Author: bugman
Date: Mon May 6 10:58:18 2013
New Revision: 19663
URL: http://svn.gna.org/viewcvs/relax?rev=19663&view=rev
Log:
Shifted the LM63 dispersion model functions into the new lib.dispersion.lm63
module.
Added:
branches/relax_disp/lib/dispersion/lm63.py
- copied, changed from r19657,
branches/relax_disp/lib/dispersion/equations.py
Modified:
branches/relax_disp/lib/dispersion/equations.py
branches/relax_disp/target_functions/relax_disp.py
Modified: branches/relax_disp/lib/dispersion/equations.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/equations.py?rev=19663&r1=19662&r2=19663&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/equations.py (original)
+++ branches/relax_disp/lib/dispersion/equations.py Mon May 6 10:58:18 2013
@@ -24,7 +24,7 @@
"""The relaxation dispersion equations."""
# Python module imports.
-from math import log, tanh
+from math import log
def calc_two_point_r2eff(relax_time=None, I_ref=None, I=None):
@@ -49,20 +49,3 @@
# Calculate and return the value (avoiding integer division problems).
return -1.0 / relax_time * log(float(I) / I_ref)
-
-
-def r2eff_LM63(params=None, cpmg_frqs=None, back_calc=None,
num_disp_points=None):
- """Back calculate R2eff.
-
- The currently supported equation is that for CPMG relaxation dispersion
in the fast exchange limit:
-
- - Millet et al., JACS, 2000, 122, 2867-2877 (equation 19)
- - Kovrigin et al., J. Mag. Res., 2006, 180, 93-104 (equation 1)
-
- In the future, back-calculation should be available for CPMG relaxation
dispersion in the slow exchange limit:
- - Tollinger et al., JACS, 2001, 123, 11341-11352 (equation 2)
- """
-
- # Loop over the time points, back calculating the R2eff value.
- for i in range(num_disp_points):
- back_calc[i] = params[0] + params[1] * (1 - 2 * tanh(params[2] / (2
* 4 * cpmg_frqs[i])) * ((4 * cpmg_frqs[i] ) / params[2]))
Copied: branches/relax_disp/lib/dispersion/lm63.py (from r19657,
branches/relax_disp/lib/dispersion/equations.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/lm63.py?p2=branches/relax_disp/lib/dispersion/lm63.py&p1=branches/relax_disp/lib/dispersion/equations.py&r1=19657&r2=19663&rev=19663&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/equations.py (original)
+++ branches/relax_disp/lib/dispersion/lm63.py Mon May 6 10:58:18 2013
@@ -21,48 +21,49 @@
###############################################################################
# Module docstring.
-"""The relaxation dispersion equations."""
+"""The Luz and Meiboom (1963) 2-site fast exchange model.
+
+This module is for the function, gradient and Hessian of the LM63 model.
The model is named after the reference:
+
+ Luz, S. and Meiboom S., 1963, Nuclear Magnetic Resonance study of
protolysis of trimethylammonium ion in aqueous solution - order of reaction
with respect to solvent, J. Chem. Phys. 1963, 39, 366-370 (U{DOI:
10.1063/1.1734254<http://dx.doi.org/10.1063/1.1734254>}).
+
+The equation used is:
+
+ phi_ex / 4 * nu_cpmg / kex \ \
+ R2eff = R20 + ------ * | 1 - ----------- * tanh | ----------- | | ,
+ kex \ kex \ 4 * nu_cpmg / /
+
+where:
+
+ phi_ex = pA * pB * delta_omega^2 ,
+
+kex is the chemical exchange rate constant, pA and pB are the populations of
states A and B, and delta_omega is the chemical shift difference between the
two states.
+"""
# Python module imports.
-from math import log, tanh
+from math import tanh
-def calc_two_point_r2eff(relax_time=None, I_ref=None, I=None):
- """Calculate the R2eff/R1rho value for the fixed relaxation time data.
+def r2eff_LM63(r20=None, phi_ex=None, kex=None, cpmg_frqs=None,
back_calc=None, num_points=None):
+ """Calculate the R2eff values for the LM63 model.
- The formula is:
-
- -1 / I1 \
- R2eff = ------- * ln | -- | ,
- relax_T \ I0 /
-
- where relax_T is the fixed delay time, I0 is the reference peak
intensity when relax_T is zero, and I1 is the peak intensity in a spectrum of
interest.
+ See the module docstring for details.
- @keyword relax_time: The fixed relaxation delay time in seconds.
- @type relax_time: float
- @keyword I_ref: The peak intensity in the reference spectrum.
- @type I_ref: float
- @keyword I: The peak intensity of interest.
- @type I: float
+ @keyword r20: The R20 parameter value (R2 with no exchange).
+ @type r20: float
+ @keyword phi_ex: The phi_ex parameter value (pA * pB *
delta_omega^2).
+ @type phi_ex: float
+ @keyword kex: The kex parameter value (the exchange rate in
rad/s).
+ @type kex: float
+ @keyword cpmg_frqs: The CPMG nu1 frequencies.
+ @type cpmg_frqs: numpy rank-1 float array
+ @keyword back_calc: The array for holding the back calculated R2eff
values. Each element corresponds to one of the CPMG nu1 frequencies.
+ @type back_calc: numpy rank-1 float array
+ @keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs and back_calc arguments.
+ @type num_poinst: int
"""
- # Calculate and return the value (avoiding integer division problems).
- return -1.0 / relax_time * log(float(I) / I_ref)
-
-
-def r2eff_LM63(params=None, cpmg_frqs=None, back_calc=None,
num_disp_points=None):
- """Back calculate R2eff.
-
- The currently supported equation is that for CPMG relaxation dispersion
in the fast exchange limit:
-
- - Millet et al., JACS, 2000, 122, 2867-2877 (equation 19)
- - Kovrigin et al., J. Mag. Res., 2006, 180, 93-104 (equation 1)
-
- In the future, back-calculation should be available for CPMG relaxation
dispersion in the slow exchange limit:
- - Tollinger et al., JACS, 2001, 123, 11341-11352 (equation 2)
- """
-
- # Loop over the time points, back calculating the R2eff value.
- for i in range(num_disp_points):
- back_calc[i] = params[0] + params[1] * (1 - 2 * tanh(params[2] / (2
* 4 * cpmg_frqs[i])) * ((4 * cpmg_frqs[i] ) / params[2]))
+ # Loop over the time points, back calculating the R2eff values.
+ for i in range(num_points):
+ back_calc[i] = r20 + phi_ex / kex * (1.0 - (4.0 * cpmg_frqs[i] /
params[2]) * tanh(kex / (4 * cpmg_frqs[i])))
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=19663&r1=19662&r2=19663&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Mon May 6 10:58:18
2013
@@ -27,7 +27,7 @@
from numpy import dot, float64, zeros
# relax module imports.
-from lib.dispersion.equations import r2eff_LM63
+from lib.dispersion.lm63 import r2eff_LM63
from lib.errors import RelaxError
from target_functions.chi2 import chi2
from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_LM63,
MODEL_R2EFF
@@ -117,7 +117,7 @@
# Loop over the spectrometer frequencies.
for frq_index in range(self.num_frq):
# Back calculate the R2eff values.
- r2eff_LM63(params=params, cpmg_frqs=self.cpmg_frqs,
back_calc=self.back_calc[spin_index, frq_index],
num_disp_points=self.num_disp_points)
+ r2eff_LM63(r20=params[0], phi_ex=params[1], kex=params[2],
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points)
# Calculate and return the chi-squared value.
chi2_sum += chi2(values[spin_index, frq_index],
back_calc[spin_index, frq_index], sd[spin_index, frq_index])
r19663 - in /branches/relax_disp: lib/dispersion/equations.py lib/dispersion/lm63.py target_functions/relax_disp.py