r23929 - /branches/disp_spin_speed/lib/dispersion/lm63.py -- June 13, 2014 - 13:03

Author: tlinnet
Date: Fri Jun 13 13:03:16 2014
New Revision: 23929

URL: http://svn.gna.org/viewcvs/relax?rev=23929&view=rev
Log:
Methods to replace math domain errors in model LM63, has been replaced with 
numpy masks.

number of points has been removed, as the masks utility replaces this.

Documentation is also fixed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
models for Clustered analysis.

Modified:
    branches/disp_spin_speed/lib/dispersion/lm63.py

Modified: branches/disp_spin_speed/lib/dispersion/lm63.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63.py?rev=23929&r1=23928&r2=23929&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/lm63.py     (original)
+++ branches/disp_spin_speed/lib/dispersion/lm63.py     Fri Jun 13 13:03:16 
2014
@@ -64,38 +64,36 @@
 """
 
 # Python module imports.
-from numpy import array, isfinite, sum, tanh
+from numpy import any, array, isfinite, sum, tanh
 
 
-def r2eff_LM63(r20=None, phi_ex=None, kex=None, cpmg_frqs=None, 
back_calc=None, num_points=None):
+def r2eff_LM63(r20=None, phi_ex=None, kex=None, cpmg_frqs=None, 
back_calc=None):
     """Calculate the R2eff values for the LM63 model.
 
     See the module docstring for details.
 
 
     @keyword r20:           The R20 parameter value (R2 with no exchange).
-    @type r20:              float
+    @type r20:              numpy float array of rank [NE][NS][[NM][NO][ND]
     @keyword phi_ex:        The phi_ex parameter value (pA * pB * 
delta_omega^2).
-    @type phi_ex:           float
+    @type phi_ex:           numpy float array of rank [NE][NS][[NM][NO][ND]
     @keyword kex:           The kex parameter value (the exchange rate in 
rad/s).
     @type kex:              float
     @keyword cpmg_frqs:     The CPMG nu1 frequencies.
-    @type cpmg_frqs:        numpy rank-1 float array
+    @type cpmg_frqs:        numpy float array of rank [NE][NS][[NM][NO][ND]
     @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.
-    @type num_points:       int
+    @type back_calc:        numpy float array of rank [NE][NS][[NM][NO][ND]
     """
 
     # Catch divide with zeros (to avoid pointless mathematical operations).
     if kex == 0.0:
-        back_calc[:] = array([r20]*num_points)
+        back_calc[:] = r20
         return
 
     # Catch zeros (to avoid pointless mathematical operations).
     # This will result in no exchange, returning flat lines.
-    if phi_ex == 0.0:
-        back_calc[:] = array([r20]*num_points)
+    if any(phi_ex) == 0.0:
+        back_calc[:] = r20
         return
 
     # Repetitive calculations (to speed up calculations).
@@ -103,11 +101,10 @@
     kex_4 = 4.0 / kex
 
     # Calculate R2eff.
-    R2eff = r20 + rex * (1.0 - kex_4 * cpmg_frqs * tanh(kex / (4.0 * 
cpmg_frqs)))
+    back_calc[:] = r20 + rex * (1.0 - kex_4 * cpmg_frqs * tanh(kex / (4.0 * 
cpmg_frqs)))
 
     # 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)):
-        R2eff = array([1e100]*num_points)
-
-    back_calc[:] = R2eff
+    if not isfinite(sum(back_calc)):
+        # Replaces nan, inf, etc. with fill value.
+        fix_invalid(back_calc, copy=False, fill_value=1e100)