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