It's rather insane, this result! And for your work it'll make quite a difference. The speed ups are huge, now we have to work out how to present it to the relax user community. This is not a suggestion, but it would be interesting to compare the speed of relax now to other dispersion software. I wouldn't be surprised if relax is faster than them all, and for all models.
Regards, Edward On 17 June 2014 20:28, Troels Emtekær Linnet <[email protected]> wrote: > Phoooooowwwwww..... > > This has been one loooooong marathon for a week intensive coding. > > But I am done now! > > A little out of power, but happy with the result! > > Best > Troels > > > > 2014-06-17 19:35 GMT+02:00 Edward d'Auvergne <[email protected]>: >> >> That commit message might be a bit misleading when I present it to all >> relax users. It sounds like the 'NS R1rho 3-site' model is new. You >> have to be a bit more careful what you write, as I present your text >> in all of the relax announcements. >> >> Regards, >> >> Edward >> >> >> >> On 17 June 2014 19:27, <[email protected]> wrote: >> > Author: tlinnet >> > Date: Tue Jun 17 19:27:10 2014 >> > New Revision: 24056 >> > >> > URL: http://svn.gna.org/viewcvs/relax?rev=24056&view=rev >> > Log: >> > Implemented the target function for ns r1rho 3site. >> > >> > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion >> > models for Clustered analysis. >> > >> > Modified: >> > branches/disp_spin_speed/target_functions/relax_disp.py >> > >> > Modified: branches/disp_spin_speed/target_functions/relax_disp.py >> > URL: >> > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24056&r1=24055&r2=24056&view=diff >> > >> > ============================================================================== >> > --- branches/disp_spin_speed/target_functions/relax_disp.py >> > (original) >> > +++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun >> > 17 19:27:10 2014 >> > @@ -784,35 +784,26 @@ >> > k_AC = pC * kex_AC / pA_pC >> > dw_AC = dw_AB + dw_BC >> > >> > - # Initialise. >> > - chi2_sum = 0.0 >> > - >> > - # Loop over the spins. >> > - for si in range(self.num_spins): >> > - # Loop over the spectrometer frequencies. >> > - for mi in range(self.num_frq): >> > - # The R20 index. >> > - r20_index = mi + si*self.num_frq >> > - >> > - # Convert dw from ppm to rad/s. >> > - dw_AB_frq = dw_AB[si] * self.frqs[0, si, mi, 0, 0] >> > - dw_AC_frq = dw_AC[si] * self.frqs[0, si, mi, 0, 0] >> > - >> > - # Loop over the offsets. >> > - for oi in range(self.num_offsets[0, si, mi]): >> > - # Back calculate the R2eff values for each >> > experiment type. >> > - ns_r1rho_3site(M0=self.M0, matrix=self.matrix, >> > r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[0, si, mi, >> > oi, 0], offset=self.offset[0, si, mi, oi, 0], r1=self.r1[0, si, mi, oi, 0], >> > pA=pA, pB=pB, pC=pC, dw_AB=dw_AB_frq, dw_AC=dw_AC_frq, k_AB=k_AB, >> > k_BA=k_BA, >> > k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA, >> > spin_lock_fields=self.spin_lock_omega1[0, si, mi, oi], >> > relax_time=self.relax_times[0, si, mi, oi], >> > inv_relax_time=self.inv_relax_times[0, si, mi, oi], >> > back_calc=self.back_calc[0, si, mi, oi], num_points=self.num_disp_points[0, >> > si, mi, oi]) >> > - >> > - # For all missing data points, set the >> > back-calculated value to the measured values so that it has no effect on >> > the >> > chi-squared value. >> > - for di in range(self.num_disp_points[0, si, mi, >> > oi]): >> > - if self.missing[0, si, mi, oi, di]: >> > - self.back_calc[0, si, mi, oi, di] = >> > self.values[0, si, mi, oi, di] >> > - >> > - # Calculate and return the chi-squared value. >> > - chi2_sum += chi2(self.values[0, si, mi, oi], >> > self.back_calc[0, si, mi, oi], self.errors[0, si, mi, oi]) >> > + # Convert dw from ppm to rad/s. Use the out argument, to pass >> > directly to structure. >> > + multiply( multiply.outer( dw_AB.reshape(1, self.NS), >> > self.nm_no_nd_ones ), self.frqs, out=self.dw_AB_struct ) >> > + multiply( multiply.outer( dw_AC.reshape(1, self.NS), >> > self.nm_no_nd_ones ), self.frqs, out=self.dw_AC_struct ) >> > + >> > + # Reshape R20 to per experiment, spin and frequency. >> > + self.r20_struct[:] = multiply.outer( >> > r1rho_prime.reshape(self.NE, self.NS, self.NM), self.no_nd_ones ) >> > + >> > + # Back calculate the R2eff values for each experiment type. >> > + ns_r1rho_3site(M0=self.M0, matrix=self.matrix, >> > r1rho_prime=self.r20_struct, omega=self.chemical_shifts, >> > offset=self.offset, >> > r1=self.r1, pA=pA, pB=pB, pC=pC, dw_AB=self.dw_AB_struct, >> > dw_AC=self.dw_AC_struct, k_AB=k_AB, k_BA=k_BA, k_BC=k_BC, k_CB=k_CB, >> > k_AC=k_AC, k_CA=k_CA, spin_lock_fields=self.spin_lock_omega1, >> > relax_time=self.relax_times, inv_relax_time=self.inv_relax_times, >> > back_calc=self.back_calc, num_points=self.num_disp_points) >> > + >> > + # Clean the data for all values, which is left over at the end >> > of arrays. >> > + self.back_calc = self.back_calc*self.disp_struct >> > + >> > + ## For all missing data points, set the back-calculated value >> > to the measured values so that it has no effect on the chi-squared value. >> > + if self.has_missing: >> > + # Replace with values. >> > + self.back_calc[self.mask_replace_blank.mask] = >> > self.values[self.mask_replace_blank.mask] >> > >> > # Return the total chi-squared value. >> > - return chi2_sum >> > + return chi2_rankN(self.values, self.back_calc, self.errors) >> > >> > >> > def experiment_type_setup(self): >> > >> > >> > _______________________________________________ >> > 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
