Author: tlinnet
Date: Wed Jun 18 17:52:07 2014
New Revision: 24114
URL: http://svn.gna.org/viewcvs/relax?rev=24114&view=rev
Log:
Moved the paramter conversions of k_AB, k_BA and pB into lib function of NS
MMQ 2site.
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_mmq_2site.py
branches/disp_spin_speed/target_functions/relax_disp.py
Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24114&r1=24113&r2=24114&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Wed Jun 18
17:52:07 2014
@@ -83,7 +83,7 @@
matrix[1, 1] = -k_BA + 1.j*dw - R20B
-def r2eff_ns_mmq_2site_mq(M0=None, F_vector=array([1, 0], float64), m1=None,
m2=None, R20A=None, R20B=None, pA=None, pB=None, dw=None, dwH=None,
k_AB=None, k_BA=None, inv_tcpmg=None, tcp=None, back_calc=None,
num_points=None, power=None):
+def r2eff_ns_mmq_2site_mq(M0=None, F_vector=array([1, 0], float64), m1=None,
m2=None, R20A=None, R20B=None, pA=None, dw=None, dwH=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 for MQ
data.
The notation used here comes from:
@@ -111,16 +111,12 @@
@type R20B: numpy float array of rank [NS][NM][NO][ND]
@keyword pA: The population of state A.
@type pA: float
- @keyword pB: The population of state B.
- @type pB: float
@keyword dw: The chemical exchange difference between states
A and B in rad/s.
@type dw: numpy float array of rank [NS][NM][NO][ND]
@keyword dwH: The proton chemical exchange difference between
states A and B in rad/s.
@type dwH: 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 kex: The kex parameter value (the exchange rate in
rad/s).
+ @type kex: float
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
@type inv_tcpmg: numpy float array of rank [NS][NM][NO][ND]
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@@ -133,6 +129,15 @@
@type power: numpy int array of rank [NS][NM][NO][ND]
"""
+ # Once off parameter conversions.
+ pB = 1.0 - pA
+ k_BA = pA * kex
+ k_AB = pB * kex
+
+ # This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
+ M0[0] = pA
+ M0[1] = pB
+
# Extract shape of experiment.
NS, NM, NO = num_points.shape
@@ -236,7 +241,7 @@
back_calc[si, mi, oi, i]= -inv_tcpmg[si, mi, oi, i]
* log(Mx / pA)
-def r2eff_ns_mmq_2site_sq_dq_zq(M0=None, F_vector=array([1, 0], float64),
m1=None, m2=None, R20A=None, R20B=None, pA=None, pB=None, dw=None, dwH=None,
k_AB=None, k_BA=None, inv_tcpmg=None, tcp=None, back_calc=None,
num_points=None, power=None):
+def r2eff_ns_mmq_2site_sq_dq_zq(M0=None, F_vector=array([1, 0], float64),
m1=None, m2=None, R20A=None, R20B=None, pA=None, dw=None, dwH=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 for SQ,
ZQ, and DQ data.
The notation used here comes from:
@@ -260,16 +265,12 @@
@type R20B: numpy float array of rank [NS][NM][NO][ND]
@keyword pA: The population of state A.
@type pA: float
- @keyword pB: The population of state B.
- @type pB: float
@keyword dw: The combined chemical exchange difference
between states A and B in rad/s. It should be set to dwH for 1H SQ data, dw
for heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
@type dw: numpy float array of rank [NS][NM][NO][ND]
@keyword dwH: Unused - this is simply to match the
r2eff_ns_mmq_2site_mq() function arguments.
@type dwH: 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 kex: The kex parameter value (the exchange rate in
rad/s).
+ @type kex: float
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
@type inv_tcpmg: numpy float array of rank [NS][NM][NO][ND]
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@@ -282,6 +283,14 @@
@type power: numpy int array of rank [NS][NM][NO][ND]
"""
+ # Once off parameter conversions.
+ pB = 1.0 - pA
+ k_BA = pA * kex
+ k_AB = pB * kex
+
+ # This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
+ M0[0] = pA
+ M0[1] = pB
# Extract shape of experiment.
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=24114&r1=24113&r2=24114&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18
17:52:07 2014
@@ -1497,20 +1497,11 @@
pA = params[self.end_index[2]]
kex = params[self.end_index[2]+1]
- # Once off parameter conversions.
- pB = 1.0 - pA
- k_BA = pA * kex
- k_AB = pB * kex
-
multiply( multiply.outer( dw.reshape(1, self.NS), self.nm_no_nd_ones
), self.frqs, out=self.dw_struct )
multiply( multiply.outer( dwH.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs_H, out=self.dwH_struct )
# Reshape R20 to per experiment, spin and frequency.
self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS,
self.NM), self.no_nd_ones )
-
- # This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
- self.M0[0] = pA
- self.M0[1] = pB
# Initialise.
chi2_sum = 0.0
@@ -1540,7 +1531,7 @@
aliased_dwH = dw_frq
# Back calculate the R2eff values for each experiment type.
- self.r2eff_ns_mmq[ei](M0=self.M0, m1=self.m1, m2=self.m2,
R20A=r20, R20B=r20, pA=pA, pB=pB, dw=aliased_dw, dwH=aliased_dwH, k_AB=k_AB,
k_BA=k_BA, inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei],
back_calc=self.back_calc[ei], num_points=self.num_disp_points[ei],
power=self.power[ei])
+ self.r2eff_ns_mmq[ei](M0=self.M0, m1=self.m1, m2=self.m2,
R20A=r20, R20B=r20, pA=pA, dw=aliased_dw, dwH=aliased_dwH, kex=kex,
inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei],
back_calc=self.back_calc[ei], num_points=self.num_disp_points[ei],
power=self.power[ei])
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc = self.back_calc*self.disp_struct
r24114 - in /branches/disp_spin_speed: lib/dispersion/ns_mmq_2site.py target_functions/relax_disp.py