Author: tlinnet
Date: Tue May 20 22:29:41 2014
New Revision: 23271
URL: http://svn.gna.org/viewcvs/relax?rev=23271&view=rev
Log:
Math-domain catching for model TAP03.
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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target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/tap03.py
branches/disp_speed/target_functions/relax_disp.py
Modified: branches/disp_speed/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/tap03.py?rev=23271&r1=23270&r2=23271&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/tap03.py (original)
+++ branches/disp_speed/lib/dispersion/tap03.py Tue May 20 22:29:41 2014
@@ -60,10 +60,10 @@
"""
# Python module imports.
-from numpy import arctan2, array, isfinite, sin, sqrt, sum
+from numpy import abs, arctan2, array, isfinite, min, sin, sqrt, sum
-def r1rho_TAP03(r1rho_prime=None, omega=None, offset=None, pA=None, pB=None,
dw=None, kex=None, R1=0.0, spin_lock_fields=None, spin_lock_fields2=None,
back_calc=None, num_points=None):
+def r1rho_TAP03(r1rho_prime=None, omega=None, offset=None, pA=None, pB=None,
dw=None, kex=None, R1=0.0, spin_lock_fields=None, spin_lock_fields2=None,
num_points=None):
"""Calculate the R1rho' values for the TP02 model.
See the module docstring for details. This is the Trott, Abergel and
Palmer (2003) equation.
@@ -89,9 +89,7 @@
@type spin_lock_fields: numpy rank-1 float array
@keyword spin_lock_fields2: The R1rho spin-lock field strengths squared
(in rad^2.s^-2). This is for speed.
@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
"""
@@ -113,7 +111,16 @@
# The gamma factor.
sigma = pB*da + pA*db
sigma2 = sigma**2
- gamma = 1.0 + phi_ex*(sigma2 - kex2 + spin_lock_fields2) / (sigma2 +
kex2 + spin_lock_fields2)**2
+ gamma_denom = (sigma2 + kex2 + spin_lock_fields2)**2
+
+ # Catch math domain error of dividing with 0.
+ # This is when gamma_denom =0.
+ if min(abs(gamma_denom)) == 0:
+ R1rho = array([1e100]*num_points)
+
+ return R1rho
+
+ gamma = 1.0 + phi_ex*(sigma2 - kex2 + spin_lock_fields2) / gamma_denom
# Special omega values.
waeff2 = gamma*spin_lock_fields2 + da**2 # Effective field at A.
@@ -133,6 +140,20 @@
# Denominator.
denom = waeff2*wbeff2/weff2 + kex2 - 2.0*hat_sin_theta2*phi_ex + (1.0 -
gamma)*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
+
+ # Catch math domain error of dividing with 0.
+ # This is when gamma =0.
+ if min(abs(gamma)) == 0:
+ R1rho = array([1e100]*num_points)
+
+ return R1rho
+
# R1rho calculation.
R1rho = R1_cos_theta2 + R1rho_prime_sin_theta2 + hat_sin_theta2 * numer
/ denom / gamma
@@ -141,6 +162,4 @@
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=23271&r1=23270&r2=23271&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Tue May 20 22:29:41
2014
@@ -1823,7 +1823,7 @@
# Loop over the offsets.
for oi in range(self.num_offsets[0][si][mi]):
# Back calculate the R1rho values.
- r1rho_TAP03(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[0][si][mi], offset=self.offset[0][si][mi][oi],
pA=pA, pB=pB, dw=dw_frq, kex=kex, R1=self.r1[si, mi],
spin_lock_fields=self.spin_lock_omega1[0][mi][oi],
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_TAP03(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[0][si][mi], offset=self.offset[0][si][mi][oi],
pA=pA, pB=pB, dw=dw_frq, kex=kex, R1=self.r1[si, mi],
spin_lock_fields=self.spin_lock_omega1[0][mi][oi],
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]):
r23271 - in /branches/disp_speed: lib/dispersion/tap03.py target_functions/relax_disp.py