Author: tlinnet
Date: Thu May 29 12:33:36 2014
New Revision: 23588
URL: http://svn.gna.org/viewcvs/relax?rev=23588&view=rev
Log:
Converting back to having back_calc as a function argument to model TSMFK01.
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/tsmfk01.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
Modified: branches/disp_speed/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/tsmfk01.py?rev=23588&r1=23587&r2=23588&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/tsmfk01.py (original)
+++ branches/disp_speed/lib/dispersion/tsmfk01.py Thu May 29 12:33:36
2014
@@ -70,7 +70,7 @@
from numpy import array, min, sin, isfinite, sum
-def r2eff_TSMFK01(r20a=None, dw=None, k_AB=None, tcp=None, num_points=None):
+def r2eff_TSMFK01(r20a=None, dw=None, k_AB=None, tcp=None, back_calc=None,
num_points=None):
"""Calculate the R2eff values for the TSMFK01 model.
See the module docstring for details.
@@ -84,13 +84,16 @@
@type k_AB: float
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@type tcp: 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 k_AB == 0.0:
- return array([r20a]*num_points)
+ back_calc[:] = array([r20a]*num_points)
+ return
# Denominator.
denom = dw * tcp
@@ -101,7 +104,8 @@
# Catch zeros (to avoid pointless mathematical operations).
# This will result in no exchange, returning flat lines.
if min(numer) == 0.0:
- return array([r20a + k_AB]*num_points)
+ back_calc[:] = array([r20a + k_AB]*num_points)
+ return
# Calculate R2eff.
R2eff = r20a + k_AB - k_AB * numer / denom
@@ -111,4 +115,4 @@
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=23588&r1=23587&r2=23588&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Thu May 29 12:33:36
2014
@@ -1921,7 +1921,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R2eff values.
- self.back_calc[0][si][mi][0] =
r2eff_TSMFK01(r20a=R20A[r20a_index], dw=dw_frq, k_AB=k_AB,
tcp=self.tau_cpmg[0][mi], num_points=self.num_disp_points[0][si][mi][0])
+ r2eff_TSMFK01(r20a=R20A[r20a_index], dw=dw_frq, k_AB=k_AB,
tcp=self.tau_cpmg[0][mi], 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_tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py?rev=23588&r1=23587&r2=23588&view=diff
==============================================================================
---
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
(original)
+++
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
Thu May 29 12:33:36 2014
@@ -45,6 +45,7 @@
relax_times = 0.04
self.cpmg_frqs = self.ncyc / relax_times
self.tau_cpmg = 0.25 / self.cpmg_frqs
+ 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_TSMFK01(r20a=self.r20a, dw=dw_frq, k_AB=k_AB,
tcp=self.cpmg_frqs, num_points=self.num_points)
+ r2eff_TSMFK01(r20a=self.r20a, dw=dw_frq, k_AB=k_AB,
tcp=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):
r23588 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/