r23275 - in /branches/disp_speed: lib/dispersion/it99.py target_functions/relax_disp.py -- May 20, 2014 - 22:29

Author: tlinnet
Date: Tue May 20 22:29:49 2014
New Revision: 23275

URL: http://svn.gna.org/viewcvs/relax?rev=23275&view=rev
Log:
Math-domain catching for model IT99.

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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target 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/it99.py
    branches/disp_speed/target_functions/relax_disp.py

Modified: branches/disp_speed/lib/dispersion/it99.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/it99.py?rev=23275&r1=23274&r2=23275&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/it99.py  (original)
+++ branches/disp_speed/lib/dispersion/it99.py  Tue May 20 22:29:49 2014
@@ -73,10 +73,10 @@
 """
 
 # Python module imports.
-from numpy import array, isfinite, sqrt, sum
+from numpy import abs, array, isfinite, min, sqrt, sum
 
 
-def r2eff_IT99(r20=None, pA=None, pB=None, dw=None, tex=None, 
cpmg_frqs=None, back_calc=None, num_points=None):
+def r2eff_IT99(r20=None, pA=None, pB=None, dw=None, tex=None, 
cpmg_frqs=None, num_points=None):
     """Calculate the R2eff values for the IT99 model.
 
     See the module docstring for details.
@@ -94,9 +94,7 @@
     @type tex:              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
     """
 
@@ -116,6 +114,13 @@
     omega_a2 = sqrt(omega_1eff4 + pa2dw4)
     denom = 1.0 + omega_a2 * tex2
 
+    # Catch math domain error of dividing with 0.
+    # This is when denom=0.
+    if min(abs(denom)) == 0:
+        R2eff = array([1e100]*num_points)
+
+        return R2eff
+
     # R2eff calculation.
     R2eff = r20 + numer / denom
 
@@ -124,6 +129,4 @@
     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=23275&r1=23274&r2=23275&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py  (original)
+++ branches/disp_speed/target_functions/relax_disp.py  Tue May 20 22:29:49 
2014
@@ -1015,7 +1015,7 @@
                 dw_frq = dw[si] * self.frqs[0][si][mi]
 
                 # Back calculate the R2eff values.
-                r2eff_IT99(r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq, 
tex=tex, 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_IT99(r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq, tex=tex, 
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]):