Author: tlinnet
Date: Tue May 20 01:47:30 2014
New Revision: 23246
URL: http://svn.gna.org/viewcvs/relax?rev=23246&view=rev
Log:
Math-domain catching for model: 'NS CPMG 2-site expanded'.
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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target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/ns_cpmg_2site_expanded.py
branches/disp_speed/target_functions/relax_disp.py
Modified: branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py?rev=23246&r1=23245&r2=23246&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py
(original)
+++ branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py Tue
May 20 01:47:30 2014
@@ -235,14 +235,13 @@
"""
# Python module imports.
-from math import log
-from numpy import exp, power, sqrt
+from numpy import array, exp, isfinite, power, log, min, sqrt, sum
# relax module imports.
from lib.float import isNaN
-def r2eff_ns_cpmg_2site_expanded(r20=None, pA=None, dw=None, k_AB=None,
k_BA=None, relax_time=None, inv_relax_time=None, tcp=None, back_calc=None,
num_points=None, num_cpmg=None):
+def r2eff_ns_cpmg_2site_expanded(r20=None, pA=None, dw=None, k_AB=None,
k_BA=None, relax_time=None, inv_relax_time=None, tcp=None, num_points=None,
num_cpmg=None):
"""The 2-site numerical solution to the Bloch-McConnell equation using
complex conjugate matrices.
This function calculates and stores the R2eff values.
@@ -264,9 +263,7 @@
@type inv_relax_time: 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 tcp and back_calc arguments.
+ @keyword num_points: The number of points on the dispersion
curve, equal to the length of the tcp .
@type num_points: int
@keyword num_cpmg: The array of numbers of CPMG blocks.
@type num_cpmg: numpy int16, rank-1 array
@@ -342,7 +339,15 @@
t116 = power(0.5*(t97_t99 + t112), t115)
t118 = 1.0/t112
t120 = t97_nt99 + t112
- t122 = power(0.5*(t97_t99 - t112), t115)
+
+ half_t97_t99_m_t112 = 0.5*(t97_t99 - t112)
+ # Catch math domain error of power(val < 1.e-7, 40).
+ # This is when abs(half_t97_t99_m_t112) < 1.e-7.
+ if min(abs(half_t97_t99_m_t112.real)) < 1.e-7:
+ R2eff = array([1e100]*num_points)
+ return R2eff
+
+ t122 = power(half_t97_t99_m_t112, t115)
t127 = 0.5/t108
t120_t122 = t120*t122
t139 = 0.5/(k_AB + k_BA) * ((t120_t122 - t113*t116)*t118*k_BA +
(t120_t122 - t116*t120)*t127*t113*t118*k_AB)
@@ -355,8 +360,11 @@
Mx = intensity / intensity0
# Calculate the R2eff using a two-point approximation, i.e. assuming
that the decay is mono-exponential, and store it for each dispersion point.
- for i in range(num_points):
- if Mx[i] <= 0.0 or isNaN(Mx[i]):
- back_calc[i] = 1e99
- else:
- back_calc[i]= -inv_relax_time * log(Mx[i])
+ R2eff = -inv_relax_time * log(Mx)
+
+ # Catch errors, taking a sum over array is the fastest way to check for
+ # +/- inf (infinity) and nan (not a number).
+ if not isfinite(sum(R2eff)) or min(Mx) <= 0.0 or not isfinite(sum(Mx)):
+ R2eff = array([1e100]*num_points)
+
+ 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=23246&r1=23245&r2=23246&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Tue May 20 01:47:30
2014
@@ -1480,7 +1480,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R2eff values.
- r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index], pA=pA,
dw=dw_frq, k_AB=k_AB, k_BA=k_BA, relax_time=self.relax_times[0][mi],
inv_relax_time=self.inv_relax_times[0][mi], 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], num_cpmg=self.power[0][mi])
+ self.back_calc[0][si][mi][0] =
r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index], pA=pA, dw=dw_frq,
k_AB=k_AB, k_BA=k_BA, relax_time=self.relax_times[0][mi],
inv_relax_time=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi],
num_points=self.num_disp_points[0][si][mi][0], num_cpmg=self.power[0][mi])
# 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]):
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Re: r23246 - in /branches/disp_speed: lib/dispersion/ns_cpmg_2site_expanded.py target_functions/relax_disp.py