Author: bugman
Date: Sun Oct 27 18:13:04 2013
New Revision: 21253
URL: http://svn.gna.org/viewcvs/relax?rev=21253&view=rev
Log:
Converted the 'IT99' dispersion model parameters to pA and dw.
This is thanks to feedback from Nikolai Skrynnikov. I have no idea why the
phi_ex and pA.dw^2
parameters were being used in the first place. The model results after the
change are identical.
Modified:
branches/relax_disp/docs/latex/dispersion_models.tex
branches/relax_disp/lib/dispersion/it99.py
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/target_functions/relax_disp.py
branches/relax_disp/test_suite/system_tests/relax_disp.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/docs/latex/dispersion_models.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion_models.tex?rev=21253&r1=21252&r2=21253&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion_models.tex (original)
+++ branches/relax_disp/docs/latex/dispersion_models.tex Sun Oct 27 18:13:04
2013
@@ -34,7 +34,7 @@
LM63 3-site & Analytic & 3 & $\{\Rtwozero, \dots, \PhiexB,
\kB, \PhiexC, \kC\}$ & Fast exchange, $\pA > \pB$ and $\pA > \pC$ &
\citet{LuzMeiboom63} \\
CR72 & Analytic & 2 & $\{\Rtwozero, \dots, \pA, \dw,
\kex\}$ & $\pA > \pB$ &
\citet{CarverRichards72} \\
CR72 full & Analytic & 2 & $\{\RtwozeroA, \RtwozeroB,
\dots, \pA, \dw, \kex\}$ & $\pA > \pB$ &
\citet{CarverRichards72} \\
-IT99 & Analytic & 2 & $\{\Rtwozero, \dots, \Phiex,
\pA.\dw^2, \kex\}$ & $\pA \gg \pB$ &
\citet{IshimaTorchia99} \\
+IT99 & Analytic & 2 & $\{\Rtwozero, \dots, \pA, \dw,
\kex\}$ & $\pA \gg \pB$ &
\citet{IshimaTorchia99} \\
TSMFK01 & Analytic & 2 & $\{\RtwozeroA, \dots, \dw,
\kAB\}$ & $\pA \gg \pB$ &
\citet{Tollinger01} \\
NS CPMG 2-site expanded & Numeric & 2 & $\{\Rtwozero, \dots, \pA, \dw,
\kex\}$ & $\pA > \pB$ &
\citet{Tollinger01} \\
NS CPMG 2-site 3D & Numeric & 2 & $\{\Rtwozero, \dots, \pA, \dw,
\kex\}$ & $\pA > \pB$ & - \\
Modified: branches/relax_disp/lib/dispersion/it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/it99.py?rev=21253&r1=21252&r2=21253&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/it99.py (original)
+++ branches/relax_disp/lib/dispersion/it99.py Sun Oct 27 18:13:04 2013
@@ -52,7 +52,7 @@
from math import pi, sqrt
-def r2eff_IT99(r20=None, phi_ex=None, padw2=None, tex=None, cpmg_frqs=None,
back_calc=None, num_points=None):
+def r2eff_IT99(r20=None, pA=None, pB=None, dw=None, tex=None,
cpmg_frqs=None, back_calc=None, num_points=None):
"""Calculate the R2eff values for the IT99 model.
See the module docstring for details.
@@ -60,10 +60,12 @@
@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 padw2: The pA.dw^2 parameter value.
- @type padw2: 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 tex: The tex parameter value (the time of exchange in
s/rad).
@type tex: float
@keyword cpmg_frqs: The CPMG nu1 frequencies.
@@ -75,11 +77,13 @@
"""
# Repetitive calculations (to speed up calculations).
+ dw2 = dw**2
tex2 = tex**2
+ padw2 = pA * dw2
pa2dw4 = padw2**2
# The numerator.
- numer = phi_ex * tex
+ numer = padw2 * pB * tex
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=21253&r1=21252&r2=21253&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Sun Oct 27
18:13:04 2013
@@ -606,7 +606,7 @@
params = []
for frq in loop_frq():
params.append('r2')
- params += ['phi_ex', 'padw2', 'tex']
+ params += ['pA', 'dw', 'tex']
# TSMFK01 model.
elif model == MODEL_TSMFK01:
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=21253&r1=21252&r2=21253&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Sun Oct 27 18:13:04
2013
@@ -580,10 +580,13 @@
# Unpack the parameter values.
R20 = params[:self.end_index[0]]
- phi_ex = params[self.end_index[0]:self.end_index[1]]
- padw2 = params[self.end_index[1]:self.end_index[2]]
+ dw = params[self.end_index[0]:self.end_index[1]]
+ pA = params[self.end_index[1]]
tex = params[self.end_index[2]]
+ # Once off parameter conversions.
+ pB = 1.0 - pA
+
# Initialise.
chi2_sum = 0.0
@@ -594,12 +597,11 @@
# The R20 index.
r20_index = frq_index + spin_index*self.num_frq
- # Convert phi_ex and pa.dw^2 from ppm^2 to (rad/s)^2.
- phi_ex_scaled = phi_ex[spin_index] * self.frqs[spin_index,
frq_index]**2
- padw2_scaled = padw2[spin_index] * self.frqs[spin_index,
frq_index]**2
+ # Convert dw from ppm to rad/s.
+ dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
# Back calculate the R2eff values.
- r2eff_IT99(r20=R20[r20_index], phi_ex=phi_ex_scaled,
padw2=padw2_scaled, tex=tex, cpmg_frqs=self.cpmg_frqs,
back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points)
+ r2eff_IT99(r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq,
tex=tex, cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc[spin_index,
frq_index], num_points=self.num_disp_points)
# 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):
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=21253&r1=21252&r2=21253&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Sun Oct 27
18:13:04 2013
@@ -694,14 +694,14 @@
spin71 = cdp.mol[0].res[1].spin[0]
# Set the initial parameter values.
- spin70.r2 = [7, 10]
- spin70.phi_ex = 0.8
- spin70.padw2 = 260.0
- spin70.tex = 2e-4
- spin71.r2 = [5, 9]
- spin71.phi_ex = 0.1
- spin71.padw2 = 0.0001
- spin71.tex = 1e-4
+ spin70.r2 = [8.8, 16.6]
+ spin70.dw = 10.0
+ spin70.pA = 0.5
+ spin70.tex = 1000.09
+ spin71.r2 = [1, 1]
+ spin71.dw = 10.0
+ spin71.pA = 0.95
+ spin71.tex = 0.1
# Low precision optimisation.
self.interpreter.minimise(min_algor='simplex', line_search=None,
hessian_mod=None, hessian_type=None, func_tol=1e-10, grad_tol=None,
max_iter=10000, constraints=True, scaling=True, verbosity=1)
@@ -711,23 +711,23 @@
print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value
(:71)"))
print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[0],
spin71.r2[0]))
print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[1],
spin71.r2[1]))
- print("%-20s %20.15g %20.15g" % ("phi_ex", spin70.phi_ex,
spin71.phi_ex))
- print("%-20s %20.15g %20.15g" % ("padw2", spin70.padw2,
spin71.padw2))
+ print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw))
+ print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA))
print("%-20s %20.15g %20.15g" % ("tex", spin70.tex, spin71.tex))
print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
# Checks for residue :70.
self.assertAlmostEqual(spin70.r2[0], 7.24913359483782, 4)
self.assertAlmostEqual(spin70.r2[1], 10.0721943688644, 4)
- self.assertAlmostEqual(spin70.phi_ex, 0.824075664284934, 4)
- self.assertAlmostEqual(spin70.padw2, 264.941131087762, 4)
+ self.assertAlmostEqual(spin70.dw, 16.302386572665750, 4)
+ self.assertAlmostEqual(spin70.pA, 0.996889589501665, 4)
self.assertAlmostEqual(spin70.tex*1000, 0.00020445116006575*1000, 4)
self.assertAlmostEqual(spin70.chi2, 29.7980427316775, 4)
# Checks for residue :71.
self.assertAlmostEqual(spin71.r2[0], 4.96765137715714, 4)
- self.assertAlmostEqual(spin71.phi_ex, 0.16487619476159, 4)
- self.assertAlmostEqual(spin71.padw2, 0.000896297985759929, 3)
+ self.assertAlmostEqual(spin71.dw, 0.812098432417916, 4)
+ self.assertAlmostEqual(spin71.pA, 0.500000087728188, 3)
self.assertAlmostEqual(spin71.tex*1000, 0.000125225494546911*1000, 4)
self.assertAlmostEqual(spin71.chi2, 2.33683739438351, 4)
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=21253&r1=21252&r2=21253&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Sun Oct 27 18:13:04 2013
@@ -544,7 +544,7 @@
"%s: {%s, ..., %s, kB, %s, kC}" % (MODEL_LM63_3SITE, r2, phi_exB,
phi_exC),
"%s: {%s, ..., pA, %s, %s}" % (MODEL_CR72, r2, dw, kex),
"%s: {%s, %s, ..., pA, %s, %s}" % (MODEL_CR72_FULL, r2a, r2b, dw,
kex),
- "%s: {%s, ..., %s, %s, %s}" % (MODEL_IT99, r2, phi_ex, padw2, kex),
+ "%s: {%s, ..., pA, %s, %s}" % (MODEL_IT99, r2, dw, kex),
"%s: {%s, ..., %s, k_AB}" % (MODEL_TSMFK01, r2a, dw),
"%s: {%s, ..., pA, %s, %s}" % (MODEL_NS_CPMG_2SITE_3D, r2, dw, kex),
"%s: {%s, %s, ..., pA, %s, %s}" % (MODEL_NS_CPMG_2SITE_3D_FULL, r2a,
r2b, dw, kex),
@@ -595,7 +595,7 @@
uf.desc[-1].add_item_list_element("'%s'" % MODEL_LM63_3SITE, "The original
Luz and Meiboom (1963) 3-site fast exchange equation with parameters {R20,
..., phi_ex, kex, phi_ex2, kex2},")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_CR72, "The reduced Carver
and Richards (1972) 2-site equation for all time scales whereby the
simplification R20A = R20B is assumed. The parameters are {R20, ..., pA, dw,
kex},")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_CR72_FULL, "The full Carver
and Richards (1972) 2-site equation for all time scales with parameters
{R20A, R20B, ..., pA, dw, kex},")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_IT99, "The Ishima and
Torchia (1999) 2-site model for all time scales with pA >> pB and with
parameters {R20, ..., phi_ex, padw2, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_IT99, "The Ishima and
Torchia (1999) 2-site model for all time scales with pA >> pB and with
parameters {R20, ..., pA, dw, kex},")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_TSMFK01, "The Tollinger,
Kay et al. (2001) 2-site very-slow exchange model, range of microsecond to
second time scale. Applicable in the limit of slow exchange, when
|R20A-R20B| << k_AB,kB << 1/tau_CP. R20A is the transverse relaxation rate
of site A in the absence of exchange. 2*tau_CP is is the time between
successive 180 deg. pulses. The parameters are {R20A, ..., dw, k_AB}.")
uf.desc[-1].add_paragraph("The currently supported numeric models are:")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_3D, "The
reduced numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B is assumed. Its
parameters are {R20, ..., pA, dw, kex},")
r21253 - in /branches/relax_disp: docs/latex/ lib/dispersion/ specific_analyses/relax_disp/ target_functions/ test_suite/sys...