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