Re: r23010 - in /trunk: lib/dispersion/b14.py target_functions/relax_disp.py -- May 06, 2014

Hi,

This is a speed up, but there is a much better speed up.  Don't define
g_fact in the target function.  Define it in the lib.dispersion.b14
module, outside of the function (above the function).  Then it is not
calculated once for each target function call, but only once for the
entire time you run relax!  This completely eliminates the calculation
from the optimisation.

Regards,

Edward




On 6 May 2014 17:24,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Tue May  6 17:24:28 2014
New Revision: 23010

URL: http://svn.gna.org/viewcvs/relax?rev=23010&view=rev
Log:
Speed-up. Moved g_factor: g = 1/sqrt(2) outside library function to be 
calculated once.

sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014) 
B14 model - 2-site exact solution model for all time scales.

This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging


Modified:
    trunk/lib/dispersion/b14.py
    trunk/target_functions/relax_disp.py

Modified: trunk/lib/dispersion/b14.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=23010&r1=23009&r2=23010&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Tue May  6 17:24:28 2014
@@ -102,7 +102,7 @@
 from numpy import arccosh, cos, cosh, log, sin, sinh, sqrt, power


-def r2eff_B14(r20a=None, r20b=None, deltaR2=None, alpha_m=None, pA=None, 
pB=None, dw=None, zeta=None, Psi=None, kex=None, k_AB=None, k_BA=None, 
ncyc=None, inv_tcpmg=None, tcp=None, back_calc=None, num_points=None):
+def r2eff_B14(r20a=None, r20b=None, deltaR2=None, alpha_m=None, pA=None, 
pB=None, dw=None, zeta=None, Psi=None, g_fact=None, kex=None, k_AB=None, 
k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None, back_calc=None, 
num_points=None):
     """Calculate the R2eff values for the CR72 model.

     See the module docstring for details.
@@ -126,6 +126,8 @@
     @type zeta:             float
     @keyword Psi:           The Carver and Richards (1972) Psi notation. 
Psi =  alpha_m**2 + 4 * k_BA * k_AB - dw**2.
     @type Psi:              float
+    @keyword g_fact:        The factor g = 1/sqrt(2). This is calculated 
outside library function, to only be calculated once.
+    @type g_fact:           float
     @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).
@@ -151,8 +153,8 @@
     two_tcp = 2.0 * tcp

     # Get the real and imaginary components of the exchange induced shift.
-    g3 = 1/sqrt(2) * sqrt(Psi + sqrt(zeta2 + Psi2))
-    g4 = 1/sqrt(2) * sqrt(-Psi + sqrt(zeta2 + Psi2))
+    g3 = g_fact * sqrt(Psi + sqrt(zeta2 + Psi2))
+    g4 = g_fact * sqrt(-Psi + sqrt(zeta2 + Psi2))

     # Repetitive calculations (to speed up calculations).
     g32 = g3**2

Modified: trunk/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=23010&r1=23009&r2=23010&view=diff
==============================================================================
--- trunk/target_functions/relax_disp.py        (original)
+++ trunk/target_functions/relax_disp.py        Tue May  6 17:24:28 2014
@@ -27,7 +27,7 @@
 # Python module imports.
 from copy import deepcopy
 from math import pi
-from numpy import complex64, dot, float64, int16, zeros
+from numpy import complex64, dot, float64, int16, sqrt, zeros

 # relax module imports.
 from lib.dispersion.b14 import r2eff_B14
@@ -790,6 +790,7 @@
         pB = 1.0 - pA
         k_BA = pA * kex
         k_AB = pB * kex
+        g_fact = 1/sqrt(2)

         # Initialise.
         chi2_sum = 0.0
@@ -823,7 +824,7 @@
                     Psi = alpha_m**2 + 4 * k_BA * k_AB - aliased_dw**2

                     # Back calculate the R2eff values.
-                    r2eff_B14(r20a=r20a, r20b=r20b, deltaR2=deltaR2, 
alpha_m=alpha_m, pA=pA, pB=pB, dw=dw_frq, zeta=zeta, Psi=Psi, kex=kex, 
k_AB=k_AB, k_BA=k_BA, ncyc=self.power[ei][mi], 
inv_tcpmg=self.inv_relax_times[ei][mi], tcp=self.tau_cpmg[ei][mi], 
back_calc=self.back_calc[ei][si][mi][0], 
num_points=self.num_disp_points[ei][si][mi][0])
+                    r2eff_B14(r20a=r20a, r20b=r20b, deltaR2=deltaR2, 
alpha_m=alpha_m, pA=pA, pB=pB, dw=dw_frq, zeta=zeta, Psi=Psi, 
g_fact=g_fact, kex=kex, k_AB=k_AB, k_BA=k_BA, ncyc=self.power[ei][mi], 
inv_tcpmg=self.inv_relax_times[ei][mi], tcp=self.tau_cpmg[ei][mi], 
back_calc=self.back_calc[ei][si][mi][0], 
num_points=self.num_disp_points[ei][si][mi][0])

                     # For all missing data points, set the back-calculated 
value to the measured values so that it has no effect on the chi-squared 
value.
                     for di in range(self.num_disp_points[ei][si][mi][0]):


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Re: r23010 - in /trunk: lib/dispersion/b14.py target_functions/relax_disp.py

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