Author: tlinnet
Date: Wed Jun 25 02:14:42 2014
New Revision: 24297
URL: http://svn.gna.org/viewcvs/relax?rev=24297&view=rev
Log:
For model NS CPMG 2site 3d, the M0 matrix was preformed for higher
dimensionality in init of target function.
The transposes/rolled axis versions was also initiated.
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
branches/disp_spin_speed/target_functions/relax_disp.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=24297&r1=24296&r2=24297&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 Wed Jun 25
02:14:42 2014
@@ -224,7 +224,7 @@
return c_mat
-def r2eff_ns_cpmg_2site_3D(r180x=None, M0=None, r10a=0.0, r10b=0.0,
r20a=None, r20b=None, pA=None, dw=None, dw_orig=None, kex=None,
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
+def r2eff_ns_cpmg_2site_3D(r180x=None, M0=None, M0_T=None, r10a=0.0,
r10b=0.0, r20a=None, r20b=None, pA=None, dw=None, dw_orig=None, kex=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.
@@ -233,7 +233,9 @@
@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, 7D array
+ @type M0: numpy float array of rank
[NE][NS][NM][NO][ND][7][1]
+ @keyword M0_T: This is a vector that contains the initial
magnetizations corresponding to the A and B state transverse magnetizations,
where the outer two axis has been swapped for efficient dot operations.
+ @type M0_T: numpy float array of rank
[NE][NS][NM][NO][ND][1][7]
@keyword r10a: The R1 value for state A.
@type r10a: float
@keyword r10b: The R1 value for state B.
@@ -281,8 +283,10 @@
k_AB = pB * kex
# This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
- M0[1] = pA
- M0[4] = pB
+ M0_T[:, :, :, :, :, 0, 1] = pA
+ M0_T[:, :, :, :, :, 0, 4] = pB
+ M0[:, :, :, :, :, 1, 0] = pA
+ M0[:, :, :, :, :, 4, 0] = pB
# Extract the total numbers of experiments, number of spins, number of
magnetic field strength, number of offsets, maximum number of dispersion
point.
NE, NS, NM, NO, ND = back_calc.shape
@@ -316,7 +320,7 @@
r20a_si_mi_di = r20a[0, si, mi, 0, di]
# Initial magnetisation.
- Mint_i = M0
+ Mint_i = M0[0, si, mi, 0, di]
# This matrix is a propagator that will evolve the
magnetization with the matrix R for a delay tcp.
evolution_matrix_i = evolution_matrix_mat[0, si, mi, 0, di]
@@ -326,7 +330,7 @@
Mint_i = dot(evolution_matrix_i, Mint_i)
# The next lines calculate the R2eff using a two-point
approximation, i.e. assuming that the decay is mono-exponential.
- Mx = Mint_i[1] / pA
+ Mx = Mint_i[1][0] / pA
if Mx <= 0.0 or isNaN(Mx):
back_calc[0, si, mi, 0, di] = r20a_si_mi_di
else:
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=24297&r1=24296&r2=24297&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 25
02:14:42 2014
@@ -400,8 +400,11 @@
if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]:
self.M0 = zeros(3, float64)
if model in [MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL]:
- self.M0 = zeros(7, float64)
- self.M0[0] = 0.5
+ M0_0 = zeros( [self.NE, self.NS, self.NM, self.NO, self.ND,7,
1], float64)
+ M0_0[:, :, :, :, :, 0, 0] = 0.5
+ self.M0 = M0_0
+ # Transpose M0, to prepare for dot operation. Roll the last axis
one back, corresponds to a transpose for the outer two axis.
+ self.M0_T = rollaxis(self.M0, 6, 5)
if model in [MODEL_NS_R1RHO_2SITE]:
# Offset of spin-lock from A.
da_mat = self.chemical_shifts - self.offset
@@ -596,7 +599,7 @@
self.r20b_struct[:] = multiply.outer( R20B.reshape(self.NE, self.NS,
self.NM), self.no_nd_ones )
# Back calculate the R2eff values.
- r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0,
r20a=self.r20a_struct, r20b=self.r20b_struct, pA=pA, dw=self.dw_struct,
dw_orig=dw, kex=kex, inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg,
back_calc=self.back_calc, num_points=self.num_disp_points, power=self.power)
+ r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0, M0_T=self.M0_T,
r20a=self.r20a_struct, r20b=self.r20b_struct, pA=pA, dw=self.dw_struct,
dw_orig=dw, kex=kex, inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg,
back_calc=self.back_calc, num_points=self.num_disp_points, power=self.power)
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc = self.back_calc*self.disp_struct
r24297 - in /branches/disp_spin_speed: lib/dispersion/ns_cpmg_2site_3d.py target_functions/relax_disp.py