Hi Troels, Awesome work with all these speed ups!! If you are feeling really adventurous, I'll soon place a hint about an ultimate solution for speed in the thread at http://thread.gmane.org/gmane.science.nmr.relax.devel/5726. The chi2_5D() function and missing data ideas there should already give you some great speed ups as well.
Cheers, Edward On 19 May 2014 03:20, <[email protected]> wrote: > Author: tlinnet > Date: Mon May 19 03:20:53 2014 > New Revision: 23227 > > URL: http://svn.gna.org/viewcvs/relax?rev=23227&view=rev > Log: > Speed-up of model IT99. > > task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models. > > Change in speed is: > test_hansen_cpmg_data_auto_analysis > 9.74s -> 8.330s > > test_hansen_cpmg_data_to_it99 > 4.928s -> 3.138s > > Modified: > branches/disp_speed/lib/dispersion/it99.py > > Modified: branches/disp_speed/lib/dispersion/it99.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/it99.py?rev=23227&r1=23226&r2=23227&view=diff > ============================================================================== > --- branches/disp_speed/lib/dispersion/it99.py (original) > +++ branches/disp_speed/lib/dispersion/it99.py Mon May 19 03:20:53 2014 > @@ -73,7 +73,7 @@ > """ > > # Python module imports. > -from math import sqrt > +from numpy import array, isfinite, sqrt, sum > > > def r2eff_IT99(r20=None, pA=None, pB=None, dw=None, tex=None, > cpmg_frqs=None, back_calc=None, num_points=None): > @@ -109,24 +109,21 @@ > # The numerator. > numer = padw2 * pB * tex > > - # Loop over the time points, back calculating the R2eff values. > + # The effective rotating frame field. > + omega_1eff4 = 2304.0 * cpmg_frqs**4 > + > + # Denominator. > + omega_a2 = sqrt(omega_1eff4 + pa2dw4) > + denom = 1.0 + omega_a2 * tex2 > + > + # R2eff calculation. > + R2eff = r20 + numer / denom > + > + # Catch errors, taking a sum over array is the fastest way to check for > + # +/- inf (infinity) and nan (not a number). > + if not isfinite(sum(R2eff)): > + R2eff = array([1e100]*num_points) > + > + # Parse back the value to update the back_calc class object. > for i in range(num_points): > - # Catch zeros (to avoid pointless mathematical operations). > - if numer == 0.0: > - back_calc[i] = r20 > - continue > - > - # The effective rotating frame field. > - omega_1eff4 = 2304.0 * cpmg_frqs[i]**4 > - > - # Denominator. > - omega_a2 = sqrt(omega_1eff4 + pa2dw4) > - denom = 1.0 + omega_a2 * tex2 > - > - # Avoid divide by zero. > - if denom == 0.0: > - back_calc[i] = 1e100 > - continue > - > - # R2eff calculation. > - back_calc[i] = r20 + numer / denom > + back_calc[i] = R2eff[i] > > > _______________________________________________ > 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
