The change looks good. Though this has an additional change - the addition of the looping over experiment types. This should have been a separate commit, or minimally mentioned in the commit message.
Cheers, Edward On 6 May 2014 17:20, <tlin...@nmr-relax.com> wrote: > Author: tlinnet > Date: Tue May 6 17:20:53 2014 > New Revision: 23003 > > URL: http://svn.gna.org/viewcvs/relax?rev=23003&view=rev > Log: > Speed-up. Moved the Repetitive calculations of pB, k_BA and k_AB out of the > library function. > > 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#Debugging > > > Modified: > trunk/lib/dispersion/b14.py > trunk/target_functions/relax_disp.py > > Modified: trunk/lib/dispersion/b14.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=23003&r1=23002&r2=23003&view=diff > ============================================================================== > --- trunk/lib/dispersion/b14.py (original) > +++ trunk/lib/dispersion/b14.py Tue May 6 17:20:53 2014 > @@ -102,7 +102,7 @@ > from numpy import arccosh, cos, cosh, log, sin, sinh, sqrt, power > > > -def r2eff_B14(r20a=None, r20b=None, pA=None, dw=None, kex=None, ncyc=None, > inv_tcpmg=None, tcp=None, back_calc=None, num_points=None): > +def r2eff_B14(r20a=None, r20b=None, pA=None, pB=None, dw=None, kex=None, > k_AB=None, k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None, back_calc=None, > num_points=None): > """Calculate the R2eff values for the CR72 model. > > See the module docstring for details. > @@ -114,10 +114,16 @@ > @type r20b: float > @keyword pA: The population of state A. > @type pA: float > + @keyword pB: The population of state B. > + @type pB: float > @keyword dw: The chemical exchange difference between states > A and B in rad/s. > @type dw: float > @keyword kex: The kex parameter value (the exchange rate in > rad/s). > @type kex: float > + @keyword k_AB: The rate of exchange from site A to B (rad/s). > + @type k_AB: float > + @keyword k_BA: The rate of exchange from site B to A (rad/s). > + @type k_BA: float > @keyword ncyc: The matrix exponential power array. The number > of CPMG blocks. > @type ncyc: numpy int16, rank-1 array > @keyword inv_tcpmg: The inverse of the total duration of the CPMG > element (in inverse seconds). > @@ -130,12 +136,7 @@ > @type num_points: int > """ > > - # The B population. > - pB = 1.0 - pA > - > # Repetitive calculations (to speed up calculations). > - k_BA = pA * kex > - k_AB = pB * kex > dw2 = dw**2 > > ######################################################################### > > Modified: trunk/target_functions/relax_disp.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=23003&r1=23002&r2=23003&view=diff > ============================================================================== > --- trunk/target_functions/relax_disp.py (original) > +++ trunk/target_functions/relax_disp.py Tue May 6 17:20:53 2014 > @@ -786,29 +786,42 @@ > pA = params[self.end_index[2]] > kex = params[self.end_index[2]+1] > > + # Once off parameter conversions. > + pB = 1.0 - pA > + k_BA = pA * kex > + k_AB = pB * kex > + > # 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_frq = dw[si] * self.frqs[0][si][mi] > - > - # Back calculate the R2eff values. > - r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, > dw=dw_frq, kex=kex, ncyc=self.power[0][mi], > inv_tcpmg=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi], > back_calc=self.back_calc[0][si][mi][0], > num_points=self.num_disp_points[0][si][mi][0]) > - > - # 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][0]): > - if self.missing[0][si][mi][0][di]: > - self.back_calc[0][si][mi][0][di] = > self.values[0][si][mi][0][di] > - > - # Calculate and return the chi-squared value. > - chi2_sum += chi2(self.values[0][si][mi][0], > self.back_calc[0][si][mi][0], self.errors[0][si][mi][0]) > + # Loop over the experiment types. > + for ei in range(self.num_exp): > + # 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_frq = dw[si] * self.frqs[ei][si][mi] > + > + # Alias the dw frequency combinations. > + if self.exp_types[ei] == EXP_TYPE_CPMG_SQ: > + aliased_dw = dw_frq > + elif self.exp_types[ei] == EXP_TYPE_CPMG_PROTON_SQ: > + aliased_dw = dw_frq > + > + # Back calculate the R2eff values. > + r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index], > pA=pA, pB=pB, dw=dw_frq, kex=kex, k_AB=k_AB, k_BA=k_BA, > ncyc=self.power[ei][mi], inv_tcpmg=self.inv_relax_times[ei][mi], > tcp=self.tau_cpmg[ei][mi], back_calc=self.back_calc[ei][si][mi][0], > num_points=self.num_disp_points[ei][si][mi][0]) > + > + # 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[ei][si][mi][0]): > + if self.missing[ei][si][mi][0][di]: > + self.back_calc[ei][si][mi][0][di] = > self.values[ei][si][mi][0][di] > + > + # Calculate and return the chi-squared value. > + chi2_sum += chi2(self.values[ei][si][mi][0], > self.back_calc[ei][si][mi][0], self.errors[ei][si][mi][0]) > > # Return the total chi-squared value. > return chi2_sum > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > relax-comm...@gna.org > > 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 relax-devel@gna.org 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
