Author: tlinnet
Date: Tue Jun 24 16:35:01 2014
New Revision: 24286
URL: http://svn.gna.org/viewcvs/relax?rev=24286&view=rev
Log:
Speeded up ns r1rho 2site, by preforming the evolution matrices, and the M0
matrix in the init part of the target function.
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_r1rho_2site.py
branches/disp_spin_speed/target_functions/relax_disp.py
Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24286&r1=24285&r2=24286&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py Tue Jun 24
16:35:01 2014
@@ -50,8 +50,7 @@
"""
# Python module imports.
-from math import atan2
-from numpy import array, cos, dot, float64, log, multiply, sin, sum
+from numpy import array, cos, dot, einsum, float64, log, multiply, sin, sum
# relax module imports.
from lib.float import isNaN
@@ -236,6 +235,9 @@
# This matrix is a propagator that will evolve the magnetization with
the matrix R.
Rexpo_mat = matrix_exponential_rank_NE_NS_NM_NO_ND_x_x(R_mat)
+ # Magnetization evolution.
+ Rexpo_M0_mat = einsum('...ij,...jk', Rexpo_mat, M0)
+
# Loop over spins.
for si in range(NS):
# Loop over the spectrometer frequencies.
@@ -245,23 +247,19 @@
# Extract number of points.
num_points_i = num_points[0, si, mi, oi]
- # Repetitive calculations (to speed up calculations).
- # Offset of spin-lock from A.
- dA = omega[0, si, mi, oi, 0] - offset[0, si, mi, oi, 0]
-
# Loop over the time points, back calculating the R2eff
values.
for j in range(num_points_i):
- # The following lines rotate the magnetization
previous to spin-lock into the weff frame.
- theta = atan2(spin_lock_fields[0, si, mi, oi, j], dA)
- M0[0] = sin(theta) # The A state initial X
magnetisation.
- M0[2] = cos(theta) # The A state initial Z
magnetisation.
+ # Extract the preformed matrix that rotate the
magnetization previous to spin-lock into the weff frame.
+ M0_i= M0[0, si, mi, oi, j, :, 0]
# This matrix is a propagator that will evolve the
magnetization with the matrix R.
Rexpo_i = Rexpo_mat[0, si, mi, oi, j]
+ # Extract from the pre-formed Magnetization evolution
matrix.
+ Rexpo_M0_mat_i = Rexpo_M0_mat[0, si, mi, oi, j, :, 0]
+
# Magnetization evolution.
- MA = dot(Rexpo_i, M0)
- MA = dot(M0, MA)
+ MA = dot(M0_i, Rexpo_M0_mat_i)
# The next lines calculate the R1rho using a two-point
approximation, i.e. assuming that the decay is mono-exponential.
if MA <= 0.0 or isNaN(MA):
Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24286&r1=24285&r2=24286&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 24
16:35:01 2014
@@ -27,7 +27,7 @@
# Python module imports.
from copy import deepcopy
from math import pi
-from numpy import add, array, asarray, complex64, dot, float64, int16,
max, multiply, ones, sqrt, sum, tile, zeros
+from numpy import add, array, arctan2, asarray, cos, complex64, dot,
float64, int16, max, multiply, ones, sin, sqrt, sum, tile, zeros
from numpy.ma import masked_equal
# relax module imports.
@@ -404,7 +404,17 @@
self.M0 = zeros(7, float64)
self.M0[0] = 0.5
if model in [MODEL_NS_R1RHO_2SITE]:
- self.M0 = zeros(6, float64)
+ # Offset of spin-lock from A.
+ da_mat = self.chemical_shifts - self.offset
+ # The following lines rotate the magnetization previous to
spin-lock into the weff frame.
+ theta_mat = arctan2(self.spin_lock_omega1, da_mat)
+ M0_0 = zeros([6, 1], float64)
+ M0_0[0, 0] = 1
+ M0_sin = multiply.outer( sin(theta_mat), M0_0 )
+ M0_2 = zeros([6, 1], float64)
+ M0_2[2, 0] = 1
+ M0_cos = multiply.outer( cos(theta_mat), M0_2 )
+ self.M0 = M0_sin + M0_cos
if model in [MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]:
self.M0 = zeros(9, float64)
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Re: r24286 - in /branches/disp_spin_speed: lib/dispersion/ns_r1rho_2site.py target_functions/relax_disp.py