r24115 - in /branches/disp_spin_speed: lib/dispersion/ns_r1rho_2site.py target_functions/relax_disp.py -- June 18, 2014 - 17:57

Author: tlinnet
Date: Wed Jun 18 17:57:44 2014
New Revision: 24115

URL: http://svn.gna.org/viewcvs/relax?rev=24115&view=rev
Log:
Moved the parameter conversion from target function to lib function for NS 
r1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
models for Clustered analysis.

Modified:
    branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
    branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24115&r1=24114&r2=24115&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Wed Jun 18 
17:57:44 2014
@@ -59,7 +59,7 @@
 from lib.linear_algebra.matrix_exponential import matrix_exponential
 
 
-def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, pB=None, dw=None, k_AB=None, k_BA=None, 
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None, 
num_points=None):
+def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, dw=None, kex=None, spin_lock_fields=None, 
relax_time=None, inv_relax_time=None, back_calc=None, num_points=None):
     """The 2-site numerical solution to the Bloch-McConnell equation for 
R1rho data.
 
     This function calculates and stores the R1rho values.
@@ -79,14 +79,10 @@
     @type r1:                   numpy float array of rank [NS][NM][NO][ND]
     @keyword pA:                The population of state A.
     @type pA:                   float
-    @keyword pB:                The population of state B.
-    @type pB:                   float
     @keyword dw:                The chemical exchange difference between 
states A and B in rad/s.
     @type dw:                   numpy float array of rank [NS][NM][NO][ND]
-    @keyword k_AB:              The rate of exchange from site A to B 
(rad/s).
-    @type k_AB:                 float
-    @keyword k_BA:              The rate of exchange from site B to A 
(rad/s).
-    @type k_BA:                 float
+    @keyword kex:               The kex parameter value (the exchange rate 
in rad/s).
+    @type kex:                  float
     @keyword spin_lock_fields:  The R1rho spin-lock field strengths (in 
rad.s^-1).
     @type spin_lock_fields:     numpy float array of rank [NS][NM][NO][ND]
     @keyword relax_time:        The total relaxation time period for each 
spin-lock field strength (in seconds).
@@ -98,6 +94,11 @@
     @keyword num_points:        The number of points on the dispersion 
curve, equal to the length of the tcp and back_calc arguments.
     @type num_points:           numpy int array of rank [NS][NM][NO]
     """
+
+    # Once off parameter conversions.
+    pB = 1.0 - pA
+    k_BA = pA * kex
+    k_AB = pB * kex
 
     # Extract shape of experiment.
     NE, NS, NM, NO = num_points.shape

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24115&r1=24114&r2=24115&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py     (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py     Wed Jun 18 
17:57:44 2014
@@ -1621,11 +1621,6 @@
         pA = params[self.end_index[1]]
         kex = params[self.end_index[1]+1]
 
-        # Once off parameter conversions.
-        pB = 1.0 - pA
-        k_BA = pA * kex
-        k_AB = pB * kex
-
         # Convert dw from ppm to rad/s. Use the out argument, to pass 
directly to structure.
         multiply( multiply.outer( dw.reshape(1, self.NS), self.nm_no_nd_ones 
), self.frqs, out=self.dw_struct )
 
@@ -1633,7 +1628,7 @@
         self.r20_struct[:] = multiply.outer( r1rho_prime.reshape(self.NE, 
self.NS, self.NM), self.no_nd_ones )
 
         # Back calculate the R2eff values.
-        ns_r1rho_2site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, 
r1=self.r1, pA=pA, pB=pB, dw=self.dw_struct, k_AB=k_AB, k_BA=k_BA, 
spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times, 
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc, 
num_points=self.num_disp_points)
+        ns_r1rho_2site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, 
r1=self.r1, pA=pA, dw=self.dw_struct, kex=kex, 
spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times, 
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc, 
num_points=self.num_disp_points)
 
         # Clean the data for all values, which is left over at the end of 
arrays.
         self.back_calc = self.back_calc*self.disp_struct