Hi Edward. This wont work.
I need to replace all values in back_calc if just one test is violated. I tried it with the unit tests, but it cannot get solved. Best Troeles 2014-05-27 10:22 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > I have a suggestion for this change too, specifically: > > @@ -123,6 +129,8 @@ > # The next lines calculate the R2eff using a two-point > approximation, i.e. assuming that the decay is mono-exponential. > Mx = fabs(Mint[1] / pA) > if Mx <= 0.0 or isNaN(Mx): > - back_calc[i] = 1e99 > + for i in range(num_points): > + back_calc[i] = r20a > + return > else: > back_calc[i]= -inv_tcpmg * log(Mx) > > Here you have introduced a second loop over the index i inside an > index i loop. This is not the best idea, instead try: > > # The next lines calculate the R2eff using a two-point > approximation, i.e. assuming that the decay is mono-exponential. > Mx = fabs(Mint[1] / pA) > if Mx <= 0.0 or isNaN(Mx): > back_calc[i] = r20a > else: > back_calc[i]= -inv_tcpmg * log(Mx) > > There is no need to return at this point, just let the loop continue > harmlessly. Also, one hint for the commit message would be to explain > why you changed the 1e99 value to r20a. I.e. that when kex is very > large, Mx will be zero, and although the log of zero is not defined, > this is in the 'no Rex' region so it should return r20a rather than > the -1/tcpmg*log(0.0) value of -1/tcpmg*-infinity (which is positive > infinity). This makes me wonder if this numeric model is any good for > large kex values which actually do cause exchange! > > Cheers, > > Edward > > On 27 May 2014 00:08, <[email protected]> wrote: >> Author: tlinnet >> Date: Tue May 27 00:08:08 2014 >> New Revision: 23451 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=23451&view=rev >> Log: >> Critical fix for the math domain catching of model NS CPMG 2site 3D. >> >> This was discovered with the added 8 unit tests demonstrating edge case 'no >> Rex' failures. >> >> This follows from the ideas in the post >> http://article.gmane.org/gmane.science.nmr.relax.devel/5858. >> This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of >> dispersion models. >> >> This is to implement catching of math domain errors, before they occur. >> >> Modified: >> branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py >> >> Modified: branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=23451&r1=23450&r2=23451&view=diff >> ============================================================================== >> --- branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py (original) >> +++ branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py Tue May 27 >> 00:08:08 2014 >> @@ -103,6 +103,12 @@ >> @type power: numpy int16, rank-1 array >> """ >> >> + # Catch parameter values that will result in no exchange, returning >> flat R2eff = R20 lines (when kex = 0.0, k_AB = 0.0). >> + if dw == 0.0 or pA == 1.0 or k_AB == 0.0: >> + for i in range(num_points): >> + back_calc[i] = r20a >> + return >> + >> # The matrix R that contains all the contributions to the evolution, >> i.e. relaxation, exchange and chemical shift evolution. >> R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=r20a, R2B=r20b, pA=pA, pB=pB, >> dw=dw, k_AB=k_AB, k_BA=k_BA) >> >> @@ -123,6 +129,8 @@ >> # The next lines calculate the R2eff using a two-point >> approximation, i.e. assuming that the decay is mono-exponential. >> Mx = fabs(Mint[1] / pA) >> if Mx <= 0.0 or isNaN(Mx): >> - back_calc[i] = 1e99 >> + for i in range(num_points): >> + back_calc[i] = r20a >> + return >> else: >> back_calc[i]= -inv_tcpmg * log(Mx) >> >> >> _______________________________________________ >> 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
