If you are interested, there are a tonne of other code optimisations which can be performed. For example k_AB and k_BA are calculated in lib.dispersion.cr72. But this can happen at the start of the target function outside of all the looping. Other dispersion models do this. You can even pre-add them. The pB parameter as well - these only need to be calculated once, not multiple times for each spin system, each experiment type, and each magnetic field strength. r20_kex can also be calculated in the calc_CR72_chi2() method as a numpy array, and then sent in to r2eff_CR72() using the r20_index index. The speed up of the cosh+cos vs. sqrt(sqrt()) suggestion of Andy http://thread.gmane.org/gmane.science.nmr.relax.devel/5410/focus=5448 is rather small compared to these optimisations!
Regards, Edward On 3 May 2014 13:52, Edward d'Auvergne <[email protected]> wrote: > Oh, the text 2^(-3/2) is the most compact for the documentation, and > it separates it from the 1/nu_cpmg part. So I'd prefer to present it > that way for compactness and cleanliness. That can also allow us to > pre-calculate it when the target function is initialised and and send > the value of 0.35355339059327373 into the function instead. That > would remove one exponential operation, again squeezing out a little > speed. As nu_CPMG is fixed, even faster would be to pre-calculate an > array of 2**(-3/2) / nu_CPMG and sent that in instead. That would > really be the maximal optimisation for this part! > > Cheers, > > Edward > > On 3 May 2014 13:45, Edward d'Auvergne <[email protected]> wrote: >> Hi, >> >> The origin of this was exactly what Andy Baldwin said at >> http://thread.gmane.org/gmane.science.nmr.relax.devel/5410/focus=5448 >> - that there are many different tau_CPMG definitions and there is an >> error in one of the equations in the original paper. The code in >> relax is however correct. The eta_scale value should be >> 0.35355339059327373. Feel free to fix the equations in the >> documentation of the wiki, manual and lib.dispersion.cr72 docstring. >> I wrote these before the code was fully tested and hence there is now >> a mismatch. As for using 2.0**(-3.0/2.0) in the code, this is for the >> fastest operation, avoiding the square root. But now that I look at >> it, one mathematical operation can be dropped for speed and the factor >> changed to 2.0**(-1.5). >> >> Cheers, >> >> Edward >> >> >> On 3 May 2014 12:28, Troels Emtekær Linnet <[email protected]> wrote: >>> Dear Edward. >>> >>> I was inspecting the code of model CR72. >>> >>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/lib/dispersion/cr72.py?revision=HEAD >>> >>> This is calculated as: >>> >>> eta_scale = 2.0**(-3.0/2.0) = 0.35 >>> which is: 1 / sqrt(2**3). >>> >>> This differs from the definition in: >>> http://wiki.nmr-relax.com/CR72_full#Equation >>> http://www.nmr-relax.com/manual/full_CR72_2_site_CPMG_model.html >>> http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html >>> >>> where: >>> eta_scale = 2.0**(2/3) = 1.58 >>> which is {3}sqrt(2**2). >>> >>> If I compare to: >>> http://wiki.nmr-relax.com/B14#Equation_compared_to_Carver_Richards_72 >>> (DOI: 10.1016/j.jmr.2014.02.023 , eq 70,) >>> >>> And to, (DOI: 10.1016/S0076-6879(01)39315-1 , eq 25, with the twist >>> that "tcp_Pa is the delay between 180 pulses in the CPMG pulse train", >>> "delay/180/delay/delay/180/delay " so that tcp_Pa = 2xdelay >>> >>> Then really the manual should use: >>> eta_scale = 2.0**(-3/2) >>> or >>> 1 / 2 sqrt(2) >>> >>> _______________________________________________ >>> 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
