Hi Troels, For good repository management, you should try to keep separate ideas in separate commits. In this commit you actually have two separate concepts in one commit - the change of the target_functions.relax_disp to lib.dispersion API, and handling of numpy.cosh() overflows. These should really be in two commits. This is important if in the future a better solution is found for the API and we would like to revert one of the two changes.
Cheers, Edward On 19 May 2014 14:44, <[email protected]> wrote: > Author: tlinnet > Date: Mon May 19 14:44:12 2014 > New Revision: 23240 > > URL: http://svn.gna.org/viewcvs/relax?rev=23240&view=rev > Log: > Math-domain catching for model CR72. > > task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models. > > This is to implement catching of math domain errors, before they occur. > These can be found via the --numpy-raise function to the systemtests. > > To make the code look clean, the class object "back_calc" is no longer > being updated per time point, but is updated in the relax_disp target > function in > one go. > > Modified: > branches/disp_speed/lib/dispersion/cr72.py > branches/disp_speed/target_functions/relax_disp.py > > Modified: branches/disp_speed/lib/dispersion/cr72.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/cr72.py?rev=23240&r1=23239&r2=23240&view=diff > ============================================================================== > --- branches/disp_speed/lib/dispersion/cr72.py (original) > +++ branches/disp_speed/lib/dispersion/cr72.py Mon May 19 14:44:12 2014 > @@ -92,12 +92,12 @@ > """ > > # Python module imports. > -from numpy import arccosh, array, cos, cosh, isfinite, sqrt, sum > +from numpy import arccosh, array, cos, cosh, isfinite, max, sqrt, sum > > # Repetitive calculations (to speed up calculations). > eta_scale = 2.0**(-3.0/2.0) > > -def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, > cpmg_frqs=None, back_calc=None, num_points=None): > +def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, > cpmg_frqs=None, num_points=None): > """Calculate the R2eff values for the CR72 model. > > See the module docstring for details. > @@ -115,9 +115,7 @@ > @type kex: float > @keyword cpmg_frqs: The CPMG nu1 frequencies. > @type cpmg_frqs: numpy rank-1 float array > - @keyword back_calc: The array for holding the back calculated R2eff > values. Each element corresponds to one of the CPMG nu1 frequencies. > - @type back_calc: numpy rank-1 float array > - @keyword num_points: The number of points on the dispersion curve, > equal to the length of the cpmg_frqs and back_calc arguments. > + @keyword num_points: The number of points on the dispersion curve, > equal to the length of the cpmg_frqs. > @type num_points: int > """ > > @@ -151,6 +149,14 @@ > etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs > etaneg = eta_scale * sqrt(-Psi + sqrt_psi2_zeta2) / cpmg_frqs > > + # Catch math domain error of cosh(val > 710). > + # This is when etapos > 710. > + if num_points > 0: > + if max(etapos) > 700: > + R2eff = array([1e100]*num_points) > + > + return R2eff > + > # Calculate R2eff. > R2eff = r20_kex - cpmg_frqs * arccosh( Dpos * cosh(etapos) - Dneg * > cos(etaneg) ) > > @@ -159,6 +165,4 @@ > 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): > - back_calc[i] = R2eff[i] > + return R2eff > > Modified: branches/disp_speed/target_functions/relax_disp.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_speed/target_functions/relax_disp.py?rev=23240&r1=23239&r2=23240&view=diff > ============================================================================== > --- branches/disp_speed/target_functions/relax_disp.py (original) > +++ branches/disp_speed/target_functions/relax_disp.py Mon May 19 14:44:12 > 2014 > @@ -484,7 +484,7 @@ > dw_frq = dw[si] * self.frqs[0][si][mi] > > # Back calculate the R2eff values. > - r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], > pA=pA, dw=dw_frq, kex=kex, cpmg_frqs=self.cpmg_frqs[0][mi][0], > back_calc=self.back_calc[0][si][mi][0], > num_points=self.num_disp_points[0][si][mi][0]) > + self.back_calc[0][si][mi][0] = > r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, dw=dw_frq, > kex=kex, cpmg_frqs=self.cpmg_frqs[0][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]): > > > _______________________________________________ > 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
