Author: bugman
Date: Mon Nov 18 13:26:01 2013
New Revision: 21500
URL: http://svn.gna.org/viewcvs/relax?rev=21500&view=rev
Log:
The r2eff_mmq_*() functions of lib.dispersion.mmq_2site now accept different
R20A and R20B arguments.
These are set to the same thing within the dispersion target function.
Modified:
branches/relax_disp/lib/dispersion/mmq_2site.py
branches/relax_disp/target_functions/relax_disp.py
Modified: branches/relax_disp/lib/dispersion/mmq_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/mmq_2site.py?rev=21500&r1=21499&r2=21500&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/mmq_2site.py (original)
+++ branches/relax_disp/lib/dispersion/mmq_2site.py Mon Nov 18 13:26:01 2013
@@ -62,7 +62,7 @@
matrix[1, 1] = -k_BA + 1.j*dw - R20B
-def r2eff_mmq_2site_mq(M0=None, m1=None, m2=None, r20=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, n=None):
+def r2eff_mmq_2site_mq(M0=None, 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, n=None):
"""The 2-site numerical solution to the Bloch-McConnell equation for MQ
data.
The notation used here comes from:
@@ -84,8 +84,10 @@
@type m1: numpy rank-2, 2D complex64 array
@keyword m2: A complex numpy matrix to be populated.
@type m2: numpy rank-2, 2D complex64 array
- @keyword r20: The R2 value in the absence of exchange.
- @type r20: float
+ @keyword R20A: The transverse, spin-spin relaxation rate for
state A.
+ @type R20A: float
+ @keyword R20B: The transverse, spin-spin relaxation rate for
state B.
+ @type R20B: float
@keyword pA: The population of state A.
@type pA: float
@keyword pB: The population of state B.
@@ -111,8 +113,8 @@
"""
# Populate the m1 and m2 matrices (only once per function call for
speed).
- populate_matrix(matrix=m1, R20A=r20, R20B=r20, dw=dw+dwH, k_AB=k_AB,
k_BA=k_BA) # D+ matrix component.
- populate_matrix(matrix=m2, R20A=r20, R20B=r20, dw=-dw+dwH, k_AB=k_AB,
k_BA=k_BA) # Z- matrix component.
+ populate_matrix(matrix=m1, R20A=R20A, R20B=R20B, dw=dw+dwH, k_AB=k_AB,
k_BA=k_BA) # D+ matrix component.
+ populate_matrix(matrix=m2, R20A=R20A, R20B=R20B, dw=-dw+dwH, k_AB=k_AB,
k_BA=k_BA) # Z- matrix component.
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
@@ -183,7 +185,7 @@
back_calc[i]= -inv_tcpmg * log(Mx / pA)
-def r2eff_mmq_2site_sq_dq_zq(M0=None, F_vector=array([1, 0], float64),
m1=None, m2=None, r20=None, pA=None, pB=None, dwX=None, k_AB=None, k_BA=None,
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
+def r2eff_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, dwX=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 for SQ,
ZQ, and DQ data.
The notation used here comes from:
@@ -201,8 +203,10 @@
@type m1: numpy rank-2, 2D complex64 array
@keyword m2: A complex numpy matrix to be populated.
@type m2: numpy rank-2, 2D complex64 array
- @keyword r20: The R2 value in the absence of exchange.
- @type r20: float
+ @keyword R20A: The transverse, spin-spin relaxation rate for
state A.
+ @type R20A: float
+ @keyword R20B: The transverse, spin-spin relaxation rate for
state B.
+ @type R20B: float
@keyword pA: The population of state A.
@type pA: float
@keyword pB: The population of state B.
@@ -226,8 +230,8 @@
"""
# Populate the m1 and m2 matrices (only once per function call for
speed).
- populate_matrix(matrix=m1, R20A=r20, R20B=r20, dw=dwX, k_AB=k_AB,
k_BA=k_BA)
- populate_matrix(matrix=m2, R20A=r20, R20B=r20, dw=-dwX, k_AB=k_AB,
k_BA=k_BA)
+ populate_matrix(matrix=m1, R20A=R20A, R20B=R20B, dw=dwX, k_AB=k_AB,
k_BA=k_BA)
+ populate_matrix(matrix=m2, R20A=R20A, R20B=R20B, dw=-dwX, k_AB=k_AB,
k_BA=k_BA)
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
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=21500&r1=21499&r2=21500&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Mon Nov 18 13:26:01
2013
@@ -940,17 +940,17 @@
# Back calculate the R2eff values for each experiment
type.
if self.exp_types[exp_index] == EXP_TYPE_CPMG:
- r2eff_mmq_2site_sq_dq_zq(M0=self.M0, m1=self.m1,
m2=self.m2, r20=R20[r20_index], pA=pA, pB=pB, dwX=dw_frq, k_AB=k_AB,
k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
+ r2eff_mmq_2site_sq_dq_zq(M0=self.M0, m1=self.m1,
m2=self.m2, R20A=R20[r20_index], R20B=R20[r20_index], pA=pA, pB=pB,
dwX=dw_frq, k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
elif self.exp_types[exp_index] ==
EXP_TYPE_PROTON_SQ_CPMG:
- r2eff_mmq_2site_sq_dq_zq(M0=self.M0, m1=self.m1,
m2=self.m2, r20=R20[r20_index], pA=pA, pB=pB, dwX=dwH_frq, k_AB=k_AB,
k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
+ r2eff_mmq_2site_sq_dq_zq(M0=self.M0, m1=self.m1,
m2=self.m2, R20A=R20[r20_index], R20B=R20[r20_index], pA=pA, pB=pB,
dwX=dwH_frq, k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
elif self.exp_types[exp_index] == EXP_TYPE_DQ_CPMG:
- r2eff_mmq_2site_sq_dq_zq(M0=self.M0, m1=self.m1,
m2=self.m2, r20=R20[r20_index], pA=pA, pB=pB, dwX=dwH_frq+dw_frq, k_AB=k_AB,
k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
+ r2eff_mmq_2site_sq_dq_zq(M0=self.M0, m1=self.m1,
m2=self.m2, R20A=R20[r20_index], R20B=R20[r20_index], pA=pA, pB=pB,
dwX=dwH_frq+dw_frq, k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
elif self.exp_types[exp_index] == EXP_TYPE_ZQ_CPMG:
- r2eff_mmq_2site_sq_dq_zq(M0=self.M0, m1=self.m1,
m2=self.m2, r20=R20[r20_index], pA=pA, pB=pB, dwX=dwH_frq-dw_frq, k_AB=k_AB,
k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
+ r2eff_mmq_2site_sq_dq_zq(M0=self.M0, m1=self.m1,
m2=self.m2, R20A=R20[r20_index], R20B=R20[r20_index], pA=pA, pB=pB,
dwX=dwH_frq-dw_frq, k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
power=self.power[exp_index][frq_index])
elif self.exp_types[exp_index] == EXP_TYPE_MQ_CPMG:
- r2eff_mmq_2site_mq(M0=self.M0, m1=self.m1,
m2=self.m2, r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq, dwH=dwH_frq,
k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
n=self.n[exp_index][frq_index])
+ r2eff_mmq_2site_mq(M0=self.M0, m1=self.m1,
m2=self.m2, R20A=R20[r20_index], R20B=R20[r20_index], pA=pA, pB=pB,
dw=dw_frq, dwH=dwH_frq, k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
n=self.n[exp_index][frq_index])
elif self.exp_types[exp_index] ==
EXP_TYPE_PROTON_MQ_CPMG:
- r2eff_mmq_2site_mq(M0=self.M0, m1=self.m1,
m2=self.m2, r20=R20[r20_index], pA=pA, pB=pB, dw=dwH_frq, dwH=dw_frq,
k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
n=self.n[exp_index][frq_index])
+ r2eff_mmq_2site_mq(M0=self.M0, m1=self.m1,
m2=self.m2, R20A=R20[r20_index], R20B=R20[r20_index], pA=pA, pB=pB,
dw=dwH_frq, dwH=dw_frq, k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
n=self.n[exp_index][frq_index])
# 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[exp_index][frq_index]):
r21500 - in /branches/relax_disp: lib/dispersion/mmq_2site.py target_functions/relax_disp.py