Author: tlinnet
Date: Wed Jun 18 19:01:24 2014
New Revision: 24121
URL: http://svn.gna.org/viewcvs/relax?rev=24121&view=rev
Log:
Moved the parameter conversion for r1rho 3site into lib 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_3site.py
branches/disp_spin_speed/target_functions/relax_disp.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=24121&r1=24120&r2=24121&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py Wed Jun 18
19:01:24 2014
@@ -65,7 +65,7 @@
from lib.linear_algebra.matrix_exponential import matrix_exponential
-def ns_r1rho_3site(M0=None, matrix=None, r1rho_prime=None, omega=None,
offset=None, r1=0.0, pA=None, pB=None, pC=None, dw_AB=None, dw_AC=None,
k_AB=None, k_BA=None, k_BC=None, k_CB=None, k_AC=None, k_CA=None,
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None,
num_points=None):
+def ns_r1rho_3site(M0=None, matrix=None, r1rho_prime=None, omega=None,
offset=None, r1=0.0, pA=None, pB=None, dw_AB=None, dw_AC=None, kex_AB=None,
kex_BC=None, kex_AC=None, spin_lock_fields=None, relax_time=None,
inv_relax_time=None, back_calc=None, num_points=None):
"""The 3-site numerical solution to the Bloch-McConnell equation for
R1rho data.
This function calculates and stores the R1rho values.
@@ -87,24 +87,16 @@
@type pA: float
@keyword pB: The population of state B.
@type pB: float
- @keyword pC: The population of state C.
- @type pC: float
@keyword dw_AB: The chemical exchange difference between
states A and B in rad/s.
@type dw_AB: numpy float array of rank [NS][NM][NO][ND]
@keyword dw_AC: The chemical exchange difference between
states A and C in rad/s.
@type dw_AC: numpy float array of rank [NS][NM][NO][ND]
- @keyword k_AB: The rate of exchange from site A to B
(rad/s).
- @type k_AB: float
- @keyword k_BA: The rate of exchange from site B to A
(rad/s).
- @type k_BA: float
- @keyword k_BC: The rate of exchange from site B to C
(rad/s).
- @type k_BC: float
- @keyword k_CB: The rate of exchange from site C to B
(rad/s).
- @type k_CB: float
- @keyword k_AC: The rate of exchange from site A to C
(rad/s).
- @type k_AC: float
- @keyword k_CA: The rate of exchange from site C to A
(rad/s).
- @type k_CA: float
+ @keyword kex_AB: The exchange rate between sites A and B for
3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1)
+ @type kex_AB: float
+ @keyword kex_BC: The exchange rate between sites A and C for
3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1)
+ @type kex_BC: float
+ @keyword kex_AC: The exchange rate between sites B and C for
3-site exchange with kex_BC = k_BC + k_CB (rad.s^-1)
+ @type kex_AC: float
@keyword spin_lock_fields: The R1rho spin-lock field strengths (in
rad.s^-1).
@type spin_lock_fields: numpy float array of rank [NS][NM][NO][ND]
@keyword relax_time: The total relaxation time period for each
spin-lock field strength (in seconds).
@@ -116,6 +108,18 @@
@keyword num_points: The number of points on the dispersion
curve, equal to the length of the tcp and back_calc arguments.
@type num_points: numpy int array of rank [NS][NM][NO]
"""
+
+ # Once off parameter conversions.
+ pC = 1.0 - pA - pB
+ pA_pB = pA + pB
+ pA_pC = pA + pC
+ pB_pC = pB + pC
+ k_BA = pA * kex_AB / pA_pB
+ k_AB = pB * kex_AB / pA_pB
+ k_CB = pB * kex_BC / pB_pC
+ k_BC = pC * kex_BC / pB_pC
+ k_CA = pA * kex_AC / pA_pC
+ k_AC = pC * kex_AC / pA_pC
# Extract shape of experiment.
NE, NS, NM, NO = num_points.shape
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=24121&r1=24120&r2=24121&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18
19:01:24 2014
@@ -765,16 +765,6 @@
"""
# Once off parameter conversions.
- pC = 1.0 - pA - pB
- pA_pB = pA + pB
- pA_pC = pA + pC
- pB_pC = pB + pC
- k_BA = pA * kex_AB / pA_pB
- k_AB = pB * kex_AB / pA_pB
- k_CB = pB * kex_BC / pB_pC
- k_BC = pC * kex_BC / pB_pC
- k_CA = pA * kex_AC / pA_pC
- k_AC = pC * kex_AC / pA_pC
dw_AC = dw_AB + dw_BC
# Convert dw from ppm to rad/s. Use the out argument, to pass
directly to structure.
@@ -785,7 +775,7 @@
self.r20_struct[:] = multiply.outer( r1rho_prime.reshape(self.NE,
self.NS, self.NM), self.no_nd_ones )
# Back calculate the R2eff values for each experiment type.
- ns_r1rho_3site(M0=self.M0, matrix=self.matrix,
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset,
r1=self.r1, pA=pA, pB=pB, pC=pC, dw_AB=self.dw_AB_struct,
dw_AC=self.dw_AC_struct, k_AB=k_AB, k_BA=k_BA, k_BC=k_BC, k_CB=k_CB,
k_AC=k_AC, k_CA=k_CA, spin_lock_fields=self.spin_lock_omega1,
relax_time=self.relax_times, inv_relax_time=self.inv_relax_times,
back_calc=self.back_calc, num_points=self.num_disp_points)
+ ns_r1rho_3site(M0=self.M0, matrix=self.matrix,
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset,
r1=self.r1, pA=pA, pB=pB, dw_AB=self.dw_AB_struct, dw_AC=self.dw_AC_struct,
kex_AB=kex_AB, kex_BC=kex_BC, kex_AC=kex_AC,
spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times,
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc,
num_points=self.num_disp_points)
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc = self.back_calc*self.disp_struct
r24121 - in /branches/disp_spin_speed: lib/dispersion/ns_r1rho_3site.py target_functions/relax_disp.py