Author: tlinnet
Date: Wed May 7 09:45:14 2014
New Revision: 23028
URL: http://svn.gna.org/viewcvs/relax?rev=23028&view=rev
Log:
Re-inserted the library function of b14.py the calculation of:
deltaR2 = r20a - r20b
alpha_m = deltaR2 + k_AB - k_BA
zeta = 2 * dw * alpha_m
Psi = alpha_m**2 + 4 * k_BA * k_AB - dw**2
And put the g_fact = 1/sqrt(2), inside the library function.
It made no sense to put these calculations outside the library, since there
would be no skipping of a loop.
It actually makes much better sense to keep these calculation in the library
function, to preserve the possibility
to import this module in other software.
sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014)
B14 model - 2-site exact solution model for all time scales.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging
Modified:
trunk/lib/dispersion/b14.py
trunk/target_functions/relax_disp.py
Modified: trunk/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=23028&r1=23027&r2=23028&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Wed May 7 09:45:14 2014
@@ -113,8 +113,10 @@
import numpy
from numpy import arccosh, cos, cosh, log, sin, sinh, sqrt, power
-
-def r2eff_B14(r20a=None, r20b=None, deltaR2=None, alpha_m=None, pA=None,
pB=None, dw=None, zeta=None, Psi=None, g_fact=None, kex=None, k_AB=None,
k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None, back_calc=None,
num_points=None):
+# Repetitive calculations (to speed up calculations).
+g_fact = 1/sqrt(2)
+
+def r2eff_B14(r20a=None, r20b=None, pA=None, pB=None, dw=None, kex=None,
k_AB=None, k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None, back_calc=None,
num_points=None):
"""Calculate the R2eff values for the CR72 model.
See the module docstring for details.
@@ -124,22 +126,12 @@
@type r20a: float
@keyword r20b: The R20 parameter value of state B (R2 with no
exchange).
@type r20b: float
- @keyword deltaR2: The difference r20a - r20b.
- @type deltaR2: float
- @keyword alpha_m: The Carver and Richards (1972) alpha_minus short
notation. alpha_m = deltaR2 + k_AB - k_BA = r20a - r20b + k_AB - k_BA.
- @type alpha_m: 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 zeta: The Carver and Richards (1972) zeta notation.
zeta = 2 * dw * alpha_m.
- @type zeta: float
- @keyword Psi: The Carver and Richards (1972) Psi notation. Psi
= alpha_m**2 + 4 * k_BA * k_AB - dw**2.
- @type Psi: float
- @keyword g_fact: The factor g = 1/sqrt(2). This is calculated
outside library function, to only be calculated once.
- @type g_fact: float
@keyword kex: The kex parameter value (the exchange rate in
rad/s).
@type kex: float
@keyword k_AB: The rate of exchange from site A to B (rad/s).
@@ -159,6 +151,14 @@
"""
# Repetitive calculations (to speed up calculations).
+ deltaR2 = r20a - r20b
+
+ # The Carver and Richards (1972) alpha_minus short notation.
+ alpha_m = deltaR2 + k_AB - k_BA
+ zeta = 2 * dw * alpha_m
+ Psi = alpha_m**2 + 4 * k_BA * k_AB - dw**2
+
+ # Repetitive calculations (to speed up calculations).
dw2 = dw**2
zeta2 = zeta**2
Psi2 = Psi**2
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=23028&r1=23027&r2=23028&view=diff
==============================================================================
--- trunk/target_functions/relax_disp.py (original)
+++ trunk/target_functions/relax_disp.py Wed May 7 09:45:14 2014
@@ -416,7 +416,6 @@
pB = 1.0 - pA
k_BA = pA * kex
k_AB = pB * kex
- g_fact = 1/sqrt(2)
# Initialise.
chi2_sum = 0.0
@@ -427,6 +426,9 @@
for si in range(self.num_spins):
# Loop over the spectrometer frequencies.
for mi in range(self.num_frq):
+ # The R20 index.
+ r20_index = mi + si*self.num_frq
+
# Convert dw from ppm to rad/s.
dw_frq = dw[si] * self.frqs[ei][si][mi]
@@ -436,21 +438,8 @@
elif self.exp_types[ei] == EXP_TYPE_CPMG_PROTON_SQ:
aliased_dw = dw_frq
- # The R20 index.
- r20_index = mi + si*self.num_frq
-
- # Repetitive calculations (to speed up calculations).
- r20a = R20A[r20_index]
- r20b = R20B[r20_index]
- deltaR2 = r20a - r20b
-
- # The Carver and Richards (1972) alpha_minus short
notation.
- alpha_m = deltaR2 + k_AB - k_BA
- zeta = 2 * aliased_dw * alpha_m
- Psi = alpha_m**2 + 4 * k_BA * k_AB - aliased_dw**2
-
# Back calculate the R2eff values.
- r2eff_B14(r20a=r20a, r20b=r20b, deltaR2=deltaR2,
alpha_m=alpha_m, pA=pA, pB=pB, dw=dw_frq, zeta=zeta, Psi=Psi, g_fact=g_fact,
kex=kex, k_AB=k_AB, k_BA=k_BA, ncyc=self.power[ei][mi],
inv_tcpmg=self.inv_relax_times[ei][mi], tcp=self.tau_cpmg[ei][mi],
back_calc=self.back_calc[ei][si][mi][0],
num_points=self.num_disp_points[ei][si][mi][0])
+ r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index],
pA=pA, pB=pB, dw=aliased_dw, kex=kex, k_AB=k_AB, k_BA=k_BA,
ncyc=self.power[ei][mi], inv_tcpmg=self.inv_relax_times[ei][mi],
tcp=self.tau_cpmg[ei][mi], back_calc=self.back_calc[ei][si][mi][0],
num_points=self.num_disp_points[ei][si][mi][0])
# 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 di in range(self.num_disp_points[ei][si][mi][0]):
r23028 - in /trunk: lib/dispersion/b14.py target_functions/relax_disp.py