Author: tlinnet
Date: Tue May 20 22:29:38 2014
New Revision: 23269
URL: http://svn.gna.org/viewcvs/relax?rev=23269&view=rev
Log:
Math-domain catching for model TSMFK01.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
Modified:
branches/disp_speed/lib/dispersion/tsmfk01.py
branches/disp_speed/target_functions/relax_disp.py
Modified: branches/disp_speed/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/tsmfk01.py?rev=23269&r1=23268&r2=23269&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/tsmfk01.py (original)
+++ branches/disp_speed/lib/dispersion/tsmfk01.py Tue May 20 22:29:38
2014
@@ -67,10 +67,10 @@
"""
# Python module imports.
-from numpy import array, sin, isfinite, sum
+from numpy import abs, array, min, sin, isfinite, sum
-def r2eff_TSMFK01(r20a=None, dw=None, k_AB=None, tcp=None, back_calc=None,
num_points=None):
+def r2eff_TSMFK01(r20a=None, dw=None, k_AB=None, tcp=None, num_points=None):
"""Calculate the R2eff values for the TSMFK01 model.
See the module docstring for details.
@@ -83,15 +83,20 @@
@keyword k_AB: The k_AB parameter value (the forward exchange
rate in rad/s).
@type k_AB: float
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
- @type tcp: 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 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.
@type num_points: int
"""
# Denominator.
denom = dw * tcp
+
+ # Catch math domain error of dividing with 0.
+ # This is when sin(0).
+ if min(abs(denom)) == 0:
+ R2eff = array([1e100]*num_points)
+
+ return R2eff
# The numerator.
numer = sin(denom)
@@ -104,6 +109,4 @@
if not isfinite(sum(R2eff)):
R2eff = array([1e100]*num_points)
- # Parse back the value to update the back_calc class object.
- for i in range(num_points):
- back_calc[i] = R2eff[i]
+ return 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=23269&r1=23268&r2=23269&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Tue May 20 22:29:38
2014
@@ -1921,7 +1921,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R2eff values.
- 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])
+ 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])
# 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]):
r23269 - in /branches/disp_speed: lib/dispersion/tsmfk01.py target_functions/relax_disp.py