Author: bugman
Date: Wed Jul 17 11:09:56 2013
New Revision: 20347
URL: http://svn.gna.org/viewcvs/relax?rev=20347&view=rev
Log:
More changes to the numerical solution dispersion code to match relax's
conventions.
This includes the changes of df->dw, fA->wA, fB->wB, and Mgx->Mx.
Modified:
branches/relax_disp/lib/dispersion/ns_2site_3d.py
branches/relax_disp/lib/dispersion/ns_2site_star.py
branches/relax_disp/target_functions/relax_disp.py
Modified: branches/relax_disp/lib/dispersion/ns_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/ns_2site_3d.py?rev=20347&r1=20346&r2=20347&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/ns_2site_3d.py (original)
+++ branches/relax_disp/lib/dispersion/ns_2site_3d.py Wed Jul 17 11:09:56 2013
@@ -41,7 +41,7 @@
from lib.dispersion.ns_matrices import rcpmg_3d
-def r2eff_ns_2site_3D(r180x=None, M0=None, r10a=0.0, r10b=0.0, r20a=None,
r20b=None, pA=None, dw=None, k_AB=None, k_BA=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None, power=None):
+def r2eff_ns_2site_3D(r180x=None, M0=None, r10a=0.0, r10b=0.0, r20a=None,
r20b=None, pA=None, pB=None, dw=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.
This function calculates and stores the R2eff values.
@@ -61,6 +61,8 @@
@type r20b: float
@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: float
@keyword k_AB: The rate of exchange from site A to B (rad/s).
@@ -80,7 +82,7 @@
"""
# The matrix R that contains all the contributions to the evolution,
i.e. relaxation, exchange and chemical shift evolution.
- R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=r20a, R2B=r20b, df=dw, k_AB=k_AB,
k_BA=k_BA)
+ R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=r20a, R2B=r20b, pA=pA, pB=pB,
dw=dw, k_AB=k_AB, k_BA=k_BA)
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
@@ -97,8 +99,8 @@
Mint = dot(Rexpo, Mint)
# The next lines calculate the R2eff using a two-point
approximation, i.e. assuming that the decay is mono-exponential.
- Mgx = fabs(Mint[1] / pA)
- if Mgx == 0.0:
+ Mx = fabs(Mint[1] / pA)
+ if Mx == 0.0:
back_calc[i] = 1e99
else:
- back_calc[i]= -inv_tcpmg * log(Mgx)
+ back_calc[i]= -inv_tcpmg * log(Mx)
Modified: branches/relax_disp/lib/dispersion/ns_2site_star.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/ns_2site_star.py?rev=20347&r1=20346&r2=20347&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/ns_2site_star.py (original)
+++ branches/relax_disp/lib/dispersion/ns_2site_star.py Wed Jul 17 11:09:56
2013
@@ -39,7 +39,7 @@
from scipy.linalg import expm
-def r2eff_ns_2site_star(Rr=None, Rex=None, RCS=None, R=None, M0=None,
r20a=None, r20b=None, fA=None, inv_tcpmg=None, tcp=None, back_calc=None,
num_points=None, power=None):
+def r2eff_ns_2site_star(Rr=None, Rex=None, RCS=None, R=None, M0=None,
r20a=None, r20b=None, dw=None, inv_tcpmg=None, tcp=None, back_calc=None,
num_points=None, power=None):
"""The 2-site numerical solution to the Bloch-McConnell equation using
complex conjugate matrices.
This function calculates and stores the R2eff values.
@@ -59,8 +59,8 @@
@type r20a: float
@keyword r20b: The R2 value for state B in the absence of
exchange.
@type r20b: float
- @keyword fA: The frequency of state A.
- @type fA: float
+ @keyword dw: The chemical exchange difference between states
A and B in rad/s.
+ @type dw: float
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
@type inv_tcpmg: float
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@@ -77,8 +77,8 @@
Rr[0, 0] = -r20a
Rr[1, 1] = -r20b
- # The matrix that contains the chemical shift evolution. It works here
only with X magnetization, and the complex notation allows to evolve in the
transverse plane (x, y).
- RCS[1, 1] = complex(0.0, -fA)
+ # The matrix that contains the chemical shift evolution. It works here
only with X magnetization, and the complex notation allows to evolve in the
transverse plane (x, y). The chemical shift for state A is assumed to be
zero.
+ RCS[1, 1] = complex(0.0, -dw)
# The matrix R that contains all the contributions to the evolution,
i.e. relaxation, exchange and chemical shift evolution.
add(Rr, Rex, out=R)
@@ -102,8 +102,8 @@
Moft = dot(prop_total, M0)
# The next lines calculate the R2eff using a two-point
approximation, i.e. assuming that the decay is mono-exponential.
- Mgx = Moft[0].real / M0[0]
- if Mgx == 0.0:
+ Mx = Moft[0].real / M0[0]
+ if Mx == 0.0:
back_calc[i] = 1e99
else:
- back_calc[i]= -inv_tcpmg * log(Mgx)
+ back_calc[i]= -inv_tcpmg * log(Mx)
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=20347&r1=20346&r2=20347&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Wed Jul 17 11:09:56
2013
@@ -284,7 +284,7 @@
dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
# Back calculate the R2eff values.
- r2eff_ns_2site_3D(r180x=self.r180x, M0=self.M0,
r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, dw=dw_frq, k_AB=k_AB,
k_BA=k_BA, inv_tcpmg=self.inv_relax_time, tcp=self.tau_cpmg,
back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points, power=self.power)
+ r2eff_ns_2site_3D(r180x=self.r180x, M0=self.M0,
r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, pB=pB, dw=dw_frq,
k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time, tcp=self.tau_cpmg,
back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points, power=self.power)
# 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):
@@ -344,7 +344,7 @@
dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
# Back calculate the R2eff values.
- r2eff_ns_2site_star(Rr=self.Rr, Rex=self.Rex, RCS=self.RCS,
R=self.R, M0=self.M0, r20a=R20A[r20_index], r20b=R20B[r20_index], fA=dw_frq,
inv_tcpmg=self.inv_relax_time, tcp=self.tau_cpmg,
back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points, power=self.power)
+ r2eff_ns_2site_star(Rr=self.Rr, Rex=self.Rex, RCS=self.RCS,
R=self.R, M0=self.M0, r20a=R20A[r20_index], r20b=R20B[r20_index], dw=dw_frq,
inv_tcpmg=self.inv_relax_time, tcp=self.tau_cpmg,
back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points, power=self.power)
# 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):
r20347 - in /branches/relax_disp: lib/dispersion/ns_2site_3d.py lib/dispersion/ns_2site_star.py target_functions/relax_disp.py