ b/xmds2/Nlevels_with_doppler_with_z_4wm/Nlevels_with_doppler_with_z_4wm.xmds
@@ -50,7 +50,7 @@
 				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 -------------------------
@@ -59,9 +59,10 @@
 				// 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);
@@ -107,6 +108,20 @@
 					 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
+				if (Temperature == 0)
+					_LOG(_ERROR_LOG_LEVEL, "ERROR: Temperature should be >0 to provide range for Maxwell velocity distribution\n");
+				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" />
@@ -288,11 +303,6 @@
 	</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/TODO b/xmds2/TODO
index c152093..c77e332 100644
--- a/xmds2/TODO
+++ b/xmds2/TODO
@@ -1,14 +1,3 @@
-- TODO Fix  Ndens  argument treatment:  
+- TODO Fix  Temperature > 10 misbehavior
+	Suspected stiff equation at this condition
 
-Right  now  code  is oblivius  to  --Ndens
-parameter, since eta ~1/Ndens sits  in global parameter section and already
-defined. So it is not recalculated after the parameter assignment.
-
-Ugly hack  would be to  make variable  eta_times_Ndens instead of  eta, and
-recalculate  eta=eta_times_Ndens/Ndens  in the  ODE  part  around where  it
-needed. It will have performance penalty but probably not too large.
-
-
-- TODO Fix  Temperature  argument treatment:  
-
-Same problem as above