Author: tlinnet
Date: Wed May 28 19:17:11 2014
New Revision: 23564
URL: http://svn.gna.org/viewcvs/relax?rev=23564&view=rev
Log:
Converting back to having back_calc as a function argument to model CR72:
This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.
The problem is, that many numerical models can't be optimised further, since
they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put
into
a larger numpy array.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Modified:
branches/disp_speed/lib/dispersion/cr72.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
Modified: branches/disp_speed/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/cr72.py?rev=23564&r1=23563&r2=23564&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/cr72.py (original)
+++ branches/disp_speed/lib/dispersion/cr72.py Wed May 28 19:17:11 2014
@@ -97,7 +97,7 @@
# Repetitive calculations (to speed up calculations).
eta_scale = 2.0**(-3.0/2.0)
-def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None,
cpmg_frqs=None, num_points=None):
+def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None,
cpmg_frqs=None, back_calc=None, num_points=None):
"""Calculate the R2eff values for the CR72 model.
See the module docstring for details.
@@ -115,9 +115,16 @@
@type kex: float
@keyword cpmg_frqs: The CPMG nu1 frequencies.
@type cpmg_frqs: numpy rank-1 float array
- @keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs.
+ @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_points: int
"""
+
+ # Catch parameter values that will result in no exchange, returning flat
R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
+ if dw == 0.0 or pA == 1.0 or kex == 0.0:
+ back_calc[:] = array([r20a]*num_points)
+ return
# The B population.
pB = 1.0 - pA
@@ -127,10 +134,6 @@
r20_kex = (r20a + r20b + kex) / 2.0
k_BA = pA * kex
k_AB = pB * kex
-
- # Catch parameter values that will result in no exchange, returning flat
R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
- if dw == 0.0 or pA == 1.0 or k_AB == 0.0:
- return array([r20a]*num_points)
# The Psi and zeta values.
if r20a != r20b:
@@ -156,12 +159,14 @@
# Catch math domain error of cosh(val > 710).
# This is when etapos > 710.
if max(etapos) > 700:
- return array([r20a]*num_points)
+ back_calc[:] = array([r20a]*num_points)
+ return
# The arccosh argument - catch invalid values.
fact = Dpos * cosh(etapos) - Dneg * cos(etaneg)
if min(fact) < 1.0:
- return array([r20_kex]*num_points)
+ back_calc[:] = array([r20_kex]*num_points)
+ return
# Calculate R2eff.
R2eff = r20_kex - cpmg_frqs * arccosh( fact )
@@ -171,4 +176,4 @@
if not isfinite(sum(R2eff)):
R2eff = array([1e100]*num_points)
- return R2eff
+ back_calc[:] = R2eff
Modified: branches/disp_speed/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/target_functions/relax_disp.py?rev=23564&r1=23563&r2=23564&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Wed May 28 19:17:11
2014
@@ -484,7 +484,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R2eff values.
- self.back_calc[0][si][mi][0] =
r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, dw=dw_frq,
kex=kex, cpmg_frqs=self.cpmg_frqs[0][mi][0],
num_points=self.num_disp_points[0][si][mi][0])
+ r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index],
pA=pA, dw=dw_frq, kex=kex, cpmg_frqs=self.cpmg_frqs[0][mi][0], back_calc =
self.back_calc[0][si][mi][0], num_points=self.num_disp_points[0][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[0][si][mi][0]):
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py?rev=23564&r1=23563&r2=23564&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
Wed May 28 19:17:11 2014
@@ -45,6 +45,7 @@
self.ncyc = array([2, 4, 8, 10, 20, 40, 500])
relax_times = 0.04
self.cpmg_frqs = self.ncyc / relax_times
+ self.R2eff = zeros(self.num_points, float64)
# The spin Larmor frequencies.
self.sfrq = 200. * 1E6
@@ -57,11 +58,11 @@
k_AB, k_BA, pB, dw_frq = self.param_conversion(pA=self.pA,
kex=self.kex, dw=self.dw, sfrq=self.sfrq)
# Calculate the R2eff values.
- R2eff = r2eff_CR72(r20a=self.r20a, r20b=self.r20b, pA=self.pA,
dw=dw_frq, kex=self.kex, cpmg_frqs=self.cpmg_frqs, num_points=self.num_points)
+ r2eff_CR72(r20a=self.r20a, r20b=self.r20b, pA=self.pA, dw=dw_frq,
kex=self.kex, cpmg_frqs=self.cpmg_frqs, back_calc=self.R2eff,
num_points=self.num_points)
# Check all R2eff values.
for i in range(self.num_points):
- self.assertAlmostEqual(R2eff[i], self.r20a)
+ self.assertAlmostEqual(self.R2eff[i], self.r20a)
def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None):
r23564 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/