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, <tlinnet@xxxxxxxxxxxxx> 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
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Re: r23963 - /branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py