Author: tlinnet
Date: Tue May 6 17:20:53 2014
New Revision: 23003
URL: http://svn.gna.org/viewcvs/relax?rev=23003&view=rev
Log:
Speed-up. Moved the Repetitive calculations of pB, k_BA and k_AB out of the
library function.
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=23003&r1=23002&r2=23003&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Tue May 6 17:20:53 2014
@@ -102,7 +102,7 @@
from numpy import arccosh, cos, cosh, log, sin, sinh, sqrt, power
-def r2eff_B14(r20a=None, r20b=None, pA=None, dw=None, kex=None, ncyc=None,
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None):
+def r2eff_B14(r20a=None, r20b=None, pA=None, pB=None, dw=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.
@@ -114,10 +114,16 @@
@type r20b: float
@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: 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).
+ @type k_AB: float
+ @keyword k_BA: The rate of exchange from site B to A (rad/s).
+ @type k_BA: float
@keyword ncyc: The matrix exponential power array. The number
of CPMG blocks.
@type ncyc: numpy int16, rank-1 array
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
@@ -130,12 +136,7 @@
@type num_points: int
"""
- # The B population.
- pB = 1.0 - pA
-
# Repetitive calculations (to speed up calculations).
- k_BA = pA * kex
- k_AB = pB * kex
dw2 = dw**2
#########################################################################
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=23003&r1=23002&r2=23003&view=diff
==============================================================================
--- trunk/target_functions/relax_disp.py (original)
+++ trunk/target_functions/relax_disp.py Tue May 6 17:20:53 2014
@@ -786,29 +786,42 @@
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
+
# Initialise.
chi2_sum = 0.0
- # Loop over the spins.
- for si in range(self.num_spins):
- # Loop over the spectrometer frequencies.
- for mi in range(self.num_frq):
- # The R20 index.
- r20_index = mi + si*self.num_frq
-
- # Convert dw from ppm to rad/s.
- dw_frq = dw[si] * self.frqs[0][si][mi]
-
- # Back calculate the R2eff values.
- r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index],
pA=pA, dw=dw_frq, kex=kex, ncyc=self.power[0][mi],
inv_tcpmg=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi],
back_calc=self.back_calc[0][si][mi][0],
num_points=self.num_disp_points[0][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[0][si][mi][0]):
- if self.missing[0][si][mi][0][di]:
- self.back_calc[0][si][mi][0][di] =
self.values[0][si][mi][0][di]
-
- # Calculate and return the chi-squared value.
- chi2_sum += chi2(self.values[0][si][mi][0],
self.back_calc[0][si][mi][0], self.errors[0][si][mi][0])
+ # Loop over the experiment types.
+ for ei in range(self.num_exp):
+ # Loop over the spins.
+ for si in range(self.num_spins):
+ # Loop over the spectrometer frequencies.
+ for mi in range(self.num_frq):
+ # The R20 index.
+ r20_index = mi + si*self.num_frq
+
+ # Convert dw from ppm to rad/s.
+ dw_frq = dw[si] * self.frqs[ei][si][mi]
+
+ # Alias the dw frequency combinations.
+ if self.exp_types[ei] == EXP_TYPE_CPMG_SQ:
+ aliased_dw = dw_frq
+ elif self.exp_types[ei] == EXP_TYPE_CPMG_PROTON_SQ:
+ aliased_dw = dw_frq
+
+ # Back calculate the R2eff values.
+ r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index],
pA=pA, pB=pB, dw=dw_frq, 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]):
+ if self.missing[ei][si][mi][0][di]:
+ self.back_calc[ei][si][mi][0][di] =
self.values[ei][si][mi][0][di]
+
+ # Calculate and return the chi-squared value.
+ chi2_sum += chi2(self.values[ei][si][mi][0],
self.back_calc[ei][si][mi][0], self.errors[ei][si][mi][0])
# Return the total chi-squared value.
return chi2_sum
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Re: r23003 - in /trunk: lib/dispersion/b14.py target_functions/relax_disp.py