Author: tlinnet
Date: Mon May 5 20:18:34 2014
New Revision: 22973
URL: http://svn.gna.org/viewcvs/relax?rev=22973&view=rev
Log:
Pretty up the code, making space between all "+".
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
Modified: trunk/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=22973&r1=22972&r2=22973&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Mon May 5 20:18:34 2014
@@ -142,7 +142,7 @@
keg = kex * (1 - pb)
kge = kex * pb
deltaR2 = r20a - r20b
- alpha_m = r20a - r20b + kge - keg
+ alpha_m = r20a - r20b + kge - keg
# This is not used
#nu_cpmg = ncyc/Trel
#tcp = Trel/(4.0 * ncyc) #time for one free precession element
@@ -150,20 +150,20 @@
#########################################################################
#get the real and imaginary components of the exchange induced shift
g1 = 2 * dw * alpha_m #same as carver
richards zeta
- g2 = alpha_m**2+4 * keg * kge - dw**2 #same as carver richards psi
- g3 = 1/sqrt(2) * sqrt(g2+sqrt(g1**2+g2**2)) #trig faster than square
roots
- g4 = 1/sqrt(2) * sqrt(-g2+sqrt(g1**2+g2**2)) #trig faster than square
roots
+ g2 = alpha_m**2 + 4 * keg * kge - dw**2 #same as carver richards psi
+ g3 = 1/sqrt(2) * sqrt(g2 + sqrt(g1**2 + g2**2)) #trig faster than
square roots
+ g4 = 1/sqrt(2) * sqrt(-g2 + sqrt(g1**2 + g2**2)) #trig faster than
square roots
#########################################################################
#time independent factors
- N = complex(kge+g3 - kge,g4) #N = oG+oE
- NNc = (g3**2+g4**2)
- f0 = (dw**2+g3**2)/(NNc) #f0
+ N = complex(kge + g3 - kge,g4) #N = oG + oE
+ NNc = (g3**2 + g4**2)
+ f0 = (dw**2 + g3**2)/(NNc) #f0
f2 = (dw**2 - g4**2)/(NNc) #f2
- #t1 = (-dw+g4) * (complex(-dw,-g3))/(NNc) #t1
- t2 = (dw+g4) * (complex(dw, -g3))/(NNc) #t2
- t1pt2 = complex(2 * dw**2,g1)/(NNc) #t1+t2
- oGt2 = complex((-deltaR2+keg - kge - g3),(dw - g4)) * t2 #-2 * oG * t2
- Rpre = (r20a+r20b+kex)/2.0 #-1/Trel * log(LpreDyn)
+ #t1 = (-dw + g4) * (complex(-dw,-g3))/(NNc) #t1
+ t2 = (dw + g4) * (complex(dw, -g3))/(NNc) #t2
+ t1pt2 = complex(2 * dw**2,g1)/(NNc) #t1 + t2
+ oGt2 = complex((-deltaR2 + keg - kge - g3),(dw - g4)) * t2 #-2 * oG * t2
+ Rpre = (r20a + r20b + kex)/2.0 #-1/Trel * log(LpreDyn)
E0 = 2.0 * tcp * g3 #derived from relaxation #E0 = -2.0 * tcp *
(f00R - f11R)
E2 = 2.0 * tcp * g4 #derived from chemical shifts #E2 =
complex(0,-2.0 * tcp * (f00I - f11I))
E1 = (complex(g3, -g4)) * tcp #mixed term (complex) (E0 - iE2)/2
@@ -171,9 +171,9 @@
ex0c = (f0 * numpy.sinh(E0) - f2 * numpy.sin(E2) * complex(0,1.))
#complex
ex1c = (numpy.sinh(E1)) #complex
v3 = numpy.sqrt(ex0b**2 - 1) #exact result for v2v3
- y = numpy.power((ex0b - v3)/(ex0b+v3),ncyc)
- v2pPdN = (( complex(-deltaR2+kex,dw) ) * ex0c+(-oGt2 - kge * t1pt2) * 2
* ex1c) #off diagonal common factor. sinh fuctions
- Tog = (((1+y)/2+(1 - y)/(2 * v3) * (v2pPdN)/N))
+ y = numpy.power((ex0b - v3)/(ex0b + v3),ncyc)
+ v2pPdN = (( complex(-deltaR2 + kex,dw) ) * ex0c + (-oGt2 - kge * t1pt2)
* 2 * ex1c) #off diagonal common factor. sinh fuctions
+ Tog = (((1 + y)/2 + (1 - y)/(2 * v3) * (v2pPdN)/N))
Minty = Rpre - ncyc/(Trel) * numpy.arccosh((ex0b).real) - 1/Trel *
numpy.log((Tog.real)) #estimate R2eff
# Loop over the time points, back calculating the R2eff values.
r22973 - /trunk/lib/dispersion/b14.py