Hi Troels, I have a few small points about this commit:
- Each paragraph should be on one line. This is for better formatting of the API documentation (http://www.nmr-relax.com/api/). I.e. the sentences of the same paragraph should not start on a the next line. - An empty line between the text and "::" and the equation is recommended - again for formatting in the API docs. - One equation does not have the double colon :: at the end of the introducing text. This causes the API documentation build to fail (try running "scons api_manual_html" to see the "Improper paragraph indentation" warning message). - Are the CR72 model links at the end correct? Cheers, Edward On 1 May 2014 09:21, <[email protected]> wrote: > Author: tlinnet > Date: Thu May 1 09:21:29 2014 > New Revision: 22904 > > URL: http://svn.gna.org/viewcvs/relax?rev=22904&view=rev > Log: > Extended docstring in b14.py file. > > sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014) > B14 model - 2-site exact solution model for all time scales > > 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=22904&r1=22903&r2=22904&view=diff > ============================================================================== > --- trunk/lib/dispersion/b14.py (original) > +++ trunk/lib/dispersion/b14.py Thu May 1 09:21:29 2014 > @@ -1,6 +1,7 @@ > > ############################################################################### > # > # > # Copyright (C) 2014 Troels E. Linnet > # > +# Copyright (C) 2014 Andrew Baldwin > # > # > # > # This file is part of the program relax (http://www.nmr-relax.com). > # > # > # > @@ -20,7 +21,81 @@ > > ############################################################################### > > # Module docstring. > -""" > +"""The Baldwin (2014) 2-site exact solution model for all time scales > U{B14<http://wiki.nmr-relax.com/B14>}. > + > +Description > +=========== > + > +This module is for the function, gradient and Hessian of the > U{B14<http://wiki.nmr-relax.com/B14>} model. > + > + > +References > +========== > + > +The model is named after the reference: > + > + - Andrew J. Baldwin (2014). An exact solution for R2,eff in CPMG > experiments in the case of two site chemical exchange. I{J. Magn. Reson.}. > (U{DOI: 10.1016/j.jmr.2014.02.023 > <http://dx.doi.org/10.1016/j.jmr.2014.02.023>}). > + > + > +Equations > +========= > + > +The equation used is:: > + R2A0 + R2B0 + kex Ncyc 1 ( 1+y > 1-y ) > + R2eff = ------------------ - ------ * cosh^-1 * v1c - ------ ln( --- + > ------------------ * (v2 + 2*kAB*pD ) ) > + 2 Trel Trel ( 2 > 2*sqrt(v1c^2 -1 ) ) > + > + 1 ( 1+y 1-y > ) > + = R2eff(CR72) - ------ ln( --- + ------------------ * (v2 + > 2*kAB*pD ) ) > + Trel ( 2 2*sqrt(v1c^2 -1 ) > ) > + > +Which have these following definitions:: > + v1c = F0 * cosh(tauCP * E0)- F2 * cosh(tauCP * E2) > + v1s = F0 * sinh(tauCP * E0)- F2 * sinh(tauCP * E2) > + v2*N = v1s * (OB-OA) + 4OB * F1^a * sinh(tauCP * E1) > + pD N = v1s + (F1^a + F1^b) * sinh(tauCP * E1) > + v3 = ( v2^2 + 4 * kBA * kAB * pD^2 )^1/2 > + y = ( (v1c-v3)/(v1c+v3) )^NCYC > + > +Note, E2 is complex. If |x| denotes the complex modulus:<br> > + cosh(tauCP * E2) = cos(tauCP * |E2|) > + sinh(tauCP * E2) = i sin(tauCP * |E2|) > + > +The term pD is based on product of the off diagonal elements in the CPMG > propagator (Supplementary Section 3). > + > +It is interesting to consider the region of validity of the Carver Richards > result. > +The two results are equal when the correction is zero, which is true when > + > + sqrt(v1c^2-1) ~ v2 + 2*kAB * pD > + > +This occurs when 2*kAB * pD tends to zero, and so v2=v3. > +Setting "kAB * pD" to zero, amounts to neglecting magnetisation that starts > on the ground state ensemble and end on the excited state ensemble and vice > versa. > +This will be a good approximation when pA >> p_B. > + > +In practise, significant deviations from the Carver Richards equation can be > incurred if pB > 1 %. > +Incorporation of the correction term into equation (50), results in an > improved description of the CPMG experiment over the Carver Richards equation. > + > +kex is the chemical exchange rate constant, pA and pB are the populations of > states A and B, and delta_omega is the chemical shift difference between the > two states in ppm. > + > + > +Links > +===== > + > +More information on the B14 model can be found in the: > + > + - U{relax wiki<http://wiki.nmr-relax.com/B14>}, > + > +Comparison to CR72 model can be found in the: > + > + - U{relax wiki<http://wiki.nmr-relax.com/CR72>}, > + - U{relax > manual<http://www.nmr-relax.com/manual/reduced_CR72_2_site_CPMG_model.html>}, > + - U{relaxation dispersion page of the relax > website<http://www.nmr-relax.com/analyses/relaxation_dispersion.html#CR72>}. > + > +Comparison to CR72 full model can be found in the: > + > + - U{relax wiki<http://wiki.nmr-relax.com/CR72_full>}, > + - U{relax > manual<http://www.nmr-relax.com/manual/full_CR72_2_site_CPMG_model.html>}, > + - U{relaxation dispersion page of the relax > website<http://www.nmr-relax.com/analyses/relaxation_dispersion.html#CR72_full>}. > """ > > # Python module imports. > > > _______________________________________________ > 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
