Author: tlinnet Date: Tue Jun 24 14:58:07 2014 New Revision: 24280 URL: http://svn.gna.org/viewcvs/relax?rev=24280&view=rev Log: Speeded up model NS CPMG 2site star, by moving the forming of the propagator matrix out of the for loops, and preform it. 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_star.py Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py?rev=24280&r1=24279&r2=24280&view=diff ============================================================================== --- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py (original) +++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py Tue Jun 24 14:58:07 2014 @@ -57,7 +57,7 @@ """ # Python module imports. -from numpy import add, array, conj, dot, fabs, float64, isfinite, log, min, multiply, sum +from numpy import add, array, conj, dot, einsum, fabs, float64, isfinite, log, min, multiply, sum from numpy.ma import fix_invalid, masked_where # relax module imports. @@ -221,8 +221,15 @@ # The matrix R that contains all the contributions to the evolution, i.e. relaxation, exchange and chemical shift evolution. R_mat, cR2_mat, Rr_mat, Rex_mat, RCS_mat = rcpmg_star_rankN(R2A=r20a, R2B=r20b, dw=dw, k_AB=k_AB, k_BA=k_BA, tcp=tcp) + # The the essential evolution matrix. + # This matrix is a propagator that will evolve the magnetization with the matrix R for a delay tcp. eR_mat = matrix_exponential_rank_NE_NS_NM_NO_ND_x_x(R_mat) ecR2_mat = matrix_exponential_rank_NE_NS_NM_NO_ND_x_x(cR2_mat) + + # Preform the matrix. + # This is the propagator for an element of [delay tcp; 180 deg pulse; 2 times delay tcp; 180 deg pulse; delay tau], i.e. for 2 times tau-180-tau. + prop_2_mat = evolution_matrix_mat = einsum('...ij,...jk', eR_mat, ecR2_mat) + prop_2_mat = evolution_matrix_mat = einsum('...ij,...jk', prop_2_mat, eR_mat) # Loop over the spins for si in range(NS): @@ -236,16 +243,11 @@ # Extract the values from the higher dimensional arrays. power_si_mi_di = int(power[0, si, mi, 0, di]) - # This matrix is a propagator that will evolve the magnetization with the matrix R for a delay tcp. - eR_tcp = eR_mat[0, si, mi, 0, di] - ecR2_tcp = ecR2_mat[0, si, mi, 0, di] - # This is the propagator for an element of [delay tcp; 180 deg pulse; 2 times delay tcp; 180 deg pulse; delay tau], i.e. for 2 times tau-180-tau. - prop_2 = dot(eR_tcp, ecR2_tcp) - prop_2 = dot(prop_2, eR_tcp) + prop_2_i = prop_2_mat[0, si, mi, 0, di] # Now create the total propagator that will evolve the magnetization under the CPMG train, i.e. it applies the above tau-180-tau-tau-180-tau so many times as required for the CPMG frequency under consideration. - prop_total = square_matrix_power(prop_2, power_si_mi_di) + prop_total = square_matrix_power(prop_2_i, power_si_mi_di) # Now we apply the above propagator to the initial magnetization vector - resulting in the magnetization that remains after the full CPMG pulse train. It is called M of t (t is the time after the CPMG train). Moft = dot(prop_total, M0)