Hi Andy, If you do check out the relax source code with:
$ svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk you will see your original code, now well optimised and formatted by Troels, at lib/dispersion/b14.py. This is executed from the relaxation dispersion target functions in target_functions/relax_disp.py. Regards, Edward On 7 May 2014 11:09, Edward d'Auvergne <[email protected]> wrote: > Hi, > > Cheers, I thought that pDN was one variable. That is much clearer > now. Would it be better as pD.N in the paper or the N shifted to the > other side of the equations? Just say what the final change is and we > can make the same change to the relax manual to match the paper. > Appendix 1 is a nice addition. The derivation in the main text was a > little hard to follow as you needed to always jump back to the h1, h2, > h3, h4 definitions to remind yourself as to what they were. > > If you have interest in how your model is presented to relax users, > i.e. the equations and text for the two 'B14' models in the relax > manual, maybe after I release a new version of relax (3.2.0) and > update the PDF version of the manual at > http://download.gna.org/relax/manual/relax.pdf, I'll ask if you'd like > to have a look at the section for your model and advise if you'd like > any additions, modifications, etc. Troels is currently polishing up > this LaTeX code. Or I could send you the PDF of the development code > later. There are still a few little things to do for polishing it up > and adding the 'B14' models to the 2 tables in that chapter. If you > have the 'subversion' software on your system, you can download it > yourself with: > > $ svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk > > See http://www.nmr-relax.com/download.html#Source_code_repository. > You'll see the LaTeX code for your models in the > docs/latex/dispersion.tex file. To build the manual, you'll need a > LaTeX install and scons. You can even create patches by modifying the > file and running "svn diff > patch", if you really have the urge. > Feel free to suggest improvements as you wish - in the 'B14' sections > you can present your model to all relax users as you see fit. This > chapter may be the main way that many relax users are introduced to > your model, so if you are interested in expanding this, you are more > than welcome. Changing it to be more like appendix 1 might be an > option. The section should not be too long, 1-2 pages max, and this > should be a summary of the model, pointing to your paper as the > primary reference. You can also add any \url{} links you wish. > Anyway, the current B14 section is quite reasonable when compared to > the other dispersion models, so please don't feel obliged to give > feedback. > > Cheers, > > Edward > > > > > On 7 May 2014 10:30, Andrew Baldwin <[email protected]> wrote: >> Hi chaps, >> >> PdN is the product of Pd and N (N defined earlier). >> >> I see why that's not obvious. I'll add a multiply sign in the paper. The N's >> basically all cancel later. It might actually be sensible to get rid of them >> already in 45. >> >> Also the perscription in appendix 1 might look a bit different at face >> value. To define the evolution matrix (46) you need lots of things. But for >> just the ground state R2eff, you can get away with a bit less (appendix 1). >> Appendix 1 was Nikolai's idea, and with hindsight, a very good one. >> >> For summaried equation notation, I'd suggest sticking with appendix 1. >> >> Best, >> >> Andy. >> >> >> >> >> >> On 07/05/2014 09:18, Edward d'Auvergne wrote: >>> >>> Hi, >>> >>> I need to look at the paper more. I can't see where pDN from equation >>> 45 fits into equation 48 or 50, as I only see pD there. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 7 May 2014 10:02, Troels Emtekær Linnet <[email protected]> wrote: >>>> >>>> Hi Edward. >>>> >>>> >>>> What is the equation inconsistency with pD and pDN. ? >>>> I cant see it? >>>> >>>> I look at eq: 45 in the paper. >>>> >>>> Best >>>> Troels >>>> >>>> 2014-05-06 18:19 GMT+02:00 Edward d'Auvergne <[email protected]>: >>>>> >>>>> Hi Troels, >>>>> >>>>> These are just a few LaTeX tips. But first, do you think it's worth >>>>> putting simplified equations into the 'B14' model section? And what >>>>> do you think about including the comparison to the CR72 model at >>>>> http://wiki.nmr-relax.com/B14? >>>>> >>>>> For the tips: >>>>> >>>>> 1) For the R2eff equation, you could wrap this all in a block: >>>>> >>>>> \begin{subequations} >>>>> \begin{align} >>>>> R2eff ... >>>>> \end{align} >>>>> \end{subequations} >>>>> >>>>> This will give numbers to both parts. Search >>>>> docs/latex/dispersion.tex for examples. The multi-line part can be >>>>> made prettier by using a \qquad. >>>>> >>>>> 2) The align environment is much nicer than eqnarray. >>>>> >>>>> 3) For consistency, the R2eff parameter is defined in the relax.tex >>>>> file with \Rtwoeff. Also see \RtwozeroA, \RtwozeroB, \kAB, \kBA, >>>>> \kex, etc. Most dispersion parameters are defined in a consistent way >>>>> - just have a look at the relax.tex file. >>>>> >>>>> One last thing, there appears to be an equation inconsistency with pD >>>>> and pDN. >>>>> >>>>> Cheers! >>>>> >>>>> Edward >>>>> >>>>> >>>>> On 6 May 2014 17:35, <[email protected]> wrote: >>>>>> >>>>>> Author: tlinnet >>>>>> Date: Tue May 6 17:35:00 2014 >>>>>> New Revision: 23025 >>>>>> >>>>>> URL: http://svn.gna.org/viewcvs/relax?rev=23025&view=rev >>>>>> Log: >>>>>> Added model B14 description in the manual. >>>>>> >>>>>> 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#The_relax_manual >>>>>> >>>>>> >>>>>> Modified: >>>>>> trunk/docs/latex/dispersion.tex >>>>>> >>>>>> Modified: trunk/docs/latex/dispersion.tex >>>>>> URL: >>>>>> http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=23025&r1=23024&r2=23025&view=diff >>>>>> >>>>>> ============================================================================== >>>>>> --- trunk/docs/latex/dispersion.tex (original) >>>>>> +++ trunk/docs/latex/dispersion.tex Tue May 6 17:35:00 2014 >>>>>> @@ -102,6 +102,11 @@ >>>>>> $2*\taucpmg$ is the time between successive 180 degree pulses. >>>>>> Parameters are $\{\RtwozeroA, \dots, \dw, \kAB\}$. >>>>>> See Section~\ref{sect: dispersion: TSMFK01 model} on >>>>>> page~\pageref{sect: dispersion: TSMFK01 model}. >>>>>> + \item[`B14':]\index{relaxation dispersion!B14 model} The reduced >>>>>> \citet{Baldwin2014} 2-site exact solution equation for all time scales >>>>>> whereby the simplification $\RtwozeroA = \RtwozeroB$ is assumed. >>>>>> + It has the parameters $\{\Rtwozero, \dots, \pA, \dw, \kex\}$. >>>>>> + See Section~\ref{sect: dispersion: B14 model} on >>>>>> page~\pageref{sect: dispersion: B14 model}. >>>>>> + \item[`B14 full':]\index{relaxation dispersion!B14 full model} The >>>>>> full \citet{Baldwin2014} 2-site exact equation for all time scales with >>>>>> parameters $\{\RtwozeroA, \RtwozeroB, \dots, \pA, \dw, \kex\}$. >>>>>> + See Section~\ref{sect: dispersion: B14 full model} on >>>>>> page~\pageref{sect: dispersion: B14 full model}. >>>>>> \end{description} >>>>>> >>>>>> For the SQ CPMG-type experiments, the numeric models currently >>>>>> supported are: >>>>>> @@ -549,6 +554,78 @@ >>>>>> \item the relaxation dispersion page of the relax website at >>>>>> \url{http://www.nmr-relax.com/analyses/relaxation\_dispersion.html#TSMFK01}. >>>>>> \end{itemize} >>>>>> >>>>>> + >>>>>> +% Full B14 model. >>>>>> +%~~~~~~~~~~~~~~~~~ >>>>>> + >>>>>> +\subsection{The full B14 2-site CPMG model} >>>>>> +\label{sect: dispersion: B14 full model} >>>>>> +\index{relaxation dispersion!B14 full model|textbf} >>>>>> + >>>>>> +This is the model for 2-site exchange exact analytical derivation on >>>>>> all time scales (with the constraint that $\pA > \pB$), named after >>>>>> \citet{Baldwin2014}. >>>>>> +It is selected by setting the model to `B14 full'. >>>>>> +The equation is >>>>>> +\begin{equation} >>>>>> + R_{2,\textrm{eff}} = >>>>>> \frac{R_2^A+R_2^B+k_{\textrm{EX}}}{2}-\frac{N_{\textrm{CYC}}}{T_{\textrm{rel}}}\cosh{}^{-1}(v_{1c}) >>>>>> - \frac{1}{T_{\textrm{rel}}}\ln{\left( \frac{1+y}{2} + >>>>>> \frac{1-y}{2\sqrt{v_{1c}^2-1}}(v_2 + 2k_{\textrm{AB}}p_D )\right)} \\ >>>>>> + = R_{2,\textrm{eff}}^{\textrm{CR72}} - >>>>>> \frac{1}{T_{\textrm{rel}}}\ln{\left( \frac{1+y}{2} + >>>>>> \frac{1-y}{2\sqrt{v_{1c}^2-1}}(v_2 + 2k_{\textrm{AB}}p_D )\right)} , >>>>>> +\end{equation} >>>>>> + >>>>>> +where >>>>>> +\begin{equation} >>>>>> + v_{1c} = >>>>>> F_0\cosh{\left(\tau_{\textrm{CP}}E_0\right)}-F_2\cosh{\left(\tau_{\textrm{CP}}E_2\right)} >>>>>> \\ >>>>>> + v_{1s} = >>>>>> F_0\sinh{\left(\tau_{\textrm{CP}}E_0\right)}-F_2\sinh{\left(\tau_{\textrm{CP}}E_2\right)} >>>>>> \\ >>>>>> + v_{2}N = v_{1s}\left(O_B-O_A\right)+4O_B F_1^a >>>>>> \sinh{\left(\tau_{\textrm{CP}}E_1\right)} \\ >>>>>> + p_D N = v_{1s} + >>>>>> \left(F_1^a+F_1^b\right)\sinh{\left(\tau_{\textrm{CP}}E_1\right)}\\ >>>>>> + v_3 = \left( v_2^2 + 4 k_{\textrm{BA}} k_{\textrm{AB}} p_D^2 >>>>>> \right)^{1/2} \\ >>>>>> + y = \left( \frac{v_{1c}-v_3}{v_{1c}+v_3} >>>>>> \right)^{N_{\textrm{CYC}}} >>>>>> +\end{equation} >>>>>> + >>>>>> +The advantage of this code will be that you will always get the right >>>>>> answer provided you got 2-site exchange, in-phase magnetisation and >>>>>> on-resonance pulses. >>>>>> + >>>>>> +The term $$p_D$$ is based on product of the off diagonal elements in >>>>>> the CPMG propagator (Supplementary Section 3, \citet{Baldwin2014}). >>>>>> + >>>>>> +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 >>>>>> + >>>>>> +\begin{equation} >>>>>> + \sqrt{v_{1c}^2-1} \approx v_2 + 2k_{\textrm{AB}}p_D >>>>>> +\end{equation} >>>>>> + >>>>>> +This occurs when $$k_{\textrm{AB}}p_D$$ tends to zero, and so >>>>>> $$v_2=v_3$$. >>>>>> +Setting $$k_{\textrm{AB}}p_D$$ 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 $$p_A \gg p_B$$. >>>>>> +In practise, significant deviations from the Carver Richards equation >>>>>> can be incurred if $$p_B > 1\%$$. >>>>>> +Incorporation of the correction term, results in an improved >>>>>> description of the CPMG experiment over the Carver Richards equation >>>>>> \citet{CarverRichards72}. >>>>>> + >>>>>> +The reference for this equation is: >>>>>> +\begin{itemize} >>>>>> + \item \bibentry{Baldwin2014} >>>>>> +\end{itemize} >>>>>> + >>>>>> +More information about the B14 full model is available from: >>>>>> +\begin{itemize} >>>>>> + \item the relax wiki at \url{http://wiki.nmr-relax.com/B14\_full}, >>>>>> + \item the API documentation at >>>>>> \url{http://www.nmr-relax.com/api/3.1/lib.dispersion.B14-module.html}, >>>>>> + \item the relaxation dispersion page of the relax website at >>>>>> \url{http://www.nmr-relax.com/analyses/relaxation\_dispersion.html#B14\_full}. >>>>>> +\end{itemize} >>>>>> + >>>>>> + >>>>>> +% B14 model. >>>>>> +%~~~~~~~~~~~~ >>>>>> + >>>>>> +\subsection{The reduced B14 2-site CPMG model} >>>>>> +\label{sect: dispersion: B14 model} >>>>>> +\index{relaxation dispersion!B14 model|textbf} >>>>>> + >>>>>> +This is the model for 2-site exchange exact analytical derivation on >>>>>> all time scales (with the constraint that $\pA > \pB$), named after >>>>>> \citet{Baldwin2014}. >>>>>> +It is selected by setting the model to `B14'. >>>>>> +It is the same as the full B14 model described above, but with the >>>>>> simplification that $\RtwozeroA = \RtwozeroB$. >>>>>> + >>>>>> +More information about the B14 model is available from: >>>>>> +\begin{itemize} >>>>>> + \item the relax wiki at \url{http://wiki.nmr-relax.com/B14}, >>>>>> + \item the API documentation at >>>>>> \url{http://www.nmr-relax.com/api/3.1/lib.dispersion.B14-module.html}, >>>>>> + \item the relaxation dispersion page of the relax website at >>>>>> \url{http://www.nmr-relax.com/analyses/relaxation\_dispersion.html#B14}. >>>>>> +\end{itemize} >>>>>> >>>>>> >>>>>> % The numeric CPMG models. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >> >> _______________________________________________ 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
