Hi Troels, Unfortunately this one also results in zero speed ups. It is only beneficial if you can shift things to a higher loop level.
Cheers, Edward On 6 May 2014 17:23, <[email protected]> wrote: > Author: tlinnet > Date: Tue May 6 17:23:13 2014 > New Revision: 23006 > > URL: http://svn.gna.org/viewcvs/relax?rev=23006&view=rev > Log: > Moved Carver and Richards (1972) zeta and Psi notation outside library > function. > > sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014) > B14 model - 2-site exact solution model for all time scales. > > Not sure, if this speeds the calculation up. > > 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=23006&r1=23005&r2=23006&view=diff > ============================================================================== > --- trunk/lib/dispersion/b14.py (original) > +++ trunk/lib/dispersion/b14.py Tue May 6 17:23:13 2014 > @@ -102,7 +102,7 @@ > from numpy import arccosh, cos, cosh, log, sin, sinh, sqrt, power > > > -def r2eff_B14(r20a=None, r20b=None, deltaR2=None, alpha_m=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, deltaR2=None, alpha_m=None, pA=None, > pB=None, dw=None, zeta=None, Psi=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. > @@ -122,6 +122,10 @@ > @type pB: float > @keyword dw: The chemical exchange difference between states > A and B in rad/s. > @type dw: float > + @keyword zeta: The Carver and Richards (1972) zeta notation. > zeta = 2 * dw * alpha_m. > + @type zeta: float > + @keyword Psi: The Carver and Richards (1972) Psi notation. Psi > = alpha_m**2 + 4 * k_BA * k_AB - dw**2. > + @type Psi: 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). > @@ -149,10 +153,8 @@ > > ######################################################################### > #get the real and imaginary components of the exchange induced shift > - g1 = 2 * dw * alpha_m #same as carver > richards zeta > - g2 = alpha_m**2 + 4 * k_BA * k_AB - dw2 #same as carver richards psi > - g3 = 1/sqrt(2) * sqrt(g2 + sqrt(g1**2 + g2**2)) #trig faster than > square roots > - g4 = 1/sqrt(2) * sqrt(-g2 + sqrt(g1**2 + g2**2)) #trig faster than > square roots > + g3 = 1/sqrt(2) * sqrt(Psi + sqrt(zeta**2 + Psi**2)) #trig faster than > square roots > + g4 = 1/sqrt(2) * sqrt(-Psi + sqrt(zeta**2 + Psi**2)) #trig faster than > square roots > ######################################################################### > # Repetitive calculations (to speed up calculations). > g32 = g3**2 > @@ -176,7 +178,7 @@ > t2 = (dw + g4) * complex(dw, -g3) / NNc > > # t1 + t2. > - t1pt2 = complex(2 * dw2,g1) / NNc > + t1pt2 = complex(2 * dw2, zeta) / NNc > > # -2 * oG * t2. > oGt2 = complex(-alpha_m - g3, dw - g4) * t2 > > Modified: trunk/target_functions/relax_disp.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=23006&r1=23005&r2=23006&view=diff > ============================================================================== > --- trunk/target_functions/relax_disp.py (original) > +++ trunk/target_functions/relax_disp.py Tue May 6 17:23:13 2014 > @@ -800,15 +800,6 @@ > 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 > - > - # Repetitive calculations (to speed up calculations). > - r20a = R20A[r20_index] > - r20b = R20B[r20_index] > - deltaR2 = r20a - r20b > - alpha_m = deltaR2 + k_AB - k_BA > - > # Convert dw from ppm to rad/s. > dw_frq = dw[si] * self.frqs[ei][si][mi] > > @@ -818,8 +809,21 @@ > elif self.exp_types[ei] == EXP_TYPE_CPMG_PROTON_SQ: > aliased_dw = dw_frq > > + # The R20 index. > + r20_index = mi + si*self.num_frq > + > + # Repetitive calculations (to speed up calculations). > + r20a = R20A[r20_index] > + r20b = R20B[r20_index] > + deltaR2 = r20a - r20b > + > + # The Carver and Richards (1972) alpha_minus short > notation. > + alpha_m = deltaR2 + k_AB - k_BA > + zeta = 2 * aliased_dw * alpha_m > + Psi = alpha_m**2 + 4 * k_BA * k_AB - aliased_dw**2 > + > # Back calculate the R2eff values. > - r2eff_B14(r20a=r20a, r20b=r20b, deltaR2=deltaR2, > alpha_m=alpha_m, 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]) > + r2eff_B14(r20a=r20a, r20b=r20b, deltaR2=deltaR2, > alpha_m=alpha_m, pA=pA, pB=pB, dw=dw_frq, zeta=zeta, Psi=Psi, 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]): > > > _______________________________________________ > 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
