Author: tlinnet
Date: Mon May 5 20:18:29 2014
New Revision: 22970
URL: http://svn.gna.org/viewcvs/relax?rev=22970&view=rev
Log:
Pretty the code, making space between all multiplications "*".
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=22970&r1=22969&r2=22970&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Mon May 5 20:18:29 2014
@@ -139,42 +139,42 @@
##### Baldwins code.
#########################################################################
pa=(1-pb)
- keg=kex*(1-pb)
- kge=kex*pb
+ keg=kex * (1-pb)
+ kge=kex * pb
deltaR2=r20a-r20b
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
+ #tcp=Trel/(4.0 * ncyc) #time for one free precession element
#########################################################################
#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
+ 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
#########################################################################
#time independent factors
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)
- 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
- ex0b=(f0*numpy.cosh(E0)-f2*numpy.cos(E2)) #real
- ex0c=(f0*numpy.sinh(E0)-f2*numpy.sin(E2)*complex(0,1.)) #complex
+ #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
+ ex0b=(f0 * numpy.cosh(E0)-f2 * numpy.cos(E2)) #real
+ 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))
-
Minty=Rpre-ncyc/(Trel)*numpy.arccosh((ex0b).real)-1/Trel*numpy.log((Tog.real))
#estimate R2eff
+ 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.
for i in range(num_points):
r22970 - /trunk/lib/dispersion/b14.py