Re: r23240 - in /branches/disp_speed: lib/dispersion/cr72.py target_functions/relax_disp.py -- May 20, 2014

Hi Troels,

For good repository management, you should try to keep separate ideas
in separate commits.  In this commit you actually have two separate
concepts in one commit - the change of the target_functions.relax_disp
to lib.dispersion API, and handling of numpy.cosh() overflows.  These
should really be in two commits.  This is important if in the future a
better solution is found for the API and we would like to revert one
of the two changes.

Cheers,

Edward




On 19 May 2014 14:44,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Mon May 19 14:44:12 2014
New Revision: 23240

URL: http://svn.gna.org/viewcvs/relax?rev=23240&view=rev
Log:
Math-domain catching for model CR72.

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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target 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/cr72.py
    branches/disp_speed/target_functions/relax_disp.py

Modified: branches/disp_speed/lib/dispersion/cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/cr72.py?rev=23240&r1=23239&r2=23240&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/cr72.py  (original)
+++ branches/disp_speed/lib/dispersion/cr72.py  Mon May 19 14:44:12 2014
@@ -92,12 +92,12 @@
 """

 # Python module imports.
-from numpy import arccosh, array, cos, cosh, isfinite, sqrt, sum
+from numpy import arccosh, array, cos, cosh, isfinite, max, sqrt, sum

 # Repetitive calculations (to speed up calculations).
 eta_scale = 2.0**(-3.0/2.0)

-def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, 
cpmg_frqs=None, back_calc=None, num_points=None):
+def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, 
cpmg_frqs=None, num_points=None):
     """Calculate the R2eff values for the CR72 model.

     See the module docstring for details.
@@ -115,9 +115,7 @@
     @type kex:              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
     """

@@ -151,6 +149,14 @@
     etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs
     etaneg = eta_scale * sqrt(-Psi + sqrt_psi2_zeta2) / cpmg_frqs

+    # Catch math domain error of cosh(val > 710).
+    # This is when etapos > 710.
+    if num_points > 0:
+        if max(etapos) > 700:
+            R2eff = array([1e100]*num_points)
+
+            return R2eff
+
     # Calculate R2eff.
     R2eff = r20_kex - cpmg_frqs * arccosh( Dpos * cosh(etapos) - Dneg * 
cos(etaneg) )

@@ -159,6 +165,4 @@
     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=23240&r1=23239&r2=23240&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py  (original)
+++ branches/disp_speed/target_functions/relax_disp.py  Mon May 19 14:44:12 
2014
@@ -484,7 +484,7 @@
                 dw_frq = dw[si] * self.frqs[0][si][mi]

                 # Back calculate the R2eff values.
-                r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], 
pA=pA, dw=dw_frq, kex=kex, 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_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, dw=dw_frq, 
kex=kex, 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]):


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Re: r23240 - in /branches/disp_speed: lib/dispersion/cr72.py target_functions/relax_disp.py

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