Author: tlinnet
Date: Mon May 19 14:44:12 2014
New Revision: 23240
URL: http://svn.gna.org/viewcvs/relax?rev=23240&view=rev
Log:
Math-domain catching for model CR72.
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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target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/cr72.py
branches/disp_speed/target_functions/relax_disp.py
Modified: branches/disp_speed/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/cr72.py?rev=23240&r1=23239&r2=23240&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/cr72.py (original)
+++ branches/disp_speed/lib/dispersion/cr72.py Mon May 19 14:44:12 2014
@@ -92,12 +92,12 @@
"""
# Python module imports.
-from numpy import arccosh, array, cos, cosh, isfinite, sqrt, sum
+from numpy import arccosh, array, cos, cosh, isfinite, max, sqrt, sum
# 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, back_calc=None, num_points=None):
+def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None,
cpmg_frqs=None, num_points=None):
"""Calculate the R2eff values for the CR72 model.
See the module docstring for details.
@@ -115,9 +115,7 @@
@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.
+ @keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs.
@type num_points: int
"""
@@ -151,6 +149,14 @@
etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs
etaneg = eta_scale * sqrt(-Psi + sqrt_psi2_zeta2) / cpmg_frqs
+ # Catch math domain error of cosh(val > 710).
+ # This is when etapos > 710.
+ if num_points > 0:
+ if max(etapos) > 700:
+ R2eff = array([1e100]*num_points)
+
+ return R2eff
+
# Calculate R2eff.
R2eff = r20_kex - cpmg_frqs * arccosh( Dpos * cosh(etapos) - Dneg *
cos(etaneg) )
@@ -159,6 +165,4 @@
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=23240&r1=23239&r2=23240&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Mon May 19 14:44:12
2014
@@ -484,7 +484,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R2eff values.
- 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])
+ 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])
# 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]):
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
relax-commits@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits