Hi Ed. I can see that you are pushing for this.
It wont work! 2014-06-15 16:12 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > In this change, only in one line have you used the numpy.dot() out > argument: > > + dot(Rexpo, r180x, evolution_matrix) > > So it must be working. You can do this for all others, replacing: > > - evolution_matrix = dot(evolution_matrix, Rexpo) > + dot(evolution_matrix, Rexpo, evolution_matrix) > > and: > > - evolution_matrix = dot(evolution_matrix, evolution_matrix) > + dot(evolution_matrix, evolution_matrix, evolution_matrix) > > and: > > - Mint = evolution_matrix.dot(Mint) > + dot(evolution_matrix, Mint, Mint) > > This should give an observable speed increase of 2 or more. > > Regards, > > Edward > > > On 15 June 2014 15:15, <[email protected]> wrote: > > Author: tlinnet > > Date: Sun Jun 15 15:15:23 2014 > > New Revision: 23963 > > > > URL: http://svn.gna.org/viewcvs/relax?rev=23963&view=rev > > Log: > > Made the dot evolution structure faster for NS CPMG 2site 3D. > > > > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of > dispersion models for Clustered analysis. > > > > Modified: > > branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py > > > > Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py > > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=23963&r1=23962&r2=23963&view=diff > > > ============================================================================== > > --- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py > (original) > > +++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py Sun Jun > 15 15:15:23 2014 > > @@ -54,7 +54,7 @@ > > """ > > > > # Python module imports. > > -from numpy import dot, fabs, isfinite, log, min, sum > > +from numpy import asarray, dot, fabs, isfinite, log, min, sum > > from numpy.ma import fix_invalid, masked_where > > > > > > @@ -141,6 +141,9 @@ > > # The matrix R that contains all the contributions to the > evolution, i.e. relaxation, exchange and chemical shift evolution. > > R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=R2A_si_mi, > R2B=R2B_si_mi, pA=pA, pB=pB, dw=dw_si_mi, k_AB=k_AB, k_BA=k_BA) > > > > + # The essential evolution matrix. This initialises the > structure. > > + evolution_matrix = asarray(R) * 0.0 > > + > > # Loop over the time points, back calculating the R2eff > values. > > for di in range(num_points_si_mi): > > # Extract the values from the higher dimensional arrays. > > @@ -155,12 +158,18 @@ > > # This matrix is a propagator that will evolve the > magnetization with the matrix R for a delay tcp. > > Rexpo = matrix_exponential(R*tcp_si_mi_di) > > > > - # Temp matrix. > > - t_mat = > Rexpo.dot(r180x).dot(Rexpo).dot(Rexpo).dot(r180x).dot(Rexpo).dot(Rexpo).dot(r180x).dot(Rexpo).dot(Rexpo).dot(r180x).dot(Rexpo) > > + # The essential evolution matrix. > > + # This is the first round. > > + dot(Rexpo, r180x, evolution_matrix) > > + evolution_matrix = dot(evolution_matrix, Rexpo) > > + # The second round. > > + evolution_matrix = dot(evolution_matrix, > evolution_matrix) > > + # The third and fourth round, > > + evolution_matrix = dot(evolution_matrix, > evolution_matrix) > > > > # Loop over the CPMG elements, propagating the > magnetisation. > > for j in range(power_si_mi_di/2): > > - Mint = t_mat.dot(Mint) > > + Mint = evolution_matrix.dot(Mint) > > > > # The next lines calculate the R2eff using a two-point > approximation, i.e. assuming that the decay is mono-exponential. > > Mx = Mint[1] / pA > > > > > > _______________________________________________ > > 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 > _______________________________________________ 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
