Hi Troels, For Andy's script at test_suite/shared_data/dispersion/Baldwin_2014/Baldwin.py, we should add the GPL3+ copyright notice as follows:
############################################################################### # # # Copyright (C) 2014 Andrew Baldwin ([email protected]) # # # # 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/>. # # # ############################################################################### This is a simple legal formality needed to allow the script to be bundled with relax. This would start from the second line of the script. It would replace the text: # Do not distribute without permission. # Copyright (c) # Andrew Baldwin # [email protected] # University of Oxford 2014. Andy, should we also include the "University of Oxford" text? Cheers, Edward On 1 May 2014 10:47, <[email protected]> wrote: > Author: tlinnet > Date: Thu May 1 10:47:35 2014 > New Revision: 22906 > > URL: http://svn.gna.org/viewcvs/relax?rev=22906&view=rev > Log: > Added Baldwin model B14 test data. > > sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014) > B14 model - 2-site exact solution model for all time scales. > > Added: > trunk/test_suite/shared_data/dispersion/Baldwin_2014/ > trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin.py > trunk/test_suite/shared_data/dispersion/Baldwin_2014/test.out > trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_w_error.out > > Added: trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin.py?rev=22906&view=auto > ============================================================================== > --- trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin.py > (added) > +++ trunk/test_suite/shared_data/dispersion/Baldwin_2014/Baldwin.py Thu > May 1 10:47:35 2014 > @@ -0,0 +1,85 @@ > +#!/usr/bin/python > +###################################################################### > +# Script to simulate R2eff from a CPMG experiment > +# > +# Note assumption of only inphase magnetisation and 2 site exchange > +# only. > +# > +# Requires numpy. > +# > +# > +# Do not distribute without permission. > +# Copyright (c) > +# Andrew Baldwin > +# [email protected] > +# University of Oxford 2014. > +# > + > +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.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=100. #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.out > URL: > http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Baldwin_2014/test.out?rev=22906&view=auto > ============================================================================== > --- trunk/test_suite/shared_data/dispersion/Baldwin_2014/test.out > (added) > +++ trunk/test_suite/shared_data/dispersion/Baldwin_2014/test.out Thu > May 1 10:47:35 2014 > @@ -0,0 +1,7 @@ > +50.000000 10.286255 > +100.000000 10.073083 > +200.000000 9.692746 > +250.000000 9.382441 > +500.000000 6.312396 > +1000.000000 3.957029 > +12500.000000 2.880420 > > Added: trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_w_error.out > URL: > http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_w_error.out?rev=22906&view=auto > ============================================================================== > --- trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_w_error.out > (added) > +++ trunk/test_suite/shared_data/dispersion/Baldwin_2014/test_w_error.out > Thu May 1 10:47:35 2014 > @@ -0,0 +1,7 @@ > +50.000000 10.286255 1.0 > +100.000000 10.073083 1.0 > +200.000000 9.692746 1.0 > +250.000000 9.382441 1.0 > +500.000000 6.312396 1.0 > +1000.000000 3.957029 1.0 > +12500.000000 2.880420 1.0 > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
