Author: tlinnet Date: Mon May 19 14:44:10 2014 New Revision: 23239 URL: http://svn.gna.org/viewcvs/relax?rev=23239&view=rev Log: Math-domain catching for model B14.
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 To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.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/b14.py branches/disp_speed/target_functions/relax_disp.py Modified: branches/disp_speed/lib/dispersion/b14.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/b14.py?rev=23239&r1=23238&r2=23239&view=diff ============================================================================== --- branches/disp_speed/lib/dispersion/b14.py (original) +++ branches/disp_speed/lib/dispersion/b14.py Mon May 19 14:44:10 2014 @@ -110,12 +110,12 @@ """ # Python module imports. -from numpy import arccosh, array, cos, cosh, isfinite, log, power, sin, sinh, sqrt, sum +from numpy import abs, arccosh, array, cos, cosh, isfinite, log, min, power, sin, sinh, sqrt, sum # Repetitive calculations (to speed up calculations). g_fact = 1/sqrt(2) -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): +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, num_points=None): """Calculate the R2eff values for the CR72 model. See the module docstring for details. @@ -143,9 +143,7 @@ @type inv_tcpmg: float @keyword tcp: The tau_CPMG times (1 / 4.nu1). @type tcp: 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 """ @@ -215,12 +213,24 @@ # Real. The v_1c in paper. v1c = F0 * cosh(E0) - F2 * cos(E2) + # Catch math domain error of sqrt(neg val). + # This is when abs(v1c) =< 1. + if min(abs(v1c)) <= 1.: + R2eff = array([1e100]*num_points) + return R2eff + # Exact result for v2v3. v3 = sqrt(v1c**2 - 1.) y = power( (v1c - v3) / (v1c + v3), ncyc) Tog = 0.5 * (1. + y) + (1. - y) * v5 / (2. * v3 * N ) + + # Catch math domain error of log(neg val or zero). + # This is when Tog.real =< 0. + if min(Tog.real) <= 0.: + R2eff = array([1e100]*num_points) + return R2eff ## -1/Trel * log(LpreDyn). # Rpre = (r20a + r20b + kex) / 2.0 @@ -240,6 +250,4 @@ 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=23239&r1=23238&r2=23239&view=diff ============================================================================== --- branches/disp_speed/target_functions/relax_disp.py (original) +++ branches/disp_speed/target_functions/relax_disp.py Mon May 19 14:44:10 2014 @@ -439,7 +439,7 @@ aliased_dw = dw_frq # Back calculate the R2eff values. - r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, pB=pB, dw=aliased_dw, 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]) + self.back_calc[ei][si][mi][0] = r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, pB=pB, dw=aliased_dw, 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], 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]): _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@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
