Author: tlinnet
Date: Tue May 6 17:14:51 2014
New Revision: 23002
URL: http://svn.gna.org/viewcvs/relax?rev=23002&view=rev
Log:
Speed-up. Made B14 use the precalculated inverse time, instead of calculating
the inverse time inside the 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=23002&r1=23001&r2=23002&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Tue May 6 17:14:51 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,
relax_time=None, tcp=None, back_calc=None, num_points=None):
+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):
"""Calculate the R2eff values for the CR72 model.
See the module docstring for details.
@@ -120,8 +120,8 @@
@type kex: float
@keyword ncyc: The matrix exponential power array. The number
of CPMG blocks.
@type ncyc: numpy int16, rank-1 array
- @keyword relax_time: The total relaxation time period (in seconds).
- @type relax_time: float
+ @keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
+ @type inv_tcpmg: float
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@type tcp: numpy rank-1 float array
@keyword back_calc: The array for holding the back calculated R2eff
values. Each element corresponds to one of the CPMG nu1 frequencies.
@@ -210,8 +210,8 @@
Tog = (1 + y) / 2 + (1 - y) / (2 * v3) * v2pPdN / N
- # Estimate R2eff. relax_time = Trel.
- Minty = Rpre - ncyc/relax_time * arccosh(ex0b.real) - 1/relax_time *
log(Tog.real)
+ # Estimate R2eff. relax_time = Trel = 1/inv_tcpmg.
+ Minty = Rpre - ncyc * inv_tcpmg * arccosh(ex0b.real) - inv_tcpmg *
log(Tog.real)
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=23002&r1=23001&r2=23002&view=diff
==============================================================================
--- trunk/target_functions/relax_disp.py (original)
+++ trunk/target_functions/relax_disp.py Tue May 6 17:14:51 2014
@@ -321,7 +321,7 @@
self.spin_lock_omega1_squared[ei][mi][oi] =
self.spin_lock_omega1[ei][mi][oi] ** 2
# The inverted relaxation delay.
- if model in [MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE,
MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]:
+ if model in [MODEL_B14, MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE,
MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]:
self.inv_relax_times = 1.0 / relax_times
# Special storage matrices for the multi-quantum CPMG N-site
numerical models.
@@ -800,7 +800,7 @@
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],
relax_time=self.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])
+ 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]):
r23002 - in /trunk: lib/dispersion/b14.py target_functions/relax_disp.py