Author: tlinnet
Date: Mon May 5 20:18:45 2014
New Revision: 22979
URL: http://svn.gna.org/viewcvs/relax?rev=22979&view=rev
Log:
Replaced "power" with ncyc. And made user of numpy power.
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=22979&r1=22978&r2=22979&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Mon May 5 20:18:45 2014
@@ -99,10 +99,10 @@
# Python module imports.
import numpy
-from numpy import arccosh, cos, cosh, log, sin, sinh, sqrt
-
-
-def r2eff_B14(r20a=None, r20b=None, pA=None, dw=None, kex=None, power=None,
relax_time=None, tcp=None, back_calc=None, num_points=None):
+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):
"""Calculate the R2eff values for the CR72 model.
See the module docstring for details.
@@ -118,8 +118,8 @@
@type dw: float
@keyword kex: The kex parameter value (the exchange rate in
rad/s).
@type kex: float
- @keyword power: The matrix exponential power array. The number
of CPMG blocks.
- @type power: numpy int16, rank-1 array
+ @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 tcp: The tau_CPMG times (1 / 4.nu1).
@@ -133,7 +133,6 @@
# Conversion from relax parameters, to the exact code of Baldwin.
pb = 1 - pA
Trel = relax_time
- ncyc = power
#########################################################################
##### Baldwins code.
@@ -202,7 +201,7 @@
# Exact result for v2v3.
v3 = sqrt(ex0b**2 - 1)
- y = numpy.power((ex0b - v3) / (ex0b + v3), ncyc)
+ y = power((ex0b - v3) / (ex0b + v3), ncyc)
# Off diagonal common factor. sinh fuctions.
v2pPdN = (( complex(-deltaR2 + kex, dw) ) * ex0c + (-oGt2 - kge * t1pt2)
* 2 * ex1c)
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=22979&r1=22978&r2=22979&view=diff
==============================================================================
--- trunk/target_functions/relax_disp.py (original)
+++ trunk/target_functions/relax_disp.py Mon May 5 20:18:45 2014
@@ -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, power=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],
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])
# 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]):
r22979 - in /trunk: lib/dispersion/b14.py target_functions/relax_disp.py