Author: tlinnet
Date: Tue May 20 22:29:43 2014
New Revision: 23272
URL: http://svn.gna.org/viewcvs/relax?rev=23272&view=rev
Log:
Math-domain catching for model DPL94.
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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target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/dpl94.py
branches/disp_speed/target_functions/relax_disp.py
Modified: branches/disp_speed/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/dpl94.py?rev=23272&r1=23271&r2=23272&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/dpl94.py (original)
+++ branches/disp_speed/lib/dispersion/dpl94.py Tue May 20 22:29:43 2014
@@ -63,10 +63,10 @@
"""
# Python module imports.
-from numpy import array, cos, isfinite, sin, sum
+from numpy import abs, array, cos, isfinite, min, sin, sum
-def r1rho_DPL94(r1rho_prime=None, phi_ex=None, kex=None, theta=None, R1=0.0,
spin_lock_fields2=None, back_calc=None, num_points=None):
+def r1rho_DPL94(r1rho_prime=None, phi_ex=None, kex=None, theta=None, R1=0.0,
spin_lock_fields2=None, num_points=None):
"""Calculate the R1rho values for the DPL94 model.
See the module docstring for details.
@@ -84,9 +84,7 @@
@type R1: float
@keyword spin_lock_fields2: The R1rho spin-lock field strengths squared
(in rad^2.s^-2).
@type spin_lock_fields2: numpy rank-1 float array
- @keyword back_calc: The array for holding the back calculated
R1rho values. Each element corresponds to one of the spin-lock fields.
- @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 spin_lock_fields and back_calc arguments.
+ @keyword num_points: The number of points on the dispersion
curve, equal to the length of the spin_lock_fields.
@type num_points: int
"""
@@ -103,6 +101,13 @@
# Denominator.
denom = kex2 + spin_lock_fields2
+ # Catch math domain error of dividing with 0.
+ # This is when denom =0.
+ if min(abs(denom)) == 0:
+ R1rho = array([1e100]*num_points)
+
+ return R1rho
+
# R1rho calculation.
R1rho = R1_R2 + numer / denom
@@ -111,6 +116,4 @@
if not isfinite(sum(R1rho)):
R1rho = array([1e100]*num_points)
- # Parse back the value to update the back_calc class object.
- for i in range(num_points):
- back_calc[i] = R1rho[i]
+ return R1rho
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=23272&r1=23271&r2=23272&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Tue May 20 22:29:43
2014
@@ -965,7 +965,7 @@
# Loop over the offsets.
for oi in range(self.num_offsets[0][si][mi]):
# Back calculate the R2eff values.
- r1rho_DPL94(r1rho_prime=R20[r20_index],
phi_ex=phi_ex_scaled, kex=kex, theta=self.tilt_angles[0][si][mi][oi],
R1=self.r1[si, mi],
spin_lock_fields2=self.spin_lock_omega1_squared[0][mi][oi],
back_calc=self.back_calc[0][si][mi][oi],
num_points=self.num_disp_points[0][si][mi][oi])
+ self.back_calc[0][si][mi][oi] =
r1rho_DPL94(r1rho_prime=R20[r20_index], phi_ex=phi_ex_scaled, kex=kex,
theta=self.tilt_angles[0][si][mi][oi], R1=self.r1[si, mi],
spin_lock_fields2=self.spin_lock_omega1_squared[0][mi][oi],
num_points=self.num_disp_points[0][si][mi][oi])
# 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][oi]):
r23272 - in /branches/disp_speed: lib/dispersion/dpl94.py target_functions/relax_disp.py