Hi, Then the copyright text could be:
############################################################################### # # # Copyright (C) 2014 Andrew Baldwin ([email protected]), # # 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/>. # # # ############################################################################### Cheers, Edward On 2 May 2014 10:03, Andrew Baldwin <[email protected]> wrote: > Hi Both, > > If you could could include the Ox under the copyright that would probably be > good. As you note, it's entirely a formality. Ox can get prickly, so this > would assuage them. > > Best, > > Andy. > > > > > > On 02/05/2014 08:29, Edward d'Auvergne wrote: >> >> 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
