Author: bugman
Date: Thu May 29 13:55:17 2014
New Revision: 23592
URL: http://svn.gna.org/viewcvs/relax?rev=23592&view=rev
Log:
Merged revisions 23239 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
........
r23239 | tlinnet | 2014-05-19 14:44:10 +0200 (Mon, 19 May 2014) | 10 lines
Math-domain catching for model B14.
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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target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:
trunk/ (props changed)
trunk/lib/dispersion/b14.py
trunk/target_functions/relax_disp.py
Propchange: trunk/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu May 29 13:55:17 2014
@@ -1 +1 @@
-/branches/disp_speed:1-23214,23216-23229
+/branches/disp_speed:1-23214,23216-23229,23239
Modified: trunk/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=23592&r1=23591&r2=23592&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Thu May 29 13:55:17 2014
@@ -110,12 +110,12 @@
"""
# Python module imports.
-from numpy import arccosh, arctan2, array, cos, cosh, isfinite, log, power,
sin, sinh, sqrt, sum
+from numpy import abs, arccosh, arctan2, array, cos, cosh, isfinite, log,
min, power, sin, sinh, sqrt, sum
# Repetitive calculations (to speed up calculations).
g_fact = 1/sqrt(2)
-def r2eff_B14(r20a=None, r20b=None, pA=None, pB=None, dw=None, kex=None,
k_AB=None, k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None, back_calc=None,
num_points=None):
+def r2eff_B14(r20a=None, r20b=None, pA=None, pB=None, dw=None, kex=None,
k_AB=None, k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None, num_points=None):
"""Calculate the R2eff values for the CR72 model.
See the module docstring for details.
@@ -143,9 +143,7 @@
@type inv_tcpmg: 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.
+ @keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs.
@type num_points: int
"""
@@ -216,12 +214,24 @@
# Real. The v_1c in paper.
v1c = F0 * cosh(E0) - F2 * cos(E2)
+ # Catch math domain error of sqrt(neg val).
+ # This is when abs(v1c) =< 1.
+ if min(abs(v1c)) <= 1.:
+ R2eff = array([1e100]*num_points)
+ return R2eff
+
# Exact result for v2v3.
v3 = sqrt(v1c**2 - 1.)
y = power( (v1c - v3) / (v1c + v3), ncyc)
Tog = 0.5 * (1. + y) + (1. - y) * v5 / (2. * v3 * N )
+
+ # Catch math domain error of log(neg val or zero).
+ # This is when Tog.real =< 0.
+ if min(Tog.real) <= 0.:
+ R2eff = array([1e100]*num_points)
+ return R2eff
## -1/Trel * log(LpreDyn).
# Rpre = (r20a + r20b + kex) / 2.0
@@ -241,6 +251,4 @@
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: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=23592&r1=23591&r2=23592&view=diff
==============================================================================
--- trunk/target_functions/relax_disp.py (original)
+++ trunk/target_functions/relax_disp.py Thu May 29 13:55:17 2014
@@ -439,7 +439,7 @@
aliased_dw = dw_frq
# Back calculate the R2eff values.
- r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index],
pA=pA, pB=pB, dw=aliased_dw, kex=kex, k_AB=k_AB, k_BA=k_BA,
ncyc=self.power[ei][mi], inv_tcpmg=self.inv_relax_times[ei][mi],
tcp=self.tau_cpmg[ei][mi], back_calc=self.back_calc[ei][si][mi][0],
num_points=self.num_disp_points[ei][si][mi][0])
+ self.back_calc[ei][si][mi][0] =
r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, pB=pB,
dw=aliased_dw, kex=kex, k_AB=k_AB, k_BA=k_BA, ncyc=self.power[ei][mi],
inv_tcpmg=self.inv_relax_times[ei][mi], tcp=self.tau_cpmg[ei][mi],
num_points=self.num_disp_points[ei][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[ei][si][mi][0]):
r23592 - in /trunk: ./ lib/dispersion/b14.py target_functions/relax_disp.py