Author: bugman
Date: Wed Jul 17 10:55:10 2013
New Revision: 20344
URL: http://svn.gna.org/viewcvs/relax?rev=20344&view=rev
Log:
Speed ups for the 'NS 2-site 3D' model.
The pi-pulse propagator is created only once upon target function
initialisation rather than for
each function call, each spin cluster, each magnetic field strength, each
dispersion point, and each
CPMG block.
Modified:
branches/relax_disp/lib/dispersion/ns_2site_3d.py
branches/relax_disp/target_functions/relax_disp.py
Modified: branches/relax_disp/lib/dispersion/ns_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/ns_2site_3d.py?rev=20344&r1=20343&r2=20344&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/ns_2site_3d.py (original)
+++ branches/relax_disp/lib/dispersion/ns_2site_3d.py Wed Jul 17 10:55:10 2013
@@ -33,21 +33,24 @@
# Python module imports.
from math import fabs, log
+from numpy import dot
if dep_check.scipy_module:
from scipy.linalg import expm
# relax module imports.
-from lib.dispersion.ns_matrices import r180x_3d, rcpmg_3d
+from lib.dispersion.ns_matrices import rcpmg_3d
-def r2eff_ns_2site_3D(M0=None, r10a=0.0, r10b=0.0, r20a=None, r20b=None,
pA=None, dw=None, k_AB=None, k_BA=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None, power=None):
+def r2eff_ns_2site_3D(r180x=None, M0=None, r10a=0.0, r10b=0.0, r20a=None,
r20b=None, pA=None, dw=None, k_AB=None, k_BA=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None, power=None):
"""The 2-site numerical solution to the Bloch-McConnell equation.
This function calculates and stores the R2eff values.
+ @keyword r180x: The X-axis pi-pulse propagator.
+ @type r180x: numpy float64, rank-2, 7D array
@keyword M0: This is a vector that contains the initial
magnetizations corresponding to the A and B state transverse magnetizations.
- @type M0: numpy float64, rank-1, 2D array
+ @type M0: numpy float64, rank-1, 7D array
@keyword r10a: The R1 value for state A.
@type r10a: float
@keyword r10b: The R1 value for state B.
@@ -89,12 +92,12 @@
# Loop over the CPMG elements, propagating the magnetisation.
for j in range(2*power[i]):
- Mint = Rexpo * Mint
- Mint = r180x_3d() * Mint
- Mint = Rexpo * Mint
+ Mint = dot(Rexpo, Mint)
+ Mint = dot(r180x, Mint)
+ Mint = dot(Rexpo, Mint)
# The next lines calculate the R2eff using a two-point
approximation, i.e. assuming that the decay is mono-exponential.
- Mgx = fabs((Mint[1])/pA)
+ Mgx = fabs(Mint[1] / pA)
if Mgx == 0.0:
back_calc[i] = 1e99
else:
Modified: branches/relax_disp/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=20344&r1=20343&r2=20344&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Wed Jul 17 10:55:10
2013
@@ -35,6 +35,7 @@
from lib.dispersion.m61b import r1rho_M61b
from lib.dispersion.ns_2site_3d import r2eff_ns_2site_3D
from lib.dispersion.ns_2site_star import r2eff_ns_2site_star
+from lib.dispersion.ns_matrices import r180x_3d
from lib.errors import RelaxError
from target_functions.chi2 import chi2
from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_RED, MODEL_DPL94, MODEL_IT99, MODEL_LIST_FULL, MODEL_LM63,
MODEL_M61, MODEL_M61B, MODEL_NOREX, MODEL_NS_2SITE_3D, MODEL_NS_2SITE_STAR,
MODEL_NS_2SITE_STAR_RED, MODEL_R2EFF
@@ -150,6 +151,10 @@
# The matrix that contains all the contributions to the
evolution, i.e. relaxation, exchange and chemical shift evolution.
self.R = zeros((2, 2), complex64)
+ # Pi-pulse propagators.
+ if model in [MODEL_NS_2SITE_3D]:
+ self.r180x = r180x_3d()
+
# This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
if model in [MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]:
self.M0 = zeros(2, float64)
@@ -279,7 +284,7 @@
dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
# Back calculate the R2eff values.
- r2eff_ns_2site_3D(M0=self.M0, r20a=R20A[r20_index],
r20b=R20B[r20_index], pA=pA, dw=dw_frq, k_AB=k_AB, k_BA=k_BA,
inv_tcpmg=self.inv_relax_time, tcp=self.tau_cpmg,
back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points, power=self.power)
+ r2eff_ns_2site_3D(r180x=self.r180x, M0=self.M0,
r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, dw=dw_frq, k_AB=k_AB,
k_BA=k_BA, inv_tcpmg=self.inv_relax_time, tcp=self.tau_cpmg,
back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points, power=self.power)
# For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
for point_index in range(self.num_disp_points):
r20344 - in /branches/relax_disp: lib/dispersion/ns_2site_3d.py target_functions/relax_disp.py