r24113 - in /branches/disp_spin_speed: lib/dispersion/mmq_cr72.py target_functions/relax_disp.py -- June 18, 2014 - 17:39

Author: tlinnet
Date: Wed Jun 18 17:39:08 2014
New Revision: 24113

URL: http://svn.gna.org/viewcvs/relax?rev=24113&view=rev
Log:
Moved the parameter conversion of MMQ CR72 into lib function.

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

Modified:
    branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
    branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/mmq_cr72.py?rev=24113&r1=24112&r2=24113&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/mmq_cr72.py (original)
+++ branches/disp_spin_speed/lib/dispersion/mmq_cr72.py Wed Jun 18 17:39:08 
2014
@@ -52,7 +52,7 @@
 from numpy.ma import fix_invalid, masked_greater_equal, masked_where
 
 
-def r2eff_mmq_cr72(r20=None, pA=None, pB=None, dw=None, dwH=None, kex=None, 
k_AB=None, k_BA=None, cpmg_frqs=None, inv_tcpmg=None, tcp=None, 
back_calc=None):
+def r2eff_mmq_cr72(r20=None, pA=None, dw=None, dwH=None, kex=None, 
cpmg_frqs=None, inv_tcpmg=None, tcp=None, back_calc=None):
     """The CR72 model extended to MMQ CPMG data.
 
     This function calculates and stores the R2eff values.
@@ -62,18 +62,12 @@
     @type r20:              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 dwH:           The proton chemical exchange difference between 
states A and B in rad/s.
     @type dwH:              numpy float array of rank [NS][NM][NO][ND]
     @keyword kex:           The kex parameter value (the exchange rate in 
rad/s).
     @type kex:              float
-    @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 cpmg_frqs:     The CPMG nu1 frequencies.
     @type cpmg_frqs:        numpy float array of rank [NS][NM][NO][ND]
     @keyword inv_tcpmg:     The inverse of the total duration of the CPMG 
element (in inverse seconds).
@@ -83,6 +77,11 @@
     @keyword back_calc:     The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
     @type back_calc:        numpy float array of rank [NS][NM][NO][ND]
     """
+
+    # Once off parameter conversions.
+    pB = 1.0 - pA
+    k_BA = pA * kex
+    k_AB = pB * kex
 
     # Flag to tell if values should be replaced if max_etapos in cosh 
function is violated.
     t_dw_dw_H_zero = False

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=24113&r1=24112&r2=24113&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py     (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py     Wed Jun 18 
17:39:08 2014
@@ -1261,11 +1261,6 @@
         pA = params[self.end_index[2]]
         kex = params[self.end_index[2]+1]
 
-        # Once off parameter conversions.
-        pB = 1.0 - pA
-        k_BA = pA * kex
-        k_AB = pB * kex
-
         # Convert dw and dwH 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 )
         multiply( multiply.outer( dwH.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_H, out=self.dwH_struct )
@@ -1298,7 +1293,7 @@
                 aliased_dwH = dw_frq
 
             # Back calculate the R2eff values.
-            r2eff_mmq_cr72(r20=r20, pA=pA, pB=pB, dw=aliased_dw, 
dwH=aliased_dwH, kex=kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs[ei], 
inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei], 
back_calc=self.back_calc[ei])
+            r2eff_mmq_cr72(r20=r20, pA=pA, dw=aliased_dw, dwH=aliased_dwH, 
kex=kex, cpmg_frqs=self.cpmg_frqs[ei], inv_tcpmg=self.inv_relax_times[ei], 
tcp=self.tau_cpmg[ei], back_calc=self.back_calc[ei])
 
         # Clean the data for all values, which is left over at the end of 
arrays.
         self.back_calc = self.back_calc*self.disp_struct