Author: tlinnet
Date: Fri Jun 20 19:44:00 2014
New Revision: 24220
URL: http://svn.gna.org/viewcvs/relax?rev=24220&view=rev
Log:
Started using the newly multidimensional 3D exchange matrix.
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_3site.py
Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py?rev=24220&r1=24219&r2=24220&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py Fri Jun 20
19:44:00 2014
@@ -134,48 +134,22 @@
# Loop over offsets:
for oi in range(NO):
# Extract parameters from array.
- omega_i = omega[0, si, mi, oi, 0]
- offset_i = offset[0, si, mi, oi, 0]
- r1_i = r1[0, si, mi, oi, 0]
- dw_AB_i = dw_AB[0, si, mi, oi, 0]
- dw_AC_i = dw_AC[0, si, mi, oi, 0]
-
- r1rho_prime_i = r1rho_prime[0, si, mi, oi]
- spin_lock_fields_i = spin_lock_fields[0, si, mi, oi]
- relax_time_i = relax_time[0, si, mi, oi]
- inv_relax_time_i = inv_relax_time[0, si, mi, oi]
- back_calc_i = back_calc[0, si, mi, oi]
num_points_i = num_points[0, si, mi, oi]
-
- # Repetitive calculations (to speed up calculations).
- Wa = omega_i # Larmor frequency for state A
[s^-1].
- Wb = omega_i + dw_AB_i # Larmor frequency for state B
[s^-1].
- Wc = omega_i + dw_AC_i # Larmor frequency for state C
[s^-1].
- W = pA*Wa + pB*Wb + pC*Wc # Population-averaged Larmor
frequency [s^-1].
- dA = Wa - offset_i # Offset of spin-lock from A.
- dB = Wb - offset_i # Offset of spin-lock from B.
- dC = Wc - offset_i # Offset of spin-lock from C.
- d = W - offset_i # Offset of spin-lock from
population-average.
# Loop over the time points, back calculating the R2eff
values.
for j in range(num_points_i):
- # The matrix that contains all the contributions to the
evolution, i.e. relaxation, exchange and chemical shift evolution.
- rr1rho_3d_3site(matrix=matrix, R1=r1_i,
r1rho_prime=r1rho_prime_i[j], pA=pA, pB=pB, pC=pC, wA=dA, wB=dB, wC=dC,
w1=spin_lock_fields_i[j], k_AB=k_AB, k_BA=k_BA, k_BC=k_BC, k_CB=k_CB,
k_AC=k_AC, k_CA=k_CA)
-
- R_mat_i = R_mat[0, si, mi, oi]
- diff = matrix*relax_time_i[j] - R_mat_i
- if abs(sum(diff)) > 1e-12:
- print abs(sum(diff))
- print asd
-
+ # Offset of spin-lock from A.
+ dA = omega[0, si, mi, oi, j] - offset[0, si, mi, oi, j]
# The following lines rotate the magnetization previous
to spin-lock into the weff frame.
- theta = atan2(spin_lock_fields_i[j], dA)
+ 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.
+ R_mat_j = R_mat[0, si, mi, oi, j]
+
# This matrix is a propagator that will evolve the
magnetization with the matrix R.
- Rexpo = matrix_exponential(matrix*relax_time_i[j])
+ Rexpo = matrix_exponential(R_mat_j)
# Magnetization evolution.
MA = dot(M0, dot(Rexpo, M0))
@@ -184,4 +158,4 @@
if MA <= 0.0 or isNaN(MA):
back_calc[0, si, mi, oi, j] = 1e99
else:
- back_calc[0, si, mi, oi, j]= -inv_relax_time_i[j] *
log(MA)
+ back_calc[0, si, mi, oi, j]= -inv_relax_time[0, si,
mi, oi, j] * log(MA)
r24220 - /branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py