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