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
