Author: tlinnet
Date: Tue May 6 17:34:04 2014
New Revision: 23022
URL: http://svn.gna.org/viewcvs/relax?rev=23022&view=rev
Log:
Added the synthetic data for B14 model whereby the simplification R20A = R20B
is assumed.
This is used in systemtest Relax_disp.test_baldwin_synthetic.
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
Added:
trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin_r2a_eq_r2b.py
trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b.out
trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b_w_error.out
Added:
trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin_r2a_eq_r2b.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin_r2a_eq_r2b.py?rev=23022&view=auto
==============================================================================
---
trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin_r2a_eq_r2b.py
(added)
+++
trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin_r2a_eq_r2b.py
Tue May 6 17:34:04 2014
@@ -0,0 +1,102 @@
+#!/usr/bin/python
+###############################################################################
+#
#
+# Copyright (C) 2014 Andrew Baldwin (andrew.baldwin@xxxxxxxxxxxxx),
#
+# University of Oxford
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+######################################################################
+# Script to simulate R2eff from a CPMG experiment
+#
+# Note assumption of only inphase magnetisation and 2 site exchange
+# only.
+#
+# Requires numpy.
+#
+#
+#
+
+import numpy
+from math import cos,sin,atan2
+
+############################################################################
+#Note dw is in rad s-1.
+def BaldDisp(kex,pb,dw,ncyc,Trel,R2g,R2e,outfile):
+ pa=(1-pb)
+ keg=kex*(1-pb)
+ kge=kex*pb
+ deltaR2=R2e-R2g
+ nu_cpmg=ncyc/Trel
+ 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*(deltaR2+keg-kge) #same as carver richards zeta
+ g2=(deltaR2+keg-kge)**2.0+4*keg*kge-dw**2 #same as carver richards psi
+ g3=cos(0.5*atan2(g1,g2))*(g1**2.0+g2**2.0)**(1/4.0) #trig faster than
square roots
+ g4=sin(0.5*atan2(g1,g2))*(g1**2.0+g2**2.0)**(1/4.0) #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=(R2g+R2e+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
+
+ array=[]
+ for i in range(len(ncyc)):
+ array.append((nu_cpmg[i],Minty[i]))
+ if(outfile!='Null'):
+ outy=open(outfile,'w')
+ for i in range(len(array)):
+ outy.write('%f\t%f\n' % (array[i][0],array[i][1]))
+ outy.close()
+ return array
+
+
+def ppm_to_rads(ppm,dfrq):
+ return ppm*2*numpy.pi*dfrq
+
+
+if __name__ == "__main__": #run this if this file is run as standalone
+ #otherwise use the function form your own code.
+ outfile='test_r2a_eq_r2b.out' #set to 'Null' if output is not required
+ kex=1000. #exchange rate = k+ + k- (s-1)
+ pb=0.01 #fractional population of excited state k+/kex
+ dw_ppm=2. #deltaOmega in ppm
+ dfrq=200. #spectrometer frequency of nucleci (MHz)
+ ncyc=numpy.array((2,4,8,10,20,40,500,)) #number of cpmg cycles (1 cycle
= delay/180/delay/delay/180/delay)
+ R2g=2. #relaxation rate of ground (s-1)
+ R2e=2. #relaxation rate of excited (s-1)
+ Trelax=0.04 #total time of CPMG block
+ BaldDisp(kex,pb,ppm_to_rads(dw_ppm,dfrq),ncyc,Trelax,R2g,R2e,outfile)
Added:
trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b.out
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b.out?rev=23022&view=auto
==============================================================================
--- trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b.out
(added)
+++ trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b.out
Tue May 6 17:34:04 2014
@@ -0,0 +1,7 @@
+50.000000 10.367900
+100.000000 10.146849
+200.000000 9.765987
+250.000000 9.409789
+500.000000 5.829819
+1000.000000 3.191928
+12500.000000 2.008231
Added:
trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b_w_error.out
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b_w_error.out?rev=23022&view=auto
==============================================================================
---
trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b_w_error.out
(added)
+++
trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_r2a_eq_r2b_w_error.out
Tue May 6 17:34:04 2014
@@ -0,0 +1,7 @@
+50.000000 10.367900 0.1
+100.000000 10.146849 0.1
+200.000000 9.765987 0.1
+250.000000 9.409789 0.1
+500.000000 5.829819 0.1
+1000.000000 3.191928 0.1
+12500.000000 2.008231 0.1
r23022 - /trunk/test_suite/shared_data/dispersion/Baldwin_2014/